Identification of multiple distinct Snf2 subfamilies with ...

Identification of multiple distinct Snf2 subfamilieswith conserved structural motifsAndrew Flaus David M A Martin1 Geoffrey J Barton1 and Tom Owen-Hughes

Division of Gene Regulation and Expression and 1Bioinformatics and Computational Biology Research GroupSchool of Life Sciences University of Dundee Dundee DD1 5EH Scotland UK

Received February 3 2006 Revised March 18 2006 Accepted April 5 2006

ABSTRACT

The Snf2 family of helicase-related proteins includesthe catalytic subunits of ATP-dependent chromatinremodelling complexes found in all eukaryotesThese act to regulate the structure and dynamicproperties of chromatin and so influence a broadrange of nuclear processes We have exploited pro-gress in genome sequencing to assemble a compre-hensive catalogue of over 1300 Snf2 family membersMultiple sequence alignment of the helicase-relatedregions enables 24 distinct subfamilies to be identi-fied a considerable expansion over earlier surveysWhere information is known there is a good cor-relation between biological or biochemical functionand these assignments suggesting Snf2 familymotor domains are tuned for specific tasksScanningofcomplete genomes reveals all eukaryotescontain members of multiple subfamilies whereasthey are less common and not ubiquitous in eub-acteria or archaea The large sample of Snf2 pro-teins enables additional distinguishing conservedsequence blocks within the helicase-like motor tobe identified The establishment of a phylogenyfor Snf2 proteins provides an opportunity to makeinformed assignments of function and the identifi-cation of conserved motifs provides a frameworkfor understanding the mechanisms by which theseproteins function

INTRODUCTION

Some 15 years ago Gorbalenya and Koonin (12) identified alarge group of proteins sharing a series of short orderedmotifs The majority of members with known function werenucleic acid strand separating helicases so the sequences

became known as helicase motifs and were labelled sequen-tially I Ia II III IV V and VI A number of additional con-served blocks with broad distributions within thesehelicase-like proteins have subsequently been identifiedsuch as the TxGx (3) and Q motifs (4)

Proteins containing the helicase motifs are subdivided intoseveral superfamilies on the basis of similarity Structuralcharacterizations have revealed that helicase-like superfami-lies 1 and 2 (SF1 and SF2) are related with a common coreof two recA-like domains (5) The helicase-like enzymeslink ATP hydrolysis to a directed change in the relative ori-entation of these domains (6) Structural and mutagenesisstudies have shown that each of the conserved motifs in theactive site cleft between the recA-like domains plays a rolein the transformation of chemical energy from ATP hydro-lysis to mechanical motion This enzymatic process hasbeen suggested to represent one application of a more generalmechanism used in many proteins containing a recA-likedomain (7)

Proteins with a helicase-like region of similar primarysequence to Saccharomyces cerevisiae Snf2p comprise theSnf2 family within SF2 (Figure 1A) Indeed Snf2p was specif-ically aligned within SF2 by Gorbalenya and Koonin (1) Manyof the first identified Snf2 family members were ATPaseswithin chromatin remodelling complexes and it was recog-nized that the presence of a core polypeptide related to Snf2pis a defining property of ATP-dependent chromatin remod-elling (8) It is now apparent that the Snf2 family comprisesa large group of ATP-hydrolysing proteins that are ubiquitousin eukaryotes but also present in eubacteria and archaea

At least a subset of Snf2 family proteins act as ATP-dependent DNA translocases (9ndash12) Some of these proteinshave also been found to be capable of generating uncon-strained superhelical torsion in DNA (1113ndash17) proposedto occur as a result of the translocation of DNA into con-strained loops This is substantiated by recent analysis ofthe action of RSC on single DNA molecules (18) In additionto distorting DNA the ATP-dependent action of these

To whom correspondence should be addressed Tel +44 0 1382 385796 Fax +44 0 1382 388702 Email taowenhughesdundeeacukPresent addressAndrew Flaus Department of Biochemistry National University of Ireland Galway Ireland

The Author 2006 Published by Oxford University Press All rights reserved

The online version of this article has been published under an open access model Users are entitled to use reproduce disseminate or display the open accessversion of this article for non-commercial purposes provided that the original authorship is properly and fully attributed the Journal and Oxford University Pressare attributed as the original place of publication with the correct citation details given if an article is subsequently reproduced or disseminated not in its entirety butonly in part or as a derivative work this must be clearly indicated For commercial re-use please contact journalspermissionsoxfordjournalsorg

Nucleic Acids Research 2006 Vol 34 No 10 2887ndash2905doi101093nargkl295

Published online May 31 2006

proteins can disrupt chromatin as measured using a range ofdifferent assays (8) although other DNAndashprotein interactionscan also be affected For example Rad54 promotesRad51-dependent strand pairing (13) and Mot1 displacesthe TATA-binding protein (TBP) from DNA (19) Thus

although many Snf2 family proteins are likely to act toalter chromatin structure this is not the case for all membersof the family

Early biochemical studies and sequence alignmentssuggested that members of the Snf2 family could be further

Figure 1 Tree view of Snf2 family (A) Schematic diagram illustrating hierarchical classification of superfamily family and subfamily levels (B) Unrooted radialneighbour-joining tree from a multiple alignment of helicase-like region sequences excluding insertions at the minor and major insertion regions from motifs I to Iaand conserved blocks CndashK for 1306 Snf2 proteins identified in the Uniref database The clear division into subfamilies is illustrated by wedge backgrounds colouredby grouping of subfamilies Subfamilies DRD1 and JBP2 were not clearly separated as discussed in text (C) In order to illustrate the relationship betweensubfamilies a rooted tree was calculated using HMM profiles for full-length alignments of the helicase regions Groupings of subfamilies are indicated by colouringas in (B)

2888 Nucleic Acids Research 2006 Vol 34 No 10

subdivided into a number of subfamilies (20) These subfami-lies have traditionally taken the name of the archetypal mem-ber such as Scerevisiae Snf2p (Snf2 subfamily) Drosophilamelanogaster Iswi (Iswi subfamily) Mus musculus Chd1(Chd subfamily) and Scerevisiae Rad54p (Rad54 subfamily)Snf2p therefore lends its name to both the collectiveSnf2 family and a specific Snf2 subfamily (Figure 1A)

The only comprehensive analysis of the Snf2 familysequences to date was performed by Eisen et al in 1995(20) Although it has subsequently been revisited withinthe context of various biochemical studies (21ndash24) nobroad survey has been conducted for over a decade

To gain new insights into the Snf2 family we havecatalogued Snf2 family members by scanning for proteinscontaining spans with similarity in sequence over thehelicase-like region classifying them into subfamiliesanalysing the distribution of these subfamilies in completegenomes and mapping the common sequence characteristicsonto the newly available three-dimensional structures Wehave identified 24 distinct subfamilies 11 with near ubiqui-tous representation in eukaryotic genomes Many of thesesubfamilies correlate with known biological function butthere remain a significant number for which little informationis currently available The abundance of Snf2 family membersin eukaryotes in comparison to archaea and eubacteria pointsto their diversification early in eukaryote radiation Thisdiversity and the currently known functional linkages suggestthe Snf2 family helicase-like region is specifically adapted toperform distinct functions within different subfamiliesUnderlying this analysis of the conserved blocks of res-idues reveals a common core of structural features likely tobe fundamental to the mechanism of the Snf2 family motors

MATERIALS AND METHODS

Data and software sources

SwissprotUniprot (25) release 42 and Uniref100 (26)release 5 were downloaded from the European Bioinformat-ics Institute (ftpftpebiacukpubdatabasesswissprot andftpftpebiacukpubdatabasesuniprot respectively) Thesources and version details for the predicted protein comple-ments of the 54 eukaryotic 24 archaeal and 269 prokaryoticorganisms surveyed are available at the webserver httpwwwsnf2net Analyses were performed on a cluster ofdual Pentium III microcomputers running a customizedDebian Linux operating system

Sequence data were manipulated with the EMBOSS suiteversion 28 (27) Multiple sequence alignments were createdwith Muscle version 30 (28) and MAFFT version 5667 withparameters retree frac14 2 and maxiterate frac14 1000 (29) and visu-alized with Jalview version 2 (30) Phylogenetic and pairwisetrees were constructed with neighbor protdist and drawtreefrom the PHYLIP suite version 3572 (31) and additionallyvisualized with ATV version 203 (32) and Hypertree version100 (33) Hidden Markov model (HMM) constructioncalibration and searching was performed with the HMMersuite versions 211 and 22g (34) and pairwise comparisonof HMMs carried out with PRC version 153 in global-globalmode (35) Sequence LOGOs were generated with WebLogoversion 282 (36) and profile logos generated with logomat-p

using the draw_logo method version 071 (37) Protein struc-tures were visualized with PyMol version 099 (38) Datawere managed using mySQL (httpwwwmysqlcom) andPostgreSQL (httpwwwpostgresqlorg) relational databasesCalculations were carried out using default parameters exceptwhere indicated All other analyses used custom Perl orPython scripts written by the authors All supplementarydata for this report and an interactive database of the resultsare publicly available at the web server httpwwwsnf2net

Experimental methods

A full technical description of the library construction andvalidation and details of the web server will be availableelsewhere (DMA Martin and A Flaus manuscript in pre-paration) The procedure used is summarized in outline below

Global Snf2 family HMM construction

Twenty-eight biochemically characterized ScerevisiaeSnf2p-like chromatin remodelling proteins or close homo-logues were selected as seed sequences The core helicase-like region spanning from 50 amino acids N-terminal tohelicase motif I to 50 amino acids C-terminal of helicasemotif VI was excised from each protein sequence and multi-ple alignments were created with Muscle using defaultparameters An initial seed HMM was constructed followingmanual assessment of the alignment

Swissprot 42 was searched using this profile expanding theset of Snf2 family sequences to 620 candidates with matchesup to E-values of 2 although some matches near this cut-offwere helicase-like sequences which were not members ofthe Snf2 family Further iterations of HMM constructionand searching of Swissprot 42 and model organism databasesfollowed by curation of sequences to remove fragmentedsequences and other artefacts not belonging to the Snf2 fam-ily yielded a set of 948 manually curated sequences whichwere then aligned by MAFFT

The resultant profile was employed in searching Uniref100and identified 5046 sequences with a match of E-value 10or better of which 3932 had E-values below 1 and 1879had positive bit-scores This cut-off may appear generousbut was intentional to enable maximum possible inclusionof Snf2 family members It is predicated by the considerablevariation in sequence between helicase motifs III and IVgiving rise to poor alignments to the general model in thisregion and consequently lower bit scores The cut-offsselected were determined by manual inspection of the hitlists and alignments to include established Snf2 family-likeproteins but exclude more distant relatives The highestE-value for a sequence classified into a subfamily (seebelow) was 22 middot 1016

Phylogenetic analysis of helicase-like sequences

A multiple sequence alignment with Muscle followed bydistance matrix calculation and neighbour-joining tree recon-struction allowed the curation of 2305 sequences into sub-groupings in the Snf2 family based on the sequence of thehelicase-like region 1306 sequences were classified in24 individual subfamilies within the Snf2 family (Table 1)after the exclusion of 436 which were fragmentary (did notspan completely from helicase motifs I to VI) or contained

Nucleic Acids Research 2006 Vol 34 No 10 2889

unique large inserts or deletions A further 220 were assignedto the prokaryotic rapA group and the remainder to more dis-tantly related clusters or as highly truncated outliers whichcould not be reasonably aligned An overview of a neighbour-joining tree constructed from a multiple alignment excludingthe variable minor and major insertion regions (see text) andvisualized using Hypertree demonstrates the clearly distin-guishable division of subfamilies (Figure 1B) Each subfam-ily was individually examined for redundancy and furtherinternal structure (data not shown)

Construction and use of subfamily profiles

Each subfamily sequence set was realigned by MAFFTmanually curated with Jalview and an HMM profile con-structed These profiles were aligned with PRC in an all-against-all comparison Although these profile comparisonsdo not give a true phylogenetic tree the scores obtainedfrom the pairwise profile alignments can be used to constructa representational tree (Figure 1C) indicating the relationshipbetween the HMM profiles to be consistent with thesequence-based tree (Figure 1B) It was also observed thatthe subfamilies could be aggregated into some broad group-ings that correlate with functional properties where known(Figure 1)

All 24 subfamily profiles were combined in one HMMlibrary and the hmmpfam application employed in searchingindividual genomic datasets to provide phylogenomic infor-mation about the taxonomic distribution of Snf2-like proteinsThe subfamily hit with maximal bitscore gt100 was usedto assign membership in a semi-automatic procedure With

very few exceptions classification was extremely clear withstrong discrimination between the top hit and the secondbest hit (data not shown)

RESULTS AND DISCUSSION

Starting from a seed set of helicase-like region sequencesfrom 28 demonstrated Snf2p-related proteins or close homo-logues we have carried out a broad survey of Snf2 familyproteins This was achieved by iterative cycles of manualcuration of multiple alignments and neighbour-joining treesto identify Snf2 proteins by similarity construction of anHMM profile from the multiple alignments of identified pro-teins and scanning of global and model organism proteindatabases using the HMM profile to uncover furthersequences for curation Our current global Snf2 family profilescan revealed 3932 sequences with E-value under 1 (1879with bitscore gt 0) in Uniref100 release 5 [24 million entries(26)] Of these 1306 sequences were identified as belongingto the Snf2 family and to span the full helicase region frommotifs I to VI without introducing large unique insertionsor deletions A further 220 sequences fall within the rapAgroup while other hits appear to belong to more distantlyrelated groups (see below) or were too highly truncated tobe aligned Neighbour-joining trees from multiple alignmentsof the set of 1306 sequences revealed a well-defined branch-ing structure (Figure 1B) and enabled their assignment to24 distinct subfamilies (Table 1)

Subfamily-specific HMM profiles were constructedfrom these assignments and used to characterize the Snf2

Table 1 Summary of subfamilies

Subfamily Archetype gene Assigned fromUniref

Other names associated with members

Snf2 Scerevisiae SNF2 117 Snf2p Sth1p snf21 SMARCA4 BRG1 BAF190 hSNF2betaSNF2L4 SMARCA2 hBRM hSNF2a SNF2L2 SNF2LA SYD splayed psa-4 brahma

Iswi Dmelanogaster Iswi 83 Isw1p Isw2p SMARCA1 SNF2L SNF2L1 SNF2LB SMARCA5 hSNF2HLsh Mmusculus Hells 35 YFR038W SMARCA6 HELLS LSH PASG DDM1 cha101ALC1 Homo sapiens CHD1L 19 SNF2PChd1 Mmusculus Chd1 96 CHD2 CHD-Z hrp1 hrp3Mi-2 Hsapiens CHD3 88 CHD3 Mi-2a Mi2alpha ZFH PKL pickle CHD4 Mi-2b Mi2beta let-418 CHD5CHD7 Hsapiens CHD7 53 CHD6 RIGB KISH2 Kis-L kismet CHD8 HELSNF1 DUPLINSwr1 Scerevisiae SWR1 44 SRCAP Snf2-related CBP activator protein dom domino PIE1EP400 Hsapiens EP400 27 E1A binding proten p400 TNRC12 hDominoIno80 Scerevisiae INO80 34Etl1 Mmusculus Smarcad1 44 SMARCAD1 hHEL1 Fun30p snf2SRRad54 Scerevisiae RAD54 76 Rad54l hRAD54 RAD54A Rdh54p RAD54B Tid1 okr okra mus-25ATRX Hsapiens ATRX 52 XH2 XNP Hp1bp2Arip4 Mmusculus Srisnf2l 23 ARIP4DRD1 Arabidopsis thaliana DRD1 12JBP2 Tbrucei JBP2 4Rad516 Scerevisiae RAD5 RAD16 61 rhp16 rad8 SMARCA3 SNF2L3 HIP116 HLTF ZBU1 RNF80

RUSH-1alpha P113 MUG131Ris1 Scerevisiae RIS1 35Lodestar Dmelanogaster Lodestar 40 LDS TTF2 hLodestar HuF2factor 2SHPRH Hsapiens SHPRH 44 YLR247CMot1 Scerevisiae MOT1 45 TAFII170 TAF172 BTAF1 Hel89BERCC6 Hsapiens ERCC6 71 rad26 rhp26 CSB csb-1 RAD26LSSO1653 Ssolfataricus SSO1653 149 SsoRad54likeSMARCAL1 Hsapiens SMARCAL1 54 HARP DAAD ZRANB3 Marcal1

Listing subfamily name from prevailing protein name for first characterized member archetype organism and official gene name number of subfamily membersidentified in Uniref as in Materials and Methods and a non-exhaustive list of alternative names for archetype and other subfamily members


family complement for 54 complete eukaryote genomes Thecounts of predicted proteins and unique encoding genes for21 selected genomes are listed in Table 2 part A and Brespectively (see Supplementary Table S1A for full analysisof eukaryotic genomes and Supplementary Table S2for gene IDs by subfamily for seven common modelorganisms) In addition 24 complete archaeal and 269bacterial genomes were scanned (Supplementary TablesS1B and S1C)

Subfamilies within the Snf2 family

The clear distinction and significant number of subfamiliesbased on the helicase-like region (Figure 1B and Table 1)reflects both a remarkable breadth and specificity in theSnf2 family An additional level of similarity distinguishesapparent groupings of subfamilies (Figure 1) which echo cur-rent understanding of their functional diversity (Table 3)Most of the best studied Snf2 family proteins fall into agrouping of lsquoSnf2-likersquo subfamilies including proteins suchas Scerevisiae Snf2p Dmelanogaster Iswi mouse Chd1and human Mi-2 which are core subunits of the well-knownATP-dependent chromatin remodelling complexes A sepa-rate lsquoSwr1-likersquo grouping encompasses the Swr1 Ino80EP400 and Etl1 subfamilies The lsquoRad54-likersquo grouping con-tains the Rad54 subfamily relatives such as ATRX andArip4 and also includes the recently recognized DRD1 andJBP2 proteins A further unexpected lsquoRad516-likersquo group-ing links several poorly studied subfamilies three of whichcontain RING finger insertions within the helicase-like region(see below) The lsquoSSO1653-likersquo grouping of Mot1 ERCC6and SSO1653 is notable because all three subfamilies arethought to have non-chromatin substrates Finally we havelabelled SMARCAL1 proteins as lsquodistantrsquo because they lackseveral otherwise conserved sequence hallmarks of the Snf2family (see below) Although some groupings are clear fur-ther investigations will be required to verify those where theboundaries are less distinct

Since the subfamily assignments are based only on thecommon helicase-like region this suggests that the lsquomotorrsquoat the core of even large multiprotein remodeller complexesis tuned to the mechanistic requirements of its functionSuch properties are not unprecedented for motor proteinsubfamilies The ubiquitous kinesin and myosin proteins aredivided into at least 14 and 17 subfamilies respectively(3940) and those subfamilies are recognized to reflect tuningof the motors for enzymatic properties linked to particularfunctional roles As this also appears to be true for Snf2 fam-ily proteins we can anticipate that mechanistic features of themotors will be shared within subfamilies and groupings Thismay be useful in helping to predict function of poorly charac-terized proteins For example owing to the recent observationthat Swr1 functions in histone exchange (41ndash43) it is tempt-ing to speculate that the Snf2 motors within other subfamiliesin the Swr1-like grouping may be adapted for relatedpurposes

Owing to the remarkable diversity revealed by thisclassification and the occurrence of many subfamilies whichhave not been intensively investigated we briefly summarizecurrent functional and biochemical understanding and charac-teristic features of each subfamily in Table 3

Defining the Snf2 family

The survey of Snf2 family proteins enables detailed analysisof sequence conservation in the helicase-like region(Figure 2) This reveals a number of unique features distin-guishing them from other helicase superfamily SF2 membersFirst the conserved helicase motifs show a highly conservedcharacter across the Snf2 family and some motifs are exten-ded by juxtaposed residues such as conserved blocks E and G(Figure 2 and Supplementary Figure S4) Second thehelicase-like region in the Snf2 family is significantly longerthan for many other helicases primarily due to an increasedspacing between motifs III and IV of gt160 residues comparedto 38 and 78 for typical SF2 helicases NS3 and RecG respec-tively (44) Third a number of unique conserved blocks arefound in Snf2 family proteins (Figure 2 and SupplementaryTable S5) Several of these blocks have been noted pre-viously (2045ndash48) with conserved block B having been con-fused in a number of early manuscripts with motif IVConserved blocks B C and K are of particular interestbecause they are located within the characteristic extendedinter-motif IIIndashIV region (Figure 3G)

The SMARCAL1 subfamily contains classical helicasemotifs which are highly similar to the other subfamilies Italso has an extended motif IIIndashIV spacing but it neverthelesslack conserved blocks within the motif IIIndashIV region (Supple-mentary Figure S4) The rapA group has similar propertiesbut is more diverse in overall sequence and retains lesssimilarity in the classical motifs It is unclear whether theSMARCAL1 subfamily and particularly the rapA groupwill maintain the structural features of the Snf2 family andthey are therefore at the limit of the definition of the Snf2family We have also noticed further protein groupings withextended spacing between motifs III and IV and detectablesimilarity to the classical helicase-like motifs of the Snf2family sequences (Supplementary Figure S4) These includepoxvirus NPH-I related proteins involved in transcriptiontermination (49) and the FANCMMPH1Hef group of heli-cases encompassing yeast Mph1p archaeal Hef and humanFANCM proteins involved in DNA repair (50ndash52) Howeverthose proteins show low similarity to the Snf2 family betweenmotifs III and IV and appear to lack the characteristic con-served blocks C J and K of the Snf2 family Interestinglycomparison of the recently determined Pyrococcus furiosusarchaeal Hef helicase structure reveals that the MPH1Hefgroup has a related structural organization to ZebrafishRad54 but contains only a single compact alpha-helicaldomain encoded between motifs III and IV (SupplementaryFigure S6) It has been noted that this extra alpha-helicaldomain has some similarities with the thumb domain ofTaq DNA polymerase which grips the DNA minor groove(53) It is therefore likely that the SMARCAL1 subfamilyrapA group NPH-I and MPH1Hef proteins reflect a contin-uum of diversity while sharing core features with the otherSnf2 subfamilies

Evolution of Snf2 family diversity

None of the 293 scanned archaeal or bacterial genomes con-tains a protein classified in any of the eukaryotic subfamilies(Supplementary Tables S1B and S1C) All identified archaealand bacterial proteins belong to the SSO1653 subfamily and


rapA group Conversely the SSO1653 subfamily andrapA group are likely to be specific to microbial organismsbecause the only two members of these families identifiedin eukaryotes (Supplementary Table S1A) appear to befalse positives (data not shown) Over two-thirds of complete

microbial genomes contain members of the SSO1653subfamily andor rapA group This broad yet incompletedistribution suggests they perform non-essential functionsthat are sufficiently advantageous to maintain theirprevalence

Table 2 Subfamily occurrences in selected complete eukaryotic genomes

Sn

f2

Isw

i

Lsh

AL

C1

Chd

1

Mi-

2

CH

D7

Sw

r1

EP

40

0

Ino

80

Etl

1

Rad

54

AT

RX

Ari

p4

DR

D1

JBP

2

Rad

51

6

Ris

1

Lo

des

tar

SH

PR

H

Mo

t1

ER

CC

6

SS

O1

65

3

SM

AR

CA

L1

rapA

gro

up

(A) Predicted proteinsFungi

Scerevisiae 2 2 1 0 1 0 0 1 0 1 1 2 0 0 0 0 2 1 0 1 1 1 0 0 0Spombe 2 0 0 0 2 1 0 1 0 1 3 2 0 0 0 0 2 3 0 1 1 1 0 0 0Neurospora crassa 1 1 1 0 1 1 0 1 0 1 1 1 0 1 0 0 3 3 3 3 1 2 0 0 0

PlantAthaliana 6 3 1 2 1 3 0 1 0 1 1 1 1 0 6 0 5 5 0 2 1 3 0 2 0

InvertebratesCiona intestinalis 10 10 6 0 7 5 2 2 0 0 2 3 2 1 0 0 0 0 0 0 2 4 0 5 0Caenorhabditis elegans 3 1 0 0 1 2 1 1 0 0 1 2 1 1 0 0 0 0 6 2 1 1 0 4 0Apis mellifera 5 2 1 0 2 5 1 0 0 1 1 3 8 2 0 0 0 0 4 0 4 0 0 6 0Anopholes gambiae 1 1 1 0 1 1 1 1 0 1 1 2 3 2 0 0 0 0 2 1 1 0 0 1 0Dmelanogaster 4 3 0 0 1 3 1 3 0 1 1 1 2 1 0 0 0 0 2 1 1 0 0 1 0

VertebratesDanio rerio 6 5 0 2 7 16 13 1 0 6 4 1 0 1 0 0 2 0 1 1 1 6 0 1 0Tetraodon nigroviridis 3 1 1 1 2 4 3 1 2 1 1 3 2 2 0 0 1 0 1 1 2 1 0 1 0Fugu rubripes 16 2 1 1 9 15 10 4 3 1 1 3 7 2 0 0 3 0 2 1 2 4 0 3 0Xenopus tropicalis 14 11 4 0 15 13 11 1 3 5 1 6 4 2 0 0 4 0 2 3 2 4 1 4 0Gallus gallus 2 4 3 1 7 6 11 0 3 2 2 2 2 1 0 0 0 0 2 1 1 5 0 5 0

MammalsMonodelphis domestica 2 2 1 1 3 3 4 1 3 1 1 2 1 1 0 0 1 0 1 1 1 4 0 2 0Canis familiaris 7 2 1 4 5 13 8 2 4 2 1 5 1 1 0 0 2 0 1 2 2 3 0 3 0Bos taurus 4 3 1 2 2 5 4 2 1 1 1 2 1 1 0 0 1 0 1 1 1 2 0 2 0Rattus norvegicus 3 3 1 1 2 2 4 1 0 2 1 1 1 1 0 0 1 0 1 1 1 4 0 3 0Mmusculus 2 7 1 1 3 2 6 0 4 2 1 4 2 1 0 0 1 0 2 3 1 4 0 6 0Pan troglodytes 4 2 1 3 2 5 4 2 1 2 3 2 1 1 0 0 1 0 1 1 2 4 0 4 0Hsapiens 5 3 1 3 2 6 4 2 1 3 3 2 4 1 0 0 2 0 1 1 1 4 0 4 0

(B) Genes encoding predicted proteinsFungi

Scerevisiae 2 2 1 0 1 0 0 1 0 1 1 2 0 0 0 0 2 1 0 1 1 1 0 0 0Spombe 2 0 0 0 2 1 0 1 0 1 3 2 0 0 0 0 2 3 0 1 1 1 0 0 0Ncrassa 1 1 1 0 1 1 0 1 0 1 1 1 0 1 0 0 3 3 3 3 1 2 0 0 0

PlantAthaliana 4 2 1 1 1 3 0 1 0 1 1 1 1 0 6 0 5 5 0 2 1 3 0 2 0

InvertebratesCintestinalis 1 1 2 0 1 1 1 1 0 0 1 1 1 1 0 0 0 0 0 0 1 2 0 1 0Celegans 2 1 0 0 1 2 1 1 0 0 1 2 1 1 0 0 0 0 4 1 1 1 0 1 0Amellifera 1 1 1 0 1 1 1 0 0 1 1 1 1 1 0 0 0 0 1 0 1 0 0 1 0Agambiae 1 1 1 0 1 1 1 1 0 1 1 2 2 1 0 0 0 0 1 1 1 0 0 1 0Dmelanogaster 1 1 0 0 1 2 1 1 0 1 1 1 1 1 0 0 0 0 2 1 1 0 0 1 0

VertebratesDrerio 5 1 0 2 1 4 4 1 0 3 2 1 0 1 0 0 1 0 1 1 1 3 0 1 0Tnigroviridis 3 1 1 1 2 4 3 1 2 1 1 3 2 2 0 0 1 0 1 1 2 1 0 1 0Frubripes 3 1 1 1 2 4 4 1 1 1 1 2 2 2 0 0 1 0 1 1 1 3 0 2 0Xtropicalis 2 2 1 0 2 4 4 1 1 1 1 2 1 1 0 0 1 0 1 1 1 3 1 2 0Ggallus 1 2 1 1 3 2 3 0 1 1 1 2 1 1 0 0 0 0 1 1 1 3 0 2 0

MammalsMdomestica 2 2 1 1 2 3 4 1 2 1 1 2 1 1 0 0 1 0 1 1 1 4 0 2 0Cfamiliaris 2 2 1 1 2 3 4 1 1 1 1 2 1 1 0 0 1 0 1 1 1 3 0 2 0Btaurus 2 2 1 1 2 3 4 1 1 1 1 2 1 1 0 0 1 0 1 1 1 2 0 2 0Rnorvegicus 2 3 1 1 2 2 2 1 0 1 1 1 1 1 0 0 1 0 1 1 1 2 0 2 0Mmusculus 2 4 1 1 2 2 3 0 1 1 1 2 1 1 0 0 1 0 1 1 1 3 0 2 0Ptroglodytes 2 2 1 1 2 3 4 1 1 1 1 2 1 1 0 0 1 0 1 1 1 3 0 2 0Hsapiens 2 2 1 1 2 3 4 1 1 1 1 2 2 1 0 0 1 0 1 1 1 3 0 2 0

A Counts by genome of predicted proteins assigned to each subfamily for assignments based on highest positive bitscore for protein against each subfamily HMMprofile in turn where maximum bitscore gt100 For a complete list of 54 genomes see Supplementary Table S1A B Counts of unique genes encoding thepredicted proteins listed in part A Single gene encoding each protein assumed for fungal genomes Gene names for seven model organisms are tabulated inSupplementary Table S2 including official protein names where assigned


Table 3 Functional and sequence characteristics of subfamilies

Grouping Subfamily Functional characteristics

Snf2-like Snf2 The archetype of the Snf2 subfamily and the entire Snf2 family is the Scerevisiae Snf2 protein originally identified genetically(mutations that were Sucrose Non Fermenting or defective in mating type SWItching) However these genes were later found toplay roles in regulating transcription of a broader spectrum of genes and to catalyse alterations to chromatin structureSubsequently the proteins were purified as a non-essential 11 subunit multi-protein complex capable of ATP-dependent chromatindisruption termed the SWISNF complex (8)

Close sequence homologues have also been identified in many model organisms including the paralogue RSC (6061) and theorthologues Dmelanogaster Brahma (62) and human hBRM (63) and BRG1 (64) Many of these have been shown to alter thestructure of chromatin at the nucleosomal level and to be involved in transcription regulation although other nucleosome-relatedroles have also been identified (8) Recent hypotheses have centred on Snf2 subfamily members performing a generally disruptivefunction on nucleosomes leading either to sliding of the nucleosome (6566) alterations of histone DNA contacts (67) or to partial orcomplete removal of the histone octamer components (6869)

Homologues such as BRG1 and hBRM are components of megadalton-sized complexes containing other proteins that are also relatedto components of the yeast SWISNF complex (70) However Snf2 subfamily members have also been reported to interact withadditional proteins including histone deacetylases (71) methyl DNA-binding proteins (72) histone methyl transferases (73) theretinoblastoma tumor suppressor protein (7475) histone chaperones (76) Pol II (7778) and cohesin (79) These complexes may berecruited to specific regions of the genome through interactions with sequence-specific DNA-binding proteins [reviewed by (80)]or specific patterns of histone modifications (8182)

ISWI Iswi (Imitation SWI2) protein was identified in Dmelanogaster by similarity to Snf2p (83) and is at the catalytic core of both theNURF and the ACFCHRAC chromatin remodelling complexes (84ndash86) Biochemical studies favour the ability of Iswi proteins toreposition rather than disrupt nucleosomes Significantly all Iswi subfamily proteins require a particular region of the histone H4tail near the DNA surface as an allosteric effector (87ndash89)

Iswi subfamily members participate in a variety of complexes and functional interactions For example human SNF2H has beenfound as part of RSF hACFWCRF hWICH hCHRAC NoRC and also associated with cohesin while SNF2L is the catalyticsubunit of human NURF [summarized in (90)] Such complexes are involved in a variety of functions including activationrepression of the initiation and elongation of transcription replication and chromatin assembly [reviewed in (90ndash93)] Similar to theSnf2 subfamily Iswi subfamily members appear to be adaptable subunits for complexes related to the alteration of nucleosomepositioning (90)

Lsh Despite its name the archetypal mouse Lsh (lymphoid-specific helicase) protein (94) is widely expressed and without detectablehelicase activity Lsh and its human homologue are alternatively known as PASG SMARCA6 or by the official gene name HELLS(Helicase Lymphoid Specific) Mutants lead to premature aging with cells exhibiting replicative senescence (95) Importantlyglobal loss of CpG methylation is observed in both mammalian mutant cell lines and the Arabidopsis thaliana homologue DDM1(9697) Consistent with a direct role in DNA methylation Lsh is localized to heterochromatic regions (98) Evidence has beenpresented that Athaliana DDM1 can slide nucleosomes in vitro (99) The Scerevisiae subfamily member at locus YFR038W hasno assigned name and deletion strains are viable

Lsh subfamily members are detected over a very broad range of eukaryotes including not only fungi plants and animals but alsoprotists where their function is likely to be independent of DNA methylation Furthermore our genome scans also did not identifyLsh subfamily members in a number of lower animals or in Spombe This may represent functional redundancy or difficulties inassigning distant homologues relative to other subfamilies in the grouping

ALC1 The ALC1 subfamily derives its name from the observation that the human gene is lsquoAmplified in Liver Cancerrsquo (100) Two alternativebut potentially confusing names CHD1L [CHD1-like (101)] and SNF2P [SNF2-like in plants (102)] have also been used to refer tosubfamily members ALC1 subfamily members contain a helicase-like region which is relatively similar to the nucleosome-activeSnf2 Iswi and Chd1 subfamilies but which is coupled ahead to a macro domain implicated in ADPndashribose interactions (103)ALC1 subfamily members can be identified in both higher animals and plants but not in lower animals

Chd1 The archetypal lsquoChdrsquo protein is mouse Chd1 named after the presence of lsquoChromodomain Helicase and DNA bindingrsquo motifs (104)The characteristic chromodomain motifs can in principle bind diverse targets including proteins DNA and RNA (105) AlthoughSnf2 family proteins containing chromodomains are often referred to as a single lsquoChdrsquo subfamily it has previously been recognizedthey fall into the same three distinct subfamilies (106107) which we have distinguished in this analysis

Mouse Chd1 protein is the archetype of the first chromodomain-containing subfamily Chd1 proteins have been purified as singlesubunits (108109) although associations between Chd1 and other proteins have been identified subsequently (110111) YeastChd1 has been implicated in transcription elongation and termination (58112) and the human CHD1 and CHD2 proteins andDmelanogaster dChd1 have been linked to transcriptional events (113) Spombe Chd1 subfamily member hrp1 (helicase relatedprotein 1) has been linked with both transcription termination (58) and chromosome condensation (114) whereas the paralogoushrp3 has been linked with locus-specific silencing (115)

Mi-2 The second of the chromodomain-containing subfamilies is Mi-2 whose name derives from the Mi-2a and Mi-2b proteins which arethe commonly used names for the human CHD3 and CHD4 gene products respectively Mi-2 was isolated as an autoantigen in thehuman disease dermatomyositis (116) Subsequently the two proteins and their homologues in Dmelanogaster and Xenopus havebeen recognized as core subunits of NuRD complexes which link DNA methylation to chromatin remodelling and deacetylation(117) The chromodomains in Dmelanogaster Mi-2 are required for activity on nucleosome substrates (118) Human Mi-2a differsfrom Mi-2b principally by its additional C-terminal domain which directs complexes containing it for a specific transcriptionalrepression role (119) Since Mi-2 proteins are widely expressed but have specific roles it has been suggested they may be directedby incorporation of different targeting subunits (117120)

An additional human member of the Mi-2 subfamily CHD5 may have a role in neural development and neuroblastomas (121122)although its biochemical associations are unknown The Athaliana subfamily member PKL (swollen roots of mutants resemble apickle) has been shown to play a role in repressing embryonic genes during plant development (123)

CHD7 The third chromodomain-containing CHD7 subfamily includes four human genes CHD6ndashCHD9 CHD7 has recently been linked toCHARGE syndrome which is a common cause of congenital abnormalities (124) with most linked mutations resulting in majornonsense frameshift or splicing changes (125) There is little functional information available about CHD6 [originally known asCHD5 (126)] CHD8 or CHD9 [also known as CReMM (127)] The most studied member of the CHD7 subfamily is the product ofthe Dmelanogaster gene kismet The enormous 574 kDa KIS-L (but not the lsquosmallerrsquo 225 kDa KIS-S form) contains a Snf2 familyhelicase-like region (128) Although identified as a trithorax family gene acting during development a recent report suggests thatKIS-L may play a global role at an early stage in RNA pol II elongation (129)


Table 3 Continued


Swr1-like Swr1 The archetype of the Swr1 subfamily is Swr1p (SWISNF-related protein) from Scerevisiae which is part of the large SWR1 complexthat exchanges histone H2AZ-containing for wild-type H2A-containing dimers (41ndash43130) Three other characterized proteinsbelong to the subfamily PIE1 is involved in the Athaliana vernalization regulation [Photoperiod-Independent Early flowering(131)] through a pathway intimately linked with histone lysine methylation events (132) Dmelanogaster Domino is an essentialdevelopment-linked protein (133) and alleles can suppress position effect variegation implying they may be linked toheterochromatin functions Domino participates in a complex that combines components of the homologous yeast SWR1 andNuA4 complexes (134) and has been shown to function in acetylation dependent histone variant exchange within the TRRAPTIP60 complex (135) The human member SRCAP [Snf2p-related CBP activating protein (136)] acts as a transcriptionalco-activator of steroid hormone dependent genes and has recently been shown to be a component of a human TRRAPTIP60complex (137) and other complexes (see EP400 below) It also interacts with several coactivators including CBP (136138)SRCAP can rescue Dmelanogaster domino mutants (139) implying functional homology

EP400 The EP400 subfamily archetype E1A-binding protein p400 appears to have a role in regulation of E1A-activated genes (140ndash142)EP400 has been shown to interact strongly with ruvB-like helicases TAP54ab in the TRRAPTIP60 histone acetyl transferasecomplex (142)

The complex patterns of similarities and distinctions between EP400 and Swr1 subfamilies suggest a close functional relationship(Supplementary Figure S3A) Our HMM profiles clearly distinguish EP400 from Swr1 members and show that EP400 membersare restricted to vertebrates whereas Swr1 subfamily members are found in almost all eukaryotes (Table 2 and SupplementaryTable S1A) Although most vertebrate genomes contain a gene each for an Swr1 and EP400 member some have only one of thepair The consensus for the helicase-like regions of the subfamilies shows 50 identity and animal members of both contain largeproline and serinethreonine rich insertions at the major insertion site (Supplementary Figure S3A see below) Members of the twosubfamilies also contain overlapping combinations of accessory domains outside the helicase-like region DmelanogasterDominoA (Swr1 subfamily) and human EP400 (EP400 subfamily) both contain SANT domains whereas human SRCAP (Swr1subfamily) instead contains an AT hook (139) This has led to some confusion with human EP400 being referred to as hDominoalthough Dmelanogaster Domino has higher similarity to human SRCAP (142) and SRCAP can complement Domino mutants(139) In addition to the complexity in primary sequence relationships complexes of potentially overlapping composition existinvolving human EP400 and SRCAP including the NCoR-1 histone deacetylase (143) TRRAPTIP60 histone acetylase(137142144) and DMAP1 complex (145) The confusing overlap of the mammalian Swr1 and EP400 subfamily members maystem from multiple roles for Swr1 subfamily members in lower animals and fungi For example it has been suggested thatDmelanogaster alternative splice isoforms DominoA and DominoB are functional homologues of EP400 and SRCAPrespectively (139) and that Scerevisiae Eaf1p is a functional homologue of human EP400 (134) although it lacks both Snf2-relatedhelicase-like and extended proline-rich regions

Ino80 The archetype of the Ino80 subfamily is the Ino80 protein from Scerevisiae Further members have been identified by sequencesimilarity in fungi plants and animals (24) Ino80p was first isolated through its role in transcriptional regulation of inositolbiosynthesis (146147) and forms part of the large Ino80com complex (148) This complex is notable not only because it canreposition nucleosomes but also because it is the only known Snf2 family-related complex able to separate DNA strands in atraditional helicase assay (148) However the Ino80 complex contains two RuvB-like helicase subunits which may assist in thisThe human INO80 complex has recently been shown to contain many proteins homologous to Ino80com subunits including theRuvB-like helicases and to be capable of mobilizing mononucleosomes (149) Scerevisiae INO80-deleted strains are sensitive toDNA damaging agents and recent studies have implicated Ino80p directly in the events of double-stranded break repair (150151)perhaps for the eviction of nucleosomes in the vicinity of the break (152) although other remodelling complexes such as Swr1 RSCand SWISNF may also participate in this repair pathway [reviewed in (153)]

Etl1 Mouse Etl1 (Enhancer Trap Locus 1) derives its name from identification in an expression screen for loci having interesting propertiesin early development (154) Although members are present in all but the lowest eukaryotes including the human homologueSMARCAD1 (SMARCA containing DEAD box 1) (155) and Scerevisiae FUN30 (Function Unknown 30) (156) very littleattention has been focussed on these proteins Etl1 is very widely expressed but non-essential although deletion causes a variety ofsignificant developmental phenotypes (157) FUN30 deletions are viable although temperature sensitive (158) and mutants showdecreased sensitivity to UV radiation (159)

Rad54-like Rad54 The archetype of the Rad54 subfamily is the Rad54 protein from Scerevisiae which was isolated because its inactivation leads toincreased sensitivity to ionizing radiation Rad54p and its homologues in other organisms play an important but as yet incompletelyunderstood role in homologous recombination by stimulating Rad51-mediated single strand invasion into the target duplex andsubsequent steps in the process (160161) Many organisms also contain a second subfamily member such as Scerevisiae Rdh54por Spombe tid1p These are frequently implicated in mitotic repair and meiotic crossover (162) although the role of the humanhomologue RAD54B is unclear (163)

Rad54 proteins have been extensively studied in vitro They have been shown to be able to generate local changes in DNA topology insupercoiled plasmids (13164165) to translocate along DNA by biochemical (11) and other methods and to alter the accessibilityof nucleosomal DNA (11166167) However this latter activity appears inefficient compared to purified complexes from the Snf2and Iswi subfamilies The crystal structure of the zebrafish Rad54 helicase-like region has been determined recently (47) and isdiscussed in more detail in the text

ATRX The ATRX subfamily derives its name from the Alpha ThalassemiaMental Retardation syndrome X-linked genetic disorder causedby defects in the activity of the human member ATRX (168) This protein is localized to centromeric heterochromatin (169) andpurified complexes have been shown to increase the accessibility of nucleosomal DNA although with only moderate efficiency(12) ATRX has been implicated both in the regulation of transcription and heterochromatin structure (170) although themechanism by which it acts is unclear

Arip4 Mouse androgen receptor interacting protein 4 (171) can bind to DNA and generate ATP-dependent local torsion (16) Although it canalso bind nucleosomes Arip4 does not appear to be able to alter their nuclease sensitivity leading to the conclusion that nucleosomemobilization may not be its primary role (172) Interestingly mutation of the six lysine sumoylation sites in the protein destroyedDNA binding and ATPase activity (172)

DRD1 Athaliana DRD1 is named from its phenotype lsquoDefective in RNA-directed DNA methylationrsquo (173) DRD1 functions together withan atypical RNA polymerase IV to establish and also remove non-CpG DNA methylation as part of an RNA interference mediatedpathway (174175)

JBP2 The JBP2 subfamily takes its name from the Tbrucei J Binding Protein 2 which regulates insertion of an unusual glycosylatedthymine-derived base J which marks silenced telomeric DNA (176)


Table 3 Continued


Rad54-like(cont)

Both DRD1 and JBP2 are involved in processes which target modifications at the C5 position of the pyrimidine ring which will beexposed in the major groove JBP2 and DRD1 members show sequence similarity but have been conservatively assigned toseparate subfamilies due to their distinct evolutionary ranges and the limited numbers of members available for building HMMprofiles The identification of a DRD1 subfamily member in Dictyostelium suggests that the subfamilies may be more widespreadthan indicated by the current small sample set The Lmajor Tbrucei and Tcruzi genomes with JBP2 subfamily members alsocontain proteins assigned to the Arip4 subfamily whose members are otherwise found in higher fungi and animals but not inDRD1-containing plants It is possible that a relationship encompasses not only DRD1 and JBP2 but also Arip4

Rad516-like Rad516 Scerevisiae Rad5 and Rad16 proteins are distinct but dual archetypes for this subfamily and both are intimately involved in DNArepair pathways

Rad5p acts with the Ubc13pndashMms2p E2 ligase complex via its RING finger in one fate of the Rad6 pathway of replication linkedDNA damage bypass to poly-ubiquitylate PCNA in (177) It has also been suggested that Rad5p participates in double-strandedbreak repair in a role dependent on its helicase-like region but not its RING finger (178) A clear function for the helicase-like motorin either role has not been suggested

Rad16p acts in complex with Rad7p and Elc1p as the NEF4 nucleotide excision repair factor (179180) possibly scanning alongchromatin for lesions as part of non-transcribed strand repair (179) or by distorting DNA to expose the lesion for processing (17)Although the basis is not known the RING finger of Rad16p influences the stability of the Rad4 protein responsible for recognizingthe lesion (180)

Paradoxically no DNA repair link has been reported for the single member of the Rad516 subfamily present in each mammaliangenome such as human SMARCA3 (see also Lodestar and ERCC6 sections of this table) Instead under the nameRUSH1alpha some have been reported as steroid regulated transcriptional regulators (181) and under the name HLTF to besilenced in cancers (182)

Ris1 The Ris1 protein from Scerevisiae interacts with Sir4p and has a role in mating type silencing (183) Members are found in all fungiand plant genomes but not in animals or lower eukaryotes

Lodestar This subfamily is the only one within the Rad516 grouping which does not contain RING fingers in the major insertion site(Figure S3B) Dmelanogaster Lodestar protein was first identified as an essential cell-cycle regulated protein localizing tochromosomes during mitosis (184) Subsequently the human homologue TTF2 was shown to terminate elongating RNA pol I andpol II complexes independently of transcript length possibly by directly clearing Pol II from the template at the entry to mitosis(185) TTF2 may also have a role in interphase termination and in repair (185) This suggestion is interesting because no clearfunctional homologue of Scerevisiae Rad5p has been identified in the higher eukaryote genomes which Lodestar is restricted to(see also ERCC6 section of this table) TTF2 has been observed to rescue RNA polymerases stalled at lesions (186)

SHPRH SHPRH proteins derive their name from the ordered sequence of domains Snf2_N Linker_Histone (ie H1) PHD finger Zf_C3HC4(ie e RING finger) Helicase_C in the human member (187) (Supplementary Figure S3B) The Linker_Histone and PHD fingermotifs are located adjacent to each other at the minor insertion site between motifs I and Ia whereas the RING finger domain islocated at the major insertion site The linker histone-related domain in human SHPRH corresponds to the globular winged helixstructure of histone H1 (188) and transcription factor HNF3 (189190) The PHD finger motifs are specialized zinc finger structureswhich occur in a range of proteins involved in chromatin-mediated transcriptional regulation but whose exact function is unclear(191192)

Fungal SHPRH subfamily members typically do not contain the linker histone-related motif although they do contain the PHD andRING finger domains Animal SHPRH members contain an additional 50 kDa polypeptide sequence immediately upstream ofthe RING finger domain within the major insertion region (Supplementary Figure S3B) Although lacking an identifiable motif thisregion has a number of cysteines suggestive of a zinc finger type coordination and has some 30 charged residues Fungal membersalso contain a significant region of charged residues ahead of the RING finger

SSO1653-like Mot1 Scerevisiae Mot1 protein (Modifier of Transcription) (193) and homologues with highly conserved helicase-like regions are presentacross fungi and all higher eukaryotes where they are known as BTAF1 or TAF172 (194) In vitro and in vivo studies suggest thatMot1p interacts intimately with TBP (195) probably acting to recycle it from DNA-bound states (196) Mot1p is therefore thoughtto be a Snf2 family enzyme whose role is not to manipulate nucleosome structure although a possible direct involvement withchromatin has also been proposed (197)

ERCC6 Human ERCC6 protein (198) also known as Cockayne Syndrome B (CSB) and Scerevisiae homologue Rad26p (199) were initiallyregarded as repair proteins due to effects on transcription coupled nucleotide excision repair However it has more recently beensuggested that the function of these proteins may be to assist transcribing RNA polymerases to either pass or dissociate fromblocking DNA lesions (200) Such a role would not directly involve chromatin The consequent barriers to transcription elongationand sensitivity to DNA damage for non-functional mutants would explain features of Cockayne syndrome and is analogous to therole of the non-Snf2 family Mfd DNA translocase from Escherichia coli (201)

Most higher animal genomes contain three separate genes assigned to the ERCC6 subfamily along with single Lodestar and Rad516subfamily members Conversely fungal genomes typically encode a single ERCC6 member no Lodestar subfamily member butat least two Rad516 members This may reflect divergent strategies for accomplishing transcription-coupled repair

A number of mutations in the helicase region which result in Cockayne syndrome have been identified and these map to interestinglocations in the Snf2 family crystal structures (46198) In vitro purified ERCC6 protein can alter nuclease sensitivity and spacingof nucleosomes in an ATP-dependent manner (202) ERCC6 can also bind and negatively supercoil DNA in the presence ofnon-hydrolysable ATP analogues (203)

SSO1653 SSO1653 the sole Snf2 family member in archaeal Ssolfataricus is the archetype for the uniquely archaeal and eubacterial subfamilymost similar to the eukaryotic Snf2 proteins (see text) It is encoded in the P2 strain genome by juxtaposing SSO1653 and SSO1655genes which are punctuated by transposase SSO1654 inserted into the second recA domain immediately upstream of motif VAlthough it is highly unlikely that a Snf2 family enzyme would be functional with a 40 kDa transposase insertion in this conservedpart of the protein the enzyme with transposase removed can generate DNA torsion in an ATP-dependent analogous to eukaryoticSnf2 family proteins and was used successfully for structure determination (46) Since a full-length gene can be cloned withappropriate screening (M F White personal communication) the SSO1654 transposase must be active and we refer to there-fusion of SSO1653 and SSO1655 for simplicity as SSO1653 No information is available for the biological role of any memberof the subfamily although a role in an archaeal chromatin remodelling can be excluded because Ssolfataricus lacks archaealhistone-like proteins


Although rapA group proteins are distinguished by thelack of several features characteristic of eukaryotic Snf2family members (see above) the SSO1653 subfamily carriesall the Snf2 family sequence and structural hallmarks(Supplementary Figure S4) SSO1653 subfamily membersare present in both bacteria and archaea but they are notubiquitous in archaeal genomes despite the presence of tran-scription replication and repair mechanisms with significantsimilarity to those of eukaryotes (5455) There is also noobvious linkage between the presence of histone-like proteinsand SSO1653 subfamily members in archaeal genomes(Supplementary Table S1B) Furthermore the SSO1653 sub-family falls in a grouping (Figure 1C) with the eukaryoticERCC6 and Mot1 subfamilies whose biochemical roleappears not to involve chromatin directly In contrast to thelimited archaeal and bacterial distribution of Snf2 familyproteins all eukaryote genomes contain multiple Snf2 familyproteins The early branching Giardia lamblia and theminimal Encephalozooan cuniculi genomes both encode sixdifferent Snf2 family genes falling into subfamilies repre-sented across eukarya (Supplementary Table S1A) severalof which have clear linkage to chromatin transactions It istherefore possible that the microbial SSO1653 subfamilyrepresents an ancestral Snf2-like form from which theeukaryotic subfamilies radiated Such expansion of the Snf2family early in eukaryote evolution (20) could have beencoincident with the development of high-density nucleosomalpackaging (56)

Distribution of Snf2 family membersin complete genomes

The linkage between the primary sequence-based definitionsof the subfamilies and distinct biological function is stronglysupported by the presence of one or more subfamily membersin each eukaryotic genome across large evolutionary ranges(Table 2 and Supplementary Table S1A) For example acommon set of subfamilies are found in almost all fungiplant and animal genomes comprising Snf2 Iswi Chd1Swr1 Etl1 Mot1 Ino80 Rad516 ERCC6 Rad54 andSHPRH Increased genomic complexity is also paralleled byincreasing numbers of subfamilies and members Ecuniculiwith a genome encoding some 2000 gene products has6 Snf2 family members from 6 subfamilies whereas theScerevisiae genome encoding some 6000 genes has 17 Snf2family members from 13 subfamilies and the human genomeencoding some 25 000 genes has 32 Snf2 family genes from20 subfamilies (Table 2 part B)

The functional linkage across large evolutionary rangessuggests that each subfamily may have distinctive propertiesof their ATPase motors tuned to their function This issupported by recent biochemical results demonstrating thathelicase-like regions can be swapped within but not betweensubfamilies (57) However a counterpoint is that functionalredundancy can occur between subfamilies For examplesynthetic deletion of all three of the Scerevisiae ISW1ISW2 and CHD1 genes together is required to generate a

Table 3 Continued


SSO1653-like(cont)

The SSO1653 subfamily helicase-like region also shows close linkage with a zinc finger SWIM motif that may bind to nucleic acids(204205) For example coordinately regulated SSO1656 immediately downstream of SSO1653ndash1655 encodes a 26 kDa basicprotein containing the SWIM motif An SSO1653 subfamily member is present in all Bacillus and Streptococcus genomes (21) andmany of these polypeptides also carry a SWIM motif in the same polypeptide Polypeptides with a Snf2 family helicase-like regionbut lacking a SWIM motif appear to be in the same operon as a second smaller protein which carries the SWIM motif instead (204)Although the SWIM motif also occurs in eukaryotes it has not been linked to any of the eukaryotic Snf2 family proteins (204)

Distant SMARCAL1 The human SMARCAL1 (SMARCA-Like 1) protein and homologues also known as HARP (22) are unusual within the analysisbecause they include two subtypes with highly similar helicase-like regions that are flanked by completely different auxiliarydomains The first consists of proteins in higher eukaryotes related to human SMARCAL1 itself with centrally located helicase-likeregions and one or more Harp motifs immediately N-terminal to this Mutants in the helicase-like region of human SMARCAL1have been linked to a genetic disorder Schimke immuno-osseous dysplasia (206) although the molecular function of theSMARCAL1 protein is unknown The bovine homologue ADAAD is stimulated by DNA single-double strand boundaries (207)

The second subtype is found in animal plant and some protist genomes and contains SMARCAL1 subfamily members related inoverall domain organization to the human ZRANB3 protein (Zinc finger RAN-Binding domain containing 3) The helicase regionis located at the N-terminus of the polypeptide followed by an unusual zinc finger structure related to those found in Ran proteinbinding proteins (208) and a putative HNH type endonuclease domain at the C-terminus (209) No functional information aboutany proteins in this subtype is available

rapA group The rapA group includes some 220 eubacterial and archaeal members with significantly more sequence variation than othersubfamilies Subsets of sequences are qualitatively visible within multiple alignments of the rapA group but initial attempts todistinguish them have been unreliable due to the variability of microbial sequences and non-homogeneous sampling in sequencedorganisms (eg half of all complete bacterial genomes are for a limited range of firmicute and gamma proteobacterial genera)

Although the rapA group contains the conserved sequence patterns of the Snf2 family for the classical helicase-like motifs otherconserved blocks cannot be easily identified (Supplementary Figure S4) The characteristic extended span of at least 160 residuesbetween helicase motifs III and IV (44) is maintained in the rapA group but the central part of this region diverges markedly fromthe other subfamilies and lacks the highly conserved features characteristic of the Snf2 family The specific difficulty of aligningthis region has been remarked previously (20)

The rapA group also includes a number of polypeptides for which the helicase-like region comprises effectively the entirepolypeptide in contrast with other Snf2 family members which almost universally contain sequences outside the helicase-likeregion that are likely to form accessory domains or interaction surfaces

The only member of this group for which biological function has been investigated is Ecoli rapA also known as HepA (210) whichinfluences polymerase recycling under high salt conditions possibly by aiding the release of stalled polymerases (211)

Summaries of known biochemical biological and distinctive sequence of each subfamily Background colouring of subfamilies for groupings as shown in Figure 1


strong phenotype (5859) Redundancy also provides anexplanation why some genomes lack certain members thesmall genome of Schizosaccharomyces pombe lacks an Iswisubfamily member but maintains two Chd1 subfamily mem-bers In addition to the 11 subfamilies represented broadlyacross eukaryotes are a number of others restricted to specifictaxonomic ranges For example CHD7 members are foundalmost exclusively in animals and ATRX members arefound only in animals and plants

Subfamily-specific properties

A number of specific features contribute to the distinctionbetween subfamilies First the spacing between motifs IIIand IV is extended significantly beyond the minimal 160residues for a number of subfamilies (Table 4) For theRad516 Ris1 and SHPRH subfamilies the additionalsequences all include RING fingers whereas for the Swr1and EP400 subfamilies they comprise highly proline andserinethreonine-rich spans Ino80 and ATRX subfamilies

also contain large novel and distinct spans Remarkably allthese large extra insertions occur at the same location in theprimary sequence between conserved blocks C and K whichwe term the lsquomajor insertion sitersquo (Figure 3G and Supplemen-tary Figure S7A) Even for the subfamilies without largeinsertions there is variation in the length of sequence in themajor insertion site (Table 4) For example the ZebrafishRad54 structure contains some 25 more residues formingtwo additional small alpha helices compared to the Sulfolobussolfataricus SSO1653 structure When Snf2 family membersfrom different subfamilies are aligned the variability of themajor insertion region strongly disturbs the alignment suchthat a contiguous pattern becomes difficult to define Thishas led to some of the Snf2 family proteins being describedas having lsquosplitrsquo helicase-like ATPase regions The disconti-nuity is also the cause of protein motif databases such asSMART and Pfam defining Snf2 family members as match-ing a bipartite combination of SNF2_N and Helicase_C pro-files (Figure 3G) The C-terminal end of the SNF2_N profilecorresponds to conserved block C

Second subfamilies have characteristic small insertions atother sites (Table 4) Two such sites also in the motif IIIndashIVregion are located between conserved blocks H and B andbetween J and C (Figure 2) These are likely to influencethe length of the long alpha helical protrusions 1 and 2respectively (see below Figure 3C) and there is a differenceof some 40 residues between the shortest and longest subfam-ily lengths for each (Table 4) A lsquominor insertion sitersquo locatedbetween motifs I and Ia on the back of recA-like domain 1 isalso occupied by recognizable domains in a few subfamiliesfrom the Rad516-like grouping such as SHPRH (Supplemen-tary Figure S3B) A number of other small insertions map toloops between various secondary structural elements (datanot shown)

Third although adhering to a general Snf2 family-specificpattern individual subfamilies show characteristic patternsin the helicase motifs and in other conserved blocks(Supplementary Figure S4) For example the well-knownhelicase motif II with typical DEAH pattern favours DEGHin the Snf2 Mot1 and Rad54 subfamilies DEAQ in theSwr1 EP400 Ino80 and SSO1653 subfamilies or DESH inthe SMARCAL1 subfamily Likewise for the typical con-served block Emdashmotif I combined pattern ILADEMGLGKTall ATRX subfamily members have histidine instead of aspar-tate (ie ILAHEMGLGKT) and most Mot1 subfamily mem-bers have cysteine replacing alanine (ie ILCDEMGLGKT)It is also possible to identify other residues correlating withgroups of subfamilies For example members of the Snf2Iswi Chd1 Mi-2 CHD7 ALC1 Rad54 ATRX and Arip4subfamilies have an arginine immediately following themotif II DEAH In the zebrafish Rad54 structure this residueR294 interacts with the sulphate which is suggested to mimicthe ATP gamma phosphate

Conserved blocks encode the unique structuralfeatures of the Snf2 family

Two structural determinations of the helicase-like regionsof Snf2 family members have been presented recentlyzebrafish Rad54 (pdb code 1Z3I) (47) and SsolfataricusSSO1653 (pdb codes 1Z6A 1Z63 1Z5Z) (46) As expected

Figure 2 Conserved residues within Snf2 helicase-like region Sequence logoof global multiple alignment of 1306 Snf2 helicase-like region for alignmentpositions with residues in gt90 of proteins Helicase motifs are indicated insolid black boxes with roman numerals IndashIV additional conserved blocks areindicated in dashed black boxes with uppercase letters AndashN and conservedhydrophobic residues packing in the core of the structure by grey solid boxesMotif and box labels as in Thoma et al (47) with extensions A comparison toother nomenclatures is in Supplementary Table S5 See Table 4 for actualdistances between conserved blocks


for members of the Snf2 family the fold of each core recA-like domain in the Rad54 and SSO1653 structures is substan-tially similar and related to those of other known SF1 andSF2 helicases In the zebrafish Rad54 structure the two recA-

like domains are oriented equivalently to those of otherknown helicase structures (Figure 3A and B) whereas inthe Ssolfataricus SSO1653 structures recA-like domain 2 isflipped by 180 to an arrangement never previously observed

Figure 3 Conserved blocks contribute to distinctive structural features of Snf2 family proteins Structural components of Snf2 family proteins relevant to theconservation are illustrated on the zebrafish Rad54A structure [pdb 1Z3I (153)] (A) core recA-like domains 1 and 2 including colouring of helicase motifs (I in greenIa in blue II in bright red III in yellow IV in cyan V in teal and VI in dark red) (B) Q motif (pink) (C) antiparallel alpha helical protrusions 1 and 2 (red) projectingfrom recA-like domains 1 and 2 respectively (D) Linker spanning from protrusion 1 to protrusion 2 (middle blue) (E) Major insertion region behind protrusion 2(light green) (F) triangular brace (magenta) (G) Schematic diagram showing location of structural elements and helicase motifs coloured as in AndashF with conservedblocks from Figure 2 shown as white boxes Spans identified by Pfam profiles SNF2_N and Helicase_C are shown flanking the major insertion site


for a helicase (Supplementary Figure S7B) This unusualorientation in SSO1653 is observed for both the DNA freeand DNA-bound forms (46)

The most striking feature of the Snf2 family structures isthe presence of several additional structural elements graftedonto the core helicase structure These comprise antiparallelalpha helical protrusions from both recA-like domains1 and 2 (Figure 3C) a structured linker between the recA-likedomains (Figure 3D) the major insertion region at the backside of the domain 2 alpha helical protrusion (Figure 3E)and a triangular brace packed against the domain 2 alphahelical protrusion (Figure 3F) The two alpha-helical protru-sions and linker are all encoded within the enlarged spanbetween motifs III and IV The triangular brace is encodedimmediately downstream of motif VI

Remarkably the primary sequence features of the Snf2family correspond directly to the additional structural ele-ments (Figure 3G) First the bases of the protrusions fromrecA-like domains 1 and 2 are both fixed by conservedblocks For protrusion 1 this involves conserved block Hcomposed of a repeating pattern of aromatic residues withadditional involvement of aromatics from conserved blockA For protrusion 2 this involves the arrangement of con-served blocks C J and K Second the protrusions themselvesare relatively conserved in sequence and length withinsubfamilies but not across the whole Snf2 family Althoughthere is no obvious correlation between the lengths of the pro-trusions 1 and 2 the distribution of protrusion lengths adheresto multiples of the alpha helical repeat (Supplementary FigureS8) suggesting that protrusions retain structure while varyingin extension Third the Q motif structure found in many SF2proteins utilizes a different arrangement of residues to DEADbox helicases such as eIF4A where an aromatic residue

orients the adenine base ring for contacts with a downstreamglutamine (4) (Figures 3B) In the Snf2 family the aromaticresidue is contributed by conserved block F downstreamof the glutamine The Q motif affects ATP hydrolysis inDEAD box helicases and mutation of the core glutamine inyeast Snf2 subfamily member Sth1p causes slow growth(4) Fourth the linker connecting protrusions 1 and 2 containshighly conserved dual arginines in conserved block BTheir central location between the ATP-associating andDNA-associating structural elements suggests that they mayplay an important role in the mechanism of Snf2 familyenzymes Consistent with this mutation of the second argi-nine of the pair in Snf2p leads to effectively complete lossof function of the protein in vivo (48) Finally the brace iscomposed of a principal alpha helix anchored by conservedblock M into the junction at the base of protrusion 2 composedof conserved blocks C J and K

The major insertion region is immediately behind pro-trusion 2 almost diametrically opposite the ATP-bindingsite in the zebrafish Rad54 structure (Figure 3E) The nearestresidues of the major insertion region in Rad54 are some15 s from DNA phosphates for docked DNA (SupplementaryFigure S7A) However an appropriately oriented alpha helixof some 20 residues would be sufficient to reach into themajor groove so large insertions at the major insertion sitecould potentially interact with DNA or other DNA-bindingproteins bound in the groove In the flipped conformationof domain 2 observed in the SSO1653 structure the majorinsertion region is juxtaposed immediately adjacent to theDNA such that two non-conserved arginines from the majorinsertion region make direct DNA phosphate contacts

As the distinctive structural features are defined byunique and highly conserved blocks they are likely to confer

Table 4 Spacings between helicase motifs and major conserved blocks by subfamily

QndashI IndashIa IandashII IIndashIII IIIndashB BndashC CndashK KndashIV IVndashV VndashVI

Snf2 17 (00) 24 (01) 66 (07) 25 (03) 63 (18) 65 (32) 26 (40) 18 (00) 46 (02) 21 (00)Iswi 17 (00) 24 (00) 68 (72) 24 (01) 53 (17) 61 (12) 21 (03) 18 (00) 46 (23) 21 (00)Lsh 17 (00) 23 (03) 70 (77) 24 (00) 65 (117) 110 (336) 23 (44) 18 (18) 46 (12) 21 (00)ALC1 17 (00) 24 (00) 69 (42) 24 (04) 53 (29) 61 (29) 19 (25) 18 (00) 47 (53) 21 (00)Chd1 17 (05) 24 (00) 74 (83) 24 (00) 49 (42) 61 (04) 24 (24) 18 (00) 46 (00) 21 (00)Mi-2 17 (00) 24 (05) 85 (37) 24 (00) 49 (08) 61 (28) 26 (19) 18 (00) 46 (01) 21 (00)CHD7 17 (18) 23 (03) 78 (60) 24 (02) 49 (02) 62 (17) 33 (52) 18 (01) 46 (03) 21 (00)Swr1 17 (00) 24 (00) 67 (00) 24 (00) 64 (80) 60 (00) 484 (3065) 18 (00) 45 (00) 21 (00)EP400 17 (00) 40 (00) 51 (00) 24 (00) 53 (00) 60 (00) 469 (379) 18 (00) 45 (00) 24 (00)Ino80 17 (00) 24 (00) 73 (24) 24 (00) 59 (02) 69 (43) 280 (272) 18 (00) 45 (02) 21 (00)Etl1 17 (02) 24 (24) 71 (47) 24 (04) 60 (34) 67 (185) 68 (25) 18 (07) 45 (14) 21 (00)Rad54 26 (150) 29 (30) 71 (43) 24 (00) 64 (24) 60 (24) 36 (106) 19 (18) 47 (15) 20 (00)ATRX 25 (38) 25 (19) 87 (104) 24 (00) 49 (06) 75 (86) 105 (371) 18 (15) 65 (84) 21 (00)Arip4 25 (20) 25 (59) 118 (163) 24 (00) 64 (00) 59 (15) 101 (368) 18 (00) 61 (71) 21 (00)DRD1 26 (60) 42 (05) 76 (139) 24 (00) 67 (116) 59 (37) 32 (26) 18 (04) 51 (07) 21 (00)JBP2 23 (118) 31 (155) 86 (131) 24 (10) 22 (10) 92 (36) 75 (207) 18 (05) 46 (30) 21 (00)Rad516 49 (241) 68 (582) 79 (169) 24 (00) 62 (157) 70 (18) 123 (281) 20 (19) 48 (52) 20 (00)Ris1 22 (84) 50 (317) 97 (208) 24 (03) 54 (31) 72 (98) 152 (586) 30 (179) 45 (19) 21 (00)Lodestar 19 (57) 44 (198) 78 (109) 24 (04) 47 (35) 97 (174) 60 (258) 19 (32) 46 (07) 21 (00)SHPRH 60 (177) 185 (1345) 92 (118) 24 (16) 59 (229) 74 (43) 475 (1666) 21 (65) 43 (39) 21 (00)Mot1 17 (00) 33 (76) 65 (37) 24 (00) 62 (66) 70 (61) 29 (56) 33 (70) 48 (06) 21 (16)ERCC6 17 (04) 32 (100) 74 (151) 24 (00) 63 (65) 72 (146) 35 (132) 18 (24) 45 (49) 21 (01)SSO1653 17 (00) 25 (108) 63 (23) 24 (10) 51 (55) 65 (25) 12 (29) 18 (10) 44 (16) 21 (00)SMARCAL1 15 (07) 19 (01) 61 (76) 26 (13) 59 (31) 65 (88) 21 (38) 46 (55) 21 (04)

Means and standard deviations (in parentheses) by subfamily for the number of amino acids between helicase motifs and the conserved blocks B C and K calculatedfor 1306 Snf2 family members fromUniref assigned to subfamilies (Table 1) Spacings arecalculated from the edgesof the core conserved residuesof motifsas markedin Supplementary Figure S4


properties to the ATPase motor that adapts the action of thecore recA-like domains for a unique mechanism We antici-pate that while some features of the Snf2 family mechanismwill be common to SF2 translocases other aspects will bedistinctive Knowledge of the conserved residues and theirstructural location provides important information for under-standing these distinctions

Other levels of Snf2 family identity

We have demonstrated that the common helicase-likeregion is sufficient to enable classification of Snf2 familymembers However almost all Snf2 family polypeptides con-tain significant additional sequences likely to harbour acces-sory domains For some subfamilies there is good correlationwith the presence of particular accessory domain combina-tions (Supplementary Table S9) For example almost allSnf2 subfamily members contain a bromodomain ISWImembers contain a SANT domain and Chd1 Mi-2 andCHD7 members contain a chromodomain However manydomain profiles in resources used for domain analysis haveunidentified function or are unreliable in the context ofSnf2 proteins For example Pfam lacks a SANT-specificprofile and detects lt10 of SANT domains with a more gen-eric general lsquoMyb_DNA-bindingrsquo profile We are currentlyundertaking further analysis to improve the relevant profilesand analyse the linkage of Snf2 family accessory domainsin detail

Finally many Snf2 family proteins are part of largermulti-protein complexes Accessory motifs within these com-plexes are also likely to adapt the function of Snf2 motors fordifferent purposes

SUPPLEMENTARY DATA

Supplementary Data are available at NAR Online

ACKNOWLEDGEMENTS

We gratefully acknowledge Chris Stockdale Charlie Bond andHelder Ferreira for comments on this manuscript and DiegoMiranda-Saavedra and Jim Procter for helpful discussionsregarding the analyses We are also indebted to AndrewWaterhouse for providing essential enhancements toJalview and to Jonathan Monk for excellent systems supportWe also thank Prof U Baumann for coordinates of eIF4Awith ADP Dr Kathleen Sandman and Prof John Reeve forproviding a table of histone-like proteins in archaeal genomesand Dr Malcolm White for communicating unpublishedobservations about the SSO1653 protein AF and TOH arefunded by a Wellcome Trust Senior Research Fellowship inBasic Biomedical Science to TOH Funding to pay the OpenAccess publication charges for this article was provided by aWellcome Trust VIP award to the School of Life Sciences inDundee

Conflict of interest statement None declared

REFERENCES

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17 YuS Owen-HughesT FriedbergEC WatersR and ReedSH(2004) The yeast Rad7Rad16Abf1 complex generates superhelicaltorsion in DNA that is required for nucleotide excision repairDNA Repair (Amst) 3 277ndash287

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30 ClampM CuffJ SearleSM and BartonGJ (2004) The JalviewJava alignment editor Bioinformatics 20 426ndash427

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41 MizuguchiG ShenX LandryJ WuWH SenS and WuC(2004) ATP-driven exchange of histone H2AZ variant catalyzed bySWR1 chromatin remodeling complex Science 303 343ndash348

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43 KroganNJ KeoghMC DattaN SawaC RyanOW DingHHawRA PootoolalJ TongA CanadienV et al (2003) A Snf2family ATPase complex required for recruitment of the histoneH2A variant Htz1 Mol Cell 12 1565ndash1576

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46 DurrH KornerC MullerM HickmannV and HopfnerKP (2005)X-ray structures of the Sulfolobus solfataricus SWI2SNF2 ATPasecore and its complex with DNA Cell 121 363ndash373

47 ThomaNH CzyzewskiBK AlexeevAA MazinAVKowalczykowskiSC and PavletichNP (2005) Structure of theSWI2SNF2 chromatin-remodeling domain of eukaryotic Rad54Nature Struct Mol Biol 12 350ndash356

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ortholog of archaeal DNA repair protein Hef is defective inFanconi anemia complementation group M Nature Genet 37958ndash963

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59 TsukiyamaT PalmerJ LandelCC ShiloachJ and WuC (1999)Characterization of the imitation switch subfamily of ATP-dependentchromatin-remodeling factors in Saccharomyces cerevisiaeGenes Dev 13 686ndash697

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61 CairnsBR LorchY LiY ZhangM LacomisL Erdjument-BromageH TempstP DuJ LaurentB and KornbergRD (1996)RSC an essential abundant chromatin-remodeling complexCell 87 1249ndash1260

62 TamkunJW DeuringR ScottMP KissingerM PattatucciAMKaufmanTC and KennisonJA (1992) brahma a regulator ofDrosophila homeotic genes structurally related to the yeasttranscriptional activator SNF2SWI2 Cell 68 561ndash572

63 MuchardtC and YanivM (1993) A human homologue ofSaccharomyces cerevisiae SNF2SWI2 and Drosophila brm genespotentiates transcriptional activation by the glucocorticoid receptorEMBO J 12 4279ndash4290

64 KhavariPA PetersonCL TamkunJW MendelDB andCrabtreeGR (1993) BRG1 contains a conserved domain of theSWI2SNF2 family necessary for normal mitotic growth andtranscription Nature 366 170ndash174

65 WhitehouseI FlausA CairnsBR WhiteMF WorkmanJL andOwen-HughesT (1999) Nucleosome mobilization catalysed by theyeast SWISNF complex Nature 400 784ndash787

66 KassabovSR ZhangB PersingerJ and BartholomewB (2003)SWISNF unwraps slides and rewraps the nucleosome Mol Cell11 391ndash403

67 NarlikarGJ PhelanML and KingstonRE (2001) Generation andinterconversion of multiple distinct nucleosomal states as amechanism for catalyzing chromatin fluidity Mol Cell8 1219ndash1230

68 LorchY ZhangM and KornbergRD (1999) Histone octamertransfer by a chromatin-remodeling complex Cell 96 389ndash392

69 BrunoM FlausA StockdaleC RencurelC FerreiraH andOwen-HughesT (2003) Histone H2AH2B dimer exchange byATP-dependent chromatin remodeling activities Mol Cell12 1599ndash1606

70 XueY CanmanJC LeeCS NieZ YangD MorenoGTYoungMK SalmonED and WangW (2000) The human SWISNF-B chromatin-remodeling complex is related to yeast rsc andlocalizes at kinetochores of mitotic chromosomes Proc NatlAcad Sci USA 97 13015ndash13020


71 SifS SaurinAJ ImbalzanoAN and KingstonRE (2001)Purification and characterization of mSin3A-containing Brg1 andhBrm chromatin remodeling complexes Genes Dev 15603ndash618

72 HarikrishnanKN ChowMZ BakerEK PalS BassalSBrasacchioD WangL CraigJM JonesPL SifS et al (2005)Brahma links the SWISNF chromatin-remodeling complex withMeCP2-dependent transcriptional silencing Nature Genet 37254ndash264

73 XuW ChoH KadamS BanayoEM AndersonS YatesJRIIIEmersonBM and EvansRM (2004) A methylation-mediatorcomplex in hormone signaling Genes Dev 18 144ndash156

74 DunaiefJL StroberBE GuhaS KhavariPA AlinK LubanJBegemannM CrabtreeGR and GoffSP (1994) Theretinoblastoma protein and BRG1 form a complex and cooperate toinduce cell cycle arrest Cell 79 119ndash130

75 ZhangHS GavinM DahiyaA PostigoAA MaD LuoRXHarbourJW and DeanDC (2000) Exit from G1 and S phase of thecell cycle is regulated by repressor complexes containingHDAC-Rb-hSWISNF and Rb-hSWISNF Cell 101 79ndash89

76 MoshkinYM ArmstrongJA MaedaRK TamkunJWVerrijzerP KennisonJA and KarchF (2002) Histone chaperoneASF1 cooperates with the Brahma chromatin-remodelling machineryGenes Dev 16 2621ndash2626

77 WilsonCJ ChaoDM ImbalzanoAN SchnitzlerGRKingstonRE and YoungRA (1996) RNA polymerase IIholoenzyme contains SWISNF regulators involved in chromatinremodeling Cell 84 235ndash244

78 MetivierR PenotG HubnerMR ReidG BrandH KosM andGannonF (2003) Estrogen receptor-alpha directs ordered cyclicaland combinatorial recruitment of cofactors on a natural targetpromoter Cell 115 751ndash763

79 HuangJ HsuJM and LaurentBC (2004) The RSCnucleosome-remodeling complex is required for Cohesinrsquos associationwith chromosome arms Mol Cell 13 739ndash750

80 PetersonCL and WorkmanJL (2000) Promoter targeting andchromatin remodeling by the SWISNF complex Curr OpinGenet Dev 10 187ndash192

81 HassanAH NeelyKE and WorkmanJL (2001) Histoneacetyltransferase complexes stabilize swisnf binding to promoternucleosomes Cell 104 817ndash827

82 AgaliotiT ChenG and ThanosD (2002) Deciphering thetranscriptional histone acetylation code for a human geneCell 111 381ndash392

83 ElfringLK DeuringR McCallumCM PetersonCL andTamkunJW (1994) Identification and characterization of Drosophilarelatives of the yeast transcriptional activator SNF2SWI2Mol Cell Biol 14 2225ndash2234

84 TsukiyamaT DanielC TamkunJ and WuC (1995) ISWI amember of the SWI2SNF2 ATPase family encodes the 140 kDasubunit of the nucleosome remodeling factor Cell 83 1021ndash1026

85 ItoT BulgerM PazinMJ KobayashiR and KadonagaJT (1997)ACF an ISWI-containing and ATP-utilizing chromatin assembly andremodeling factor Cell 90 145ndash155

86 Varga-WeiszPD WilmM BonteE DumasK MannM andBeckerPB (1997) Chromatin-remodelling factor CHRAC containsthe ATPases ISWI and topoisomerase II Nature 388 598ndash602

87 HamicheA KangJG DennisC XiaoH and WuC (2001)Histone tails modulate nucleosome mobility and regulateATP-dependent nucleosome sliding by NURF Proc NatlAcad Sci USA 98 14316ndash14321

88 ClapierCR NightingaleKP and BeckerPB (2002) A criticalepitope for substrate recognition by the nucleosome remodelingATPase ISWI Nucleic Acids Res 30 649ndash655

89 FazzioTG GelbartME and TsukiyamaT (2005) Two distinctmechanisms of chromatin interaction by the Isw2 chromatinremodeling complex in vivo Mol Cell Biol 25 9165ndash9174

90 DirscherlSS and KrebsJE (2004) Functional diversity of ISWIcomplexes Biochem Cell Biol 82 482ndash489

91 EberharterA and BeckerPB (2004) ATP-dependent nucleosomeremodelling factors and functions J Cell Sci 117 3707ndash3711

92 TsukiyamaT (2002) The in vivo functions of ATP-dependentchromatin-remodelling factors Nature Rev Mol Cell Biol 3422ndash429

93 PootRA BozhenokL van den BergDL HawkesN andVarga-WeiszPD (2005) Chromatin remodeling by WSTF-ISWI atthe replication site opening a window of opportunity for epigeneticinheritance Cell Cycle 4 543ndash546

94 JarvisCD GeimanT Vila-StormMP OsipovichO AkellaUCandeiasS NathanI DurumSK and MueggeK (1996) A novelputative helicase produced in early murine lymphocytes Gene169 203ndash207

95 SunLQ and ArceciRJ (2005) Altered epigenetic patterning leadingto replicative senescence and reduced longevity A role of a novelSNF2 factor PASG Cell Cycle 4 3ndash5

96 VongsA KakutaniT MartienssenRA and RichardsEJ (1993)Arabidopsis thaliana DNA methylation mutants Science260 1926ndash1928

97 DennisK FanT GeimanT YanQ and MueggeK (2001) Lsh amember of the SNF2 family is required for genome-widemethylation Genes Dev 15 2940ndash2944

98 MueggeK (2005) Lsh a guardian of heterochromatin at repeatelements Biochem Cell Biol 83 548ndash554

99 BrzeskiJ and JerzmanowskiA (2003) Deficient in DNAmethylation 1 (DDM1) defines a novel family ofchromatin-remodeling factors J Biol Chem 278 823ndash828

100 GuanXY FangY ShamJS KwongDL ZhangY LiangQLiH ZhouH and TrentJM (2000) Recurrent chromosomealterations in hepatocellular carcinoma detected by comparativegenomic hybridization Genes Chromosomes Cancer 29 110ndash116

101 MaoM FuG WuJS ZhangQH ZhouJ KanLX HuangQHHeKL GuBW HanZG et al (1998) Identification of genesexpressed in human CD34(+) hematopoietic stemprogenitor cells byexpressed sequence tags and efficient full-length cDNA cloningProc Natl Acad Sci USA 95 8175ndash8180

102 YanL EcheniqueV BussoC SanMiguelP RamakrishnaWBennetzenJL HarringtonS and DubcovskyJ (2002) Cereal genessimilar to Snf2 define a new subfamily that includes human andmouse genes Mol Genet Genomics 268 488ndash499

103 KarrasGI KustatscherG BuhechaHR AllenMD PugieuxCSaitF BycroftM and LadurnerAG (2005) The macro domain is anADP-ribose binding module EMBO J 24 1911ndash1920

104 DelmasV StokesDG and PerryRP (1993) A mammalianDNA-binding protein that contains a chromodomain and an SNF2SWI2-like helicase domain Proc Natl Acad Sci USA 902414ndash2418

105 BrehmA TuftelandKR AaslandR and BeckerPB (2004) Themany colours of chromodomains Bioessays 26 133ndash140

106 Tajul-ArifinK TeasdaleR RavasiT HumeDA and MattickJS(2003) Identification and analysis of chromodomain-containingproteins encoded in the mouse transcriptome Genome Res13 1416ndash1429

107 WoodageT BasraiMA BaxevanisAD HieterP and CollinsFS(1997) Characterization of the CHD family of proteins Proc NatlAcad Sci USA 94 11472ndash11477

108 TranHG StegerDJ IyerVR and JohnsonAD (2000) Thechromo domain protein chd1p from budding yeast is anATP-dependent chromatin-modifying factor EMBO J19 2323ndash2331

109 LusserA UrwinDL and KadonagaJT (2005) Distinct activities ofCHD1 and ACF in ATP-dependent chromatin assembly NatureStruct Mol Biol 12 160ndash166

110 KroganNJ KimM AhnSH ZhongG KoborMS CagneyGEmiliA ShilatifardA BuratowskiS and GreenblattJF (2002)RNA polymerase II elongation factors of Saccharomyces cerevisiae atargeted proteomics approach Mol Cell Biol 22 6979ndash6992

111 Pray-GrantMG DanielJA SchieltzD YatesJRIII andGrantPA (2005) Chd1 chromodomain links histone H3 methylationwith SAGA- and SLIK-dependent acetylation Nature 433 434ndash438

112 KroganNJ KimM TongA GolshaniA CagneyG CanadienVRichardsDP BeattieBK EmiliA BooneC et al (2003)Methylation of histone H3 by Set2 in Saccharomyces cerevisiae islinked to transcriptional elongation by RNA polymerase II Mol CellBiol 23 4207ndash4218

113 KelleyDE StokesDG and PerryRP (1999) CHD1 interacts withSSRP1 and depends on both its chromodomain and its ATPasehelicase-like domain for proper association with chromatinChromosoma 108 10ndash25


114 WalfridssonJ BjerlingP ThalenM YooEJ ParkSD andEkwallK (2005) The CHD remodeling factor Hrp1 stimulatesCENP-A loading to centromeres Nucleic Acids Res 33 2868ndash2879

115 Jae YooE Kyu JangY Ae LeeM BjerlingP Bum KimJEkwallK Hyun SeongR and Dai ParkS (2002) Hrp3 achromodomain helicaseATPase DNA binding protein is required forheterochromatin silencing in fission yeast Biochem Biophys ResCommun 295 970ndash974

116 SeeligHP MoosbruggerI EhrfeldH FinkT RenzM andGenthE (1995) The major dermatomyositis-specific Mi-2autoantigen is a presumed helicase involved in transcriptionalactivation Arthritis Rheum 38 1389ndash1399

117 BowenNJ FujitaN KajitaM and WadePA (2004) Mi-2NuRDmultiple complexes for many purposes Biochim Biophys Acta1677 52ndash57

118 BouazouneK MitterwegerA LangstG ImhofA AkhtarABeckerPB and BrehmA (2002) The dMi-2 chromodomains areDNA binding modules important for ATP-dependent nucleosomemobilization EMBO J 21 2430ndash2440

119 SchultzDC FriedmanJR and RauscherFJIII (2001) Targetinghistone deacetylase complexes via KRAB-zinc finger proteins thePHD and bromodomains of KAP-1 form a cooperative unit thatrecruits a novel isoform of the Mi-2alpha subunit of NuRDGenes Dev 15 428ndash443

120 KorenjakM Taylor-HardingB BinneUK SatterleeJSStevauxO AaslandR White-CooperH DysonN and BrehmA(2004) Native E2FRBF complexes contain Myb-interacting proteinsand repress transcription of developmentally controlled E2F targetgenes Cell 119 181ndash193

121 WhitePS ThompsonPM GotohT OkawaER IgarashiJKokM WinterC GregorySG HogartyMD MarisJM et al(2005) Definition and characterization of a region of 1p363consistently deleted in neuroblastoma Oncogene 24 2684ndash2694

122 ThompsonPM GotohT KokM WhitePS and BrodeurGM(2003) CHD5 a new member of the chromodomain gene family ispreferentially expressed in the nervous system Oncogene22 1002ndash1011

123 OgasJ KaufmannS HendersonJ and SomervilleC (1999)PICKLE is a CHD3 chromatin-remodeling factor that regulates thetransition from embryonic to vegetative development in ArabidopsisProc Natl Acad Sci USA 96 13839ndash13844

124 VissersLE van RavenswaaijCM AdmiraalR HurstJAde VriesBB JanssenIM van der VlietWA HuysEHde JongPJ HamelBC et al (2004) Mutations in a new member ofthe chromodomain gene family cause CHARGE syndrome NatureGenet 36 955ndash957

125 JongmansM AdmiraalR van der DonkK VissersL BaasAKapustaL van HagenA DonnaiD de RavelT VeltmanJ et al(2006) CHARGE syndrome the phenotypic spectrum of mutations inthe CHD7 gene J Med Genet 43 306ndash314

126 SchusterEF and StogerR (2002) CHD5 defines a new subfamily ofchromodomain-SWI2SNF2-like helicases Mamm Genome13 117ndash119

127 ShurI and BenayahuD (2005) Characterization and functionalanalysis of CReMM a novel chromodomain helicase DNA-bindingprotein J Mol Biol 352 646ndash655

128 DaubresseG DeuringR MooreL PapoulasO ZakrajsekIWaldripWR ScottMP KennisonJA and TamkunJW (1999)The Drosophila kismet gene is related to chromatin-remodelingfactors and is required for both segmentation and segment identityDevelopment 126 1175ndash1187

129 SrinivasanS ArmstrongJA DeuringR DahlsveenIKMcNeillH and TamkunJW (2005) The Drosophila trithorax groupprotein Kismet facilitates an early step in transcriptional elongation byRNA Polymerase II Development 132 1623ndash1635

130 WuWH AlamiS LukE WuCH SenS MizuguchiG WeiDand WuC (2005) Swc2 is a widely conserved H2AZ-binding moduleessential for ATP-dependent histone exchange Nature StructMol Biol 12 1064ndash1071

131 NohYS and AmasinoRM (2003) PIE1 an ISWI family gene isrequired for FLC activation and floral repression in ArabidopsisPlant Cell 15 1671ndash1682

132 HeY and AmasinoRM (2005) Role of chromatin modification inflowering-time control Trends Plant Sci 10 30ndash35

133 RuhfML BraunA PapoulasO TamkunJW RandsholtN andMeisterM (2001) The domino gene of Drosophila encodes novelmembers of the SWI2SNF2 family of DNA-dependent ATPaseswhich contribute to the silencing of homeotic genes Development128 1429ndash1441

134 DoyonY and CoteJ (2004) The highly conserved andmultifunctional NuA4 HAT complex Curr Opin Genet Dev 14147ndash154

135 KuschT FlorensL MacdonaldWH SwansonSK GlaserRLYatesJRIII AbmayrSM WashburnMP and WorkmanJL(2004) Acetylation by Tip60 is required for selective histone variantexchange at DNA lesions Science 306 2084ndash2087

136 JohnstonH KneerJ ChackalaparampilI YaciukP and ChriviaJ(1999) Identification of a novel SNF2SWI2 protein family memberSRCAP which interacts with CREB-binding protein J Biol Chem274 16370ndash16376

137 CaiY JinJ FlorensL SwansonSK KuschT LiBWorkmanJL WashburnMP ConawayRC and ConawayJW(2005) The mammalian YL1 protein is a shared subunit of theTRRAPTIP60 histone acetyltransferase and SRCAP complexesJ Biol Chem 280 13665ndash13670

138 MonroyMA SchottNM CoxL ChenJD RuhM andChriviaJC (2003) SNF2-related CBP activator protein (SRCAP)functions as a coactivator of steroid receptor-mediated transcriptionthrough synergistic interactions with CARM-1 and GRIP-1Mol Endocrinol 17 2519ndash2528

139 EissenbergJC WongM and ChriviaJC (2005) Human SRCAPand Drosophila melanogaster DOM are homologs that function in thenotch signaling pathway Mol Cell Biol 25 6559ndash6569

140 SamuelsonAV NaritaM ChanHM JinJ de StanchinaEMcCurrachME FuchsM LivingstonDM and LoweSW (2005)p400 is required for E1A to promote apoptosis J Biol Chem280 21915ndash21923

141 ChanHM NaritaM LoweSW and LivingstonDM (2005) Thep400 E1A-associated protein is a novel component of the p53 p21senescence pathway Genes Dev 19 196ndash201

142 FuchsM GerberJ DrapkinR SifS IkuraT OgryzkoVLaneWS NakataniY and LivingstonDM (2001) The p400complex is an essential E1A transformation target Cell106 297ndash307

143 UnderhillC QutobMS YeeSP and TorchiaJ (2000) A novelnuclear receptor corepressor complex N-CoR contains componentsof the mammalian SWISNF complex and the corepressor KAP-1J Biol Chem 275 40463ndash40470

144 CaiY JinJ Tomomori-SatoC SatoS SorokinaI ParmelyTJConawayRC and ConawayJW (2003) Identification of newsubunits of the multiprotein mammalian TRRAPTIP60-containinghistone acetyltransferase complex J Biol Chem 27842733ndash42736

145 DoyonY SelleckW LaneWS TanS and CoteJ (2004)Structural and functional conservation of the NuA4 histoneacetyltransferase complex from yeast to humans Mol Cell Biol24 1884ndash1896

146 BachhawatN OuyangQ and HenrySA (1995) Functionalcharacterization of an inositol-sensitive upstream activation sequencein yeast A cis-regulatory element responsible for inositol-cholinemediated regulation of phospholipid biosynthesis J Biol Chem270 25087ndash25095

147 EbbertR BirkmannA and SchullerHJ (1999) The product of theSNF2SWI2 paralogue INO80 of Saccharomyces cerevisiae requiredfor efficient expression of various yeast structural genes is part of ahigh-molecular-weight protein complex Mol Microbiol32 741ndash751

148 ShenX MizuguchiG HamicheA and WuC (2000) A chromatinremodelling complex involved in transcription and DNA processingNature 406 541ndash544

149 JinJ CaiY YaoT GottschalkAJ FlorensL SwansonSKGutierrezJL ColemanMK WorkmanJL MushegianA et al(2005) A mammalian chromatin remodeling complex with similaritiesto the yeast INO80 complex J Biol Chem 280 41207ndash41212

150 MorrisonAJ HighlandJ KroganNJ Arbel-EdenAGreenblattJF HaberJE and ShenX (2004) INO80 andgamma-H2AX interaction links ATP-dependent chromatinremodeling to DNA damage repair Cell 119 767ndash775


151 van AttikumH FritschO HohnB and GasserSM (2004)Recruitment of the INO80 complex by H2A phosphorylation linksATP-dependent chromatin remodeling with DNA double-strand breakrepair Cell 119 777ndash788

152 TsukudaT FlemingAB NickoloffJA and OsleyMA (2005)Chromatin remodelling at a DNA double-strand break site inSaccharomyces cerevisiae Nature 438 379ndash383

153 DownsJA and CoteJ (2005) Dynamics of chromatin during therepair of DNA double-strand breaks Cell Cycle 41373ndash1376

154 SoininenR SchoorM HenselingU TepeC Kisters-WoikeBRossantJ and GosslerA (1992) The mouse Enhancer trap locus1 (Etl-1) a novel mammalian gene related to Drosophila and yeasttranscriptional regulator genes Mech Dev 39 111ndash123

155 AdraCN DonatoJL BadovinacR SyedF KherajR CaiHMoranC KolkerMT TurnerH WeremowiczS et al (2000)SMARCAD1 a novel human helicase family-defining memberassociated with genetic instability cloning expression and mappingto 4q22ndashq23 a band rich in breakpoints and deletion mutants involvedin several human diseases Genomics 69 162ndash173

156 ClarkMW ZhongWW KengT StormsRK BartonAKabackDB and BusseyH (1992) Identification of a Saccharomycescerevisiae homolog of the SNF2 transcriptional regulator in the DNAsequence of an 86 kb region in the LTE1-CYS1 interval on the leftarm of chromosome I Yeast 8 133ndash145

157 SchoorM Schuster-GosslerK RoopenianD and GosslerA (1999)Skeletal dysplasias growth retardation reduced postnatal survivaland impaired fertility in mice lacking the SNF2SWI2 family memberETL1 Mech Dev 85 73ndash83

158 OuspenskiII ElledgeSJ and BrinkleyBR (1999) New yeast genesimportant for chromosome integrity and segregation identified bydosage effects on genome stability Nucleic Acids Res27 3001ndash3008

159 BartonAB and KabackDB (1994) Molecular cloning ofchromosome I DNA from Saccharomyces cerevisiae analysis of thegenes in the FUN38-MAK16-SPO7 region J Bacteriol176 1872ndash1880

160 TanTL KanaarR and WymanC (2003) Rad54 a Jack of alltrades in homologous recombination DNA Repair (Amst) 2787ndash794

161 KroghBO and SymingtonLS (2004) Recombination proteins inyeast Annu Rev Genet 38 233ndash271

162 KleinHL (1997) RDH54 a RAD54 homologue in Saccharomycescerevisiae is required for mitotic diploid-specific recombination andrepair and for meiosis Genetics 147 1533ndash1543

163 TanakaK KagawaW KinebuchiT KurumizakaH andMiyagawaK (2002) Human Rad54B is a double-strandedDNA-dependent ATPase and has biochemical properties differentfrom its structural homolog in yeast Tid1Rdh54 Nucleic Acids Res30 1346ndash1353

164 TanTL EssersJ CitterioE SwagemakersSM de WitJBensonFE HoeijmakersJH and KanaarR (1999) Mouse Rad54affects DNA conformation and DNA-damage-induced Rad51 fociformation Curr Biol 9 325ndash328

165 PetukhovaG Van KomenS VerganoS KleinH and SungP(1999) Yeast Rad54 promotes Rad51-dependent homologous DNApairing via ATP hydrolysis-driven change in DNA double helixconformation J Biol Chem 274 29453ndash29462

166 AlexeevA MazinA and KowalczykowskiSC (2003) Rad54protein possesses chromatin-remodeling activity stimulated by theRad51-ssDNA nucleoprotein filament Nature Struct Biol10 182ndash186

167 AlexiadisV and KadonagaJT (2002) Strand pairing by Rad54 andRad51 is enhanced by chromatin Genes Dev 16 2767ndash2771

168 GibbonsRJ PickettsDJ VillardL and HiggsDR (1995)Mutations in a putative global transcriptional regulator cause X-linkedmental retardation with alpha-thalassemia (ATR-X syndrome)Cell 80 837ndash845

169 McDowellTL GibbonsRJ SutherlandH OrsquoRourkeDMBickmoreWA PomboA TurleyH GatterK PickettsDJBuckleVJ et al (1999) Localization of a putative transcriptionalregulator (ATRX) at pericentromeric heterochromatin and the shortarms of acrocentric chromosomes Proc Natl Acad Sci USA96 13983ndash13988

170 GibbonsRJ McDowellTL RamanS OrsquoRourkeDM GarrickDAyyubH and HiggsDR (2000) Mutations in ATRX encoding aSWISNF-like protein cause diverse changes in the pattern ofDNA methylation Nature Genet 24 368ndash371

171 JanneOA MoilanenAM PoukkaH RouleauN KarvonenUKotajaN HakliM and PalvimoJJ (2000) Androgen-receptor-interacting nuclear proteins Biochem Soc Trans 28 401ndash405

172 DomanskyiA VirtanenKT PalvimoJJ and JanneOA (2006)Biochemical characterization of androgen receptor-interacting protein4 Biochem J 393 789ndash795

173 KannoT MetteMF KreilDP AufsatzW MatzkeM andMatzkeAJ (2004) Involvement of putative SNF2 chromatinremodeling protein DRD1 in RNA-directed DNA methylationCurr Biol 14 801ndash805

174 KannoT HuettelB MetteMF AufsatzW JaligotEDaxingerL KreilDP MatzkeM and MatzkeAJ (2005) AtypicalRNA polymerase subunits required for RNA-directed DNAmethylation Nature Genet 37 761ndash765

175 KannoT AufsatzW JaligotE MetteMF MatzkeM andMatzkeAJ (2005) A SNF2-like protein facilitates dynamic control ofDNA methylation EMBO Rep 6 649ndash655

176 DiPaoloC KieftR CrossM and SabatiniR (2005) Regulation oftrypanosome DNA glycosylation by a SWI2SNF2-like proteinMol Cell 17 441ndash451

177 HoegeC PfanderB MoldovanGL PyrowolakisG and JentschS(2002) RAD6-dependent DNA repair is linked to modification ofPCNA by ubiquitin and SUMO Nature 419 135ndash141

178 ChenS DaviesAA SaganD and UlrichHD (2005) The RINGfinger ATPase Rad5p of Saccharomyces cerevisiae contributes toDNA double-strand break repair in a ubiquitin-independent mannerNucleic Acids Res 33 5878ndash5886

179 GuzderSN SungP PrakashL and PrakashS (1998) TheDNA-dependent ATPase activity of yeast nucleotide excision repairfactor 4 and its role in DNA damage recognition J Biol Chem273 6292ndash6296

180 RamseyKL SmithJJ DasguptaA MaqaniN GrantP andAubleDT (2004) The NEF4 complex regulates Rad4 levels andutilizes Snf2Swi2-related ATPase activity for nucleotide excisionrepair Mol Cell Biol 24 6362ndash6378

181 HewetsonA HendrixEC MansharamaniM LeeVH andChiltonBS (2002) Identification of the RUSH consensus-bindingsite by cyclic amplification and selection of targets demonstrationthat RUSH mediates the ability of prolactin to augmentprogesterone-dependent gene expression Mol Endocrinol16 2101ndash2112

182 MoinovaHR ChenWD ShenL SmiragliaD OlechnowiczJRaviL KasturiL MyeroffL PlassC ParsonsR et al (2002)HLTF gene silencing in human colon cancer Proc Natl Acad SciUSA 99 4562ndash4567

183 ZhangZ and BuchmanAR (1997) Identification of a member of aDNA-dependent ATPase family that causes interference withsilencing Mol Cell Biol 17 5461ndash5472

184 GirdhamCH and GloverDM (1991) Chromosome tangling andbreakage at anaphase result from mutations in lodestar a Drosophilagene encoding a putative nucleoside triphosphate-binding proteinGenes Dev 5 1786ndash1799

185 JiangY LiuM SpencerCA and PriceDH (2004) Involvement oftranscription termination factor 2 in mitotic repression of transcriptionelongation Mol Cell 14 375ndash385

186 HaraR SelbyCP LiuM PriceDH and SancarA (1999) Humantranscription release factor 2 dissociates RNA polymerases I and IIstalled at a cyclobutane thymine dimer J Biol Chem 27424779ndash24786

187 SoodR MakalowskaI GaldzickiM HuP EddingsERobbinsCM MosesT NamkoongJ ChenS and TrentJM(2003) Cloning and characterization of a novel gene SHPRHencoding a conserved putative protein with SNF2helicase andPHD-finger domains from the 6q24 region Genomics 82 153ndash161

188 RamakrishnanV FinchJT GrazianoV LeePL and SweetRM(1993) Crystal structure of globular domain of histone H5 and itsimplications for nucleosome binding Nature 362 219ndash223

189 ClarkKL HalayED LaiE and BurleySK (1993) Co-crystalstructure of the HNF-3fork head DNA-recognition motif resembleshistone H5 Nature 364 412ndash420


190 BurleySK XieX ClarkKL and ShuF (1997) Histone-liketranscription factors in eukaryotes Curr Opin Struct Biol7 94ndash102

191 AaslandR GibsonTJ and StewartAF (1995) The PHD fingerimplications for chromatin-mediated transcriptional regulation TrendsBiochem Sci 20 56ndash59

192 RagvinA ValvatneH ErdalS ArskogV TuftelandKRBreenK AMOY EberharterA GibsonTJ BeckerPB et al(2004) Nucleosome binding by the bromodomain and PHD finger ofthe transcriptional cofactor p300 J Mol Biol 337 773ndash788

193 DavisJL KunisawaR and ThornerJ (1992) A presumptivehelicase (MOT1 gene product) affects gene expression and is requiredfor viability in the yeast Saccharomyces cerevisiae Mol Cell Biol12 1879ndash1892

194 ChiccaJJII AubleDT and PughBF (1998) Cloning andbiochemical characterization of TAF-172 a human homolog of yeastMot1 Mol Cell Biol 18 1701ndash1710

195 AubleDT WangD PostKW and HahnS (1997) Molecularanalysis of the SNF2SWI2 protein family member MOT1 anATP-driven enzyme that dissociates TATA-binding protein fromDNA Mol Cell Biol 17 4842ndash4851

196 DasguptaA JuedesSA SprouseRO and AubleDT (2005)Mot1-mediated control of transcription complex assembly andactivity EMBO J 24 1717ndash1729

197 TopalidouI Papamichos-ChronakisM ThireosG and TzamariasD(2004) Spt3 and Mot1 cooperate in nucleosome remodelingindependently of TBP recruitment EMBO J 23 1943ndash1948

198 TroelstraC van GoolA de WitJ VermeulenW BootsmaD andHoeijmakersJH (1992) ERCC6 a member of a subfamily of putativehelicases is involved in Cockaynersquos syndrome and preferential repairof active genes Cell 71 939ndash953

199 van GoolAJ VerhageR SwagemakersSM van de PuttePBrouwerJ TroelstraC BootsmaD and HoeijmakersJH (1994)RAD26 the functional S cerevisiae homolog of the Cockaynesyndrome B gene ERCC6 EMBO J 13 5361ndash5369

200 SvejstrupJQ (2003) Rescue of arrested RNA polymerase IIcomplexes J Cell Sci 116 447ndash451

201 ParkJS MarrMT and RobertsJW (2002) E coli transcriptionrepair coupling factor (Mfd protein) rescues arrested complexes bypromoting forward translocation Cell 109 757ndash767

202 CitterioE Van Den BoomV SchnitzlerG KanaarR BonteEKingstonRE HoeijmakersJH and VermeulenW (2000) ATP-dependent chromatin remodeling by the Cockayne syndrome B DNArepair-transcription-coupling factor Mol Cell Biol 207643ndash7653

203 BeerensN HoeijmakersJH KanaarR VermeulenW andWymanC (2005) The CSB protein actively wraps DNA J BiolChem 280 4722ndash4729

204 MakarovaKS AravindL and KooninEV (2002) SWIM a novelZn-chelating domain present in bacteria archaea and eukaryotesTrends Biochem Sci 27 384ndash386

205 LiuJ GagnonY GauthierJ FurenlidL LrsquoHeureuxPJ AugerMNurekiO YokoyamaS and LapointeJ (1995) The zinc-binding siteof Escherichia coli glutamyl-tRNA synthetase is located in theacceptor-binding domain Studies by extended x-ray absorption finestructure molecular modeling and site-directed mutagenesis J BiolChem 270 15162ndash15169

206 BoerkoelCF TakashimaH JohnJ YanJ StankiewiczPRosenbarkerL AndreJL BogdanovicR BurguetA CockfieldSet al (2002) Mutant chromatin remodeling protein SMARCAL1causes Schimke immuno-osseous dysplasia Nature Genet 30215ndash220

207 MuthuswamiR TrumanPA MesnerLD and HockensmithJW(2000) A eukaryotic SWI2SNF2 domain an exquisite detector ofdouble-stranded to single-stranded DNA transition elementsJ Biol Chem 275 7648ndash7655

208 PlambeckCA KwanAH AdamsDJ WestmanBJ van derWeydenL MedcalfRL MorrisBJ and MackayJP (2003) Thestructure of the zinc finger domain from human splicing factorZNF265 fold J Biol Chem 278 22805ndash22811

209 HsiaKC ChakKF LiangPH ChengYS KuWY andYuanHS (2004) DNA binding and degradation by the HNH proteinColE7 Structure (Camb) 12 205ndash214

210 MuzzinO CampbellEA XiaL SeverinovaE DarstSA andSeverinovK (1998) Disruption of Escherichia coli hepA an RNApolymerase-associated protein causes UV sensitivity J Biol Chem273 15157ndash15161

211 SukhodoletsMV CabreraJE ZhiH and JinDJ (2001) RapA abacterial homolog of SWI2SNF2 stimulates RNA polymeraserecycling in transcription Genes Dev 15 3330ndash3341


proteins can disrupt chromatin as measured using a range ofdifferent assays (8) although other DNAndashprotein interactionscan also be affected For example Rad54 promotesRad51-dependent strand pairing (13) and Mot1 displacesthe TATA-binding protein (TBP) from DNA (19) Thus

although many Snf2 family proteins are likely to act toalter chromatin structure this is not the case for all membersof the family

Early biochemical studies and sequence alignmentssuggested that members of the Snf2 family could be further

Figure 1 Tree view of Snf2 family (A) Schematic diagram illustrating hierarchical classification of superfamily family and subfamily levels (B) Unrooted radialneighbour-joining tree from a multiple alignment of helicase-like region sequences excluding insertions at the minor and major insertion regions from motifs I to Iaand conserved blocks CndashK for 1306 Snf2 proteins identified in the Uniref database The clear division into subfamilies is illustrated by wedge backgrounds colouredby grouping of subfamilies Subfamilies DRD1 and JBP2 were not clearly separated as discussed in text (C) In order to illustrate the relationship betweensubfamilies a rooted tree was calculated using HMM profiles for full-length alignments of the helicase regions Groupings of subfamilies are indicated by colouringas in (B)

















































Sn

f2

Isw

i

Lsh

AL

C1

Chd

1

Mi-

2

CH

D7

Sw

r1

EP

40

0

Ino

80

Etl

1

Rad

54

AT

RX

Ari

p4

DR

D1

JBP

2

Rad

51

6

Ris

1

Lo

des

tar

SH

PR

H

Mo

t1

ER

CC

6

SS

O1

65

3

SM

AR

CA

L1

rapA

gro

up



PlantAthaliana 6 3 1 2 1 3 0 1 0 1 1 1 1 0 6 0 5 5 0 2 1 3 0 2 0






PlantAthaliana 4 2 1 1 1 3 0 1 0 1 1 1 1 0 6 0 5 5 0 2 1 3 0 2 0






















Table 3 Continued














Table 3 Continued


Rad54-like(cont)




















Table 3 Continued


SSO1653-like(cont)







































SUPPLEMENTARY DATA


ACKNOWLEDGEMENTS



REFERENCES










































































































































































































































































Sn

f2

Isw

i

Lsh

AL

C1

Chd

1

Mi-

2

CH

D7

Sw

r1

EP

40

0

Ino

80

Etl

1

Rad

54

AT

RX

Ari

p4

DR

D1

JBP

2

Rad

51

6

Ris

1

Lo

des

tar

SH

PR

H

Mo

t1

ER

CC

6

SS

O1

65

3

SM

AR

CA

L1

rapA

gro

up



PlantAthaliana 6 3 1 2 1 3 0 1 0 1 1 1 1 0 6 0 5 5 0 2 1 3 0 2 0






PlantAthaliana 4 2 1 1 1 3 0 1 0 1 1 1 1 0 6 0 5 5 0 2 1 3 0 2 0






















Table 3 Continued














Table 3 Continued


Rad54-like(cont)




















Table 3 Continued


SSO1653-like(cont)







































SUPPLEMENTARY DATA


ACKNOWLEDGEMENTS



REFERENCES











































































































































































































































Table 3 Continued














Table 3 Continued


Rad54-like(cont)




















Table 3 Continued


SSO1653-like(cont)







































SUPPLEMENTARY DATA


ACKNOWLEDGEMENTS



REFERENCES



























































































































































































































Table 3 Continued


Rad54-like(cont)




















Table 3 Continued


SSO1653-like(cont)







































SUPPLEMENTARY DATA


ACKNOWLEDGEMENTS



REFERENCES































































































































































































































Table 3 Continued


SSO1653-like(cont)







































SUPPLEMENTARY DATA


ACKNOWLEDGEMENTS



REFERENCES
























































































































































































































































SUPPLEMENTARY DATA


ACKNOWLEDGEMENTS



REFERENCES



























































































































































































































Identification of multiple distinct Snf2 subfamilies with ...

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