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An Epigenetic Signaturefor Monoallelic OlfactoryReceptor ExpressionAngeliki Magklara,1 Angela Yen,4,5,7 Bradley M. Colquitt,2,7 E. Josephine Clowney,3,7 William Allen,6
Eirene Markenscoff-Papadimitriou,2 Zoe A. Evans,1 Pouya Kheradpour,4,5 George Mountoufaris,1 Catriona Carey,1
Gilad Barnea,6 Manolis Kellis,4,5 and Stavros Lomvardas1,2,3,*1Department of Anatomy2Program in Neurosciences3Program in Biomedical Sciences
University of California, San Francisco, San Francisco, CA 94158, USA4Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA5Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA6Department of Neuroscience, Brown University, Providence, RI 02912, USA7These authors contributed equally to this work
*Correspondence: stavros.lomvardas@ucsf.eduDOI 10.1016/j.cell.2011.03.040
SUMMARY
Constitutive heterochromatin is traditionally viewedas the static form of heterochromatin that silencespericentromeric and telomeric repeats in a cell cycle-and differentiation-independent manner. Here, weshowthat, in themouseolfactoryepithelium,olfactoryreceptor (OR) genes are marked in a highly dynamicfashion with the molecular hallmarks of constitutiveheterochromatin, H3K9me3 and H4K20me3. The celltype and developmentally dependent deposition ofthese marks along the OR clusters are, most likely,reversed during the process of OR choice to allowfor monogenic and monoallelic OR expression. Incontrast to the current view of OR choice, our datasuggest that OR silencing takes place before ORexpression, indicating that it is not the product of anOR-elicited feedback signal. Our findings suggestthat chromatin-mediated silencing lays a molecularfoundation uponwhich singular and stochastic selec-tion for gene expression can be applied.
INTRODUCTION
In mammals, olfactory perception is accomplished by detection
of volatile chemicals in the olfactory epithelium and transmission
of the odorant information to the brain, where it is processed.
Unlike other sensory systems, olfaction relies on a large family
of OR genes that are expressed in a monogenic and monoallelic
fashion in olfactory sensory neurons (OSNs) (Buck and Axel,
1991; Chess et al., 1994). OSNs that express the same OR
converge to the same glomerulus in the olfactory bulb (Axel,
2005). ORs participate both in odor detection and in guiding
the axons to the proper glomeruli, ascribing this way the func-
tional identity of each neuron (Imai et al., 2010). The dual role
of ORs in the wiring and physiology of the olfactory system
emphasizes the importance of their proper expression. Each
neuron faces the challenging task of expressing one OR allele
at high levels while keeping the rest of the repertoire completely
silent. The effective repression of the nonchosen alleles is crucial
for this system; due to the exceptionally high number of family
members, basal transcription from the nonchosen ORs would
result in thousands of inappropriately expressed OR molecules.
Although each individual OR would have insignificant represen-
tation, all together they would generate OR activity comparable
to the one from the chosen allele, likely resulting in wiring pertur-
bations and subsequent sensory confusion.
In the mouse, �1400 ORs are expressed in the main olfactory
epithelium (MOE) in a spatial and temporal fashion that could be
organized by positional cues. Within a zone of expression,
however, each neuron expresses only one out of several
hundred alleles that have the potential to be transcribed in that
particular region in a seemingly stochastic fashion (Shykind,
2005). Genetic experiments suggest that the production of OR
protein elicits a feedback signal that stabilizes the expression
of the encoding allele and prevents the activation of additional
OR genes (Lewcock and Reed, 2004; Serizawa et al., 2003;
Shykind et al., 2004). Moreover, there is evidence that the OR
coding sequence represses heterologous promoters, suggest-
ing that it contains important information for the regulation of
OR expression (Nguyen et al., 2007). Regulatory information is
also included in proximal promoter sequences of OR genes, as
well as in distant enhancer elements (Rothman et al., 2005;
Serizawa et al., 2003). One of them, the H enhancer, interacts
with active OR alleles in cis or trans, which led us to propose
that this interaction might be instructive for OR expression
(Lomvardas et al., 2006). However, genetic ablation of H disrupts
the expression of only three proximal ORs, disputing a model in
which H is a singular enhancer that orchestrates OR choice (Fuss
et al., 2007; Nishizumi et al., 2007). Thus, despite immense
Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc. 555
Figure 1. Genome-wide Mapping of H3K9me3 and H4K20me3 Reveals a Tissue-Dependent Heterochromatinization of the ORs in the MOE
ChIP-on-chip experiments with antibodies against H3K9me3 and H4K20me3 using native chromatin preparations from the MOE and liver. The log2 ratio of
IP/input was calculated and used for the construction of the heatmaps presented here.
556 Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc.
efforts, the molecular mechanisms regulating the activation of
one OR allele and the stable transcriptional repression of the
rest remain unknown.
Chromatin-mediated silencing constitutes an effective form of
transcriptional repression. There are distinct forms of transcrip-
tionally inactive chromatin known as heterochromatin. Faculta-
tive heterochromatin, a term assigned to the chromatin structure
of silenced genes, is generally hypoacetylated and has di- and
trimethyl groups on lysine 27 and/or dimethyl groups on lysine
9 of histone H3. This type of heterochromatin is dynamic and
appears to be developmentally regulated (Trojer and Reinberg,
2007). In contrast, constitutive heterochromatin, characterized
by the trimethylation of lysine 9 and lysine 20 of histones H3
and H4 (H3K9me3 and H4K20me3, respectively) is mostly found
on pericentromeric and telomeric repeats and remains
condensed during the cell cycle and stable during differentiation
(Fodor et al., 2010).
Here, we test the hypothesis that chromatin-mediated
silencing prevents the inappropriate expression of multiple OR
genes in each sensory neuron. Our data show that, in the
MOE, OR genes are subject to an unusual form of heterochro-
matic silencing that combines characteristics of both constitu-
tive and facultative heterochromatin. Our ChIP-on-chip experi-
ments reveal high levels of H3K9me3 and H4K20me3 on OR
loci. The cell type and differentiation-dependent deposition of
these trimethyl marks on OR clusters lead to the formation of
compacted and inaccessible heterochromatic macrodomains.
Surprisingly, heterochromatic compaction of OR clusters occurs
before OR transcription and does not require OR expression,
suggesting that it is not the product of an OR-elicited feedback
signal. The enrichment for these silent marks is significantly
reduced on an active OR allele, which is marked instead with
trimethylated lysine 4 of histone H3 (H3K4me3). Insertion of
a reporter transgene within such a heterochromatic macrodo-
main results in its effective chromatin-mediated silencing in the
majority of the olfactory neurons and the subsequent OR-like
expression of this transgene, indicating that stochastic escape
from heterochromatic silencing could be the basis of monogenic
and monoallelic gene expression.
RESULTS
Whole-Genome Analysis of H3K9me3 and H4K20me3in the MOEWe performed chromatin immunoprecipitation (ChIP) experi-
ments with antibodies against all methylated forms of H3K9,
H3K27, and H4K20 using native chromatin preparations from
MOE, hippocampus, liver, or mouse embryonic fibroblasts.
(A) Positional heatmaps of chromosomes 2, 7, and 9 are shown. Each row repres
shown as adjacent columns: liver-H3K9me3, OE-H3K9me3, liver-H4K20me3, an
chromosomes.
(B) Ranked heatmap illustrating 1000 randomly selected genes (�1 in 15 genes).
translation start site. The ORs (blue lines) make up the vast majority of the genes th
The red lines represent VRs and FPRs.
(C) Ranked heatmap, constructed as the previous one but showing the top 1000 g
genes are ORs that also rank the highest, as depicted by the blue lines next to t
See also Figure S1.
Preliminary experiments showed that the tested OR sequences
were enriched for H3K9me3 and H4K20me3 in the MOE,
whereas in the other cell types, there was significant enrichment
only for H3K9me2 (data not shown).
To examine the distribution of the two heterochromatic marks
on all ORs, we performed ChIP-on-chip experiments using
Nimblegen whole-genome tiling arrays with immunoprecipitated
DNA fromMOE and liver. We found that most ORs are hyperme-
thylated on H3K9 and H4K20 in the MOE, but not in the liver. The
distribution of the two modifications along chromosomes 2, 7,
and 9, which contain large OR genomic clusters, is depicted as
heatmaps in Figure 1A, where genes are ordered by chromo-
somal position. Most genes, independently of their transcription
status, appear to be devoid of bothmodifications in both tissues.
However, in the MOE, there is significant enrichment for
H3K9me3 and H4K20me3 on ORs. The high enrichment for the
two modifications combined with the tandem chromosomal
organization of these genes highlights the position of each OR
cluster in these three chromosomes (Figure 1A). Vomeronasal
receptor (VR) genes, which encode monoallelically expressed
receptors that detect pheromones (Dulac and Axel, 1995), are
also enriched for H3K9me3 and H4K20me3 in the MOE
(Figure 1A, chromosome 7). ORs and VRs are hypomethylated
in the liver, in agreement with published observations that report
the complete absence or the low abundance of these marks on
OR genes in numerous cell types (Celniker et al., 2009; Hawkins
et al., 2010; Larson and Yuan, 2010).
A Heterochromatic Signature for ChemoreceptorsTo obtain a global view of our ChIP-on-chip data, we ranked the
mouse genes based on the average signal intensity of H3K9me3
and H4K20me3 over a region of 2Kb (Figures 1B and 1C), using
the translational start site (TSS) as a coordinate for the alignment
of themouse genes. To present the data in a visually comprehen-
sive manner, we included only every 15th mouse gene in the
presentation, although the analysis was performed for all of the
genes. In Figure 1B, 1000 randomly selected genes are ranked
in descending order by their enrichment values for the twomodi-
fications. OR genes, depicted by blue lines at the side of the
heatmap, are clustered on the very top, showing that they are
the most enriched genes for H3K9me3 and H4K20me3 in the
MOE. In a zoomed-in view of the top 1000 genes (Figure 1C),
OR genes constitute themajority of geneswith significant enrich-
ment for both trimethyl marks (p < 10�7). Sequential ChIPs with
chromatin from the MOE confirmed the simultaneous presence
of these marks on OR chromatin (Figure S1A available online).
Notably, as shown also in Figure 1A, the evolutionary older
type I OR genes that are organized in a unique cluster on
ents one gene in 1 kb windows from �5 kb to +5 kb of the TSS. Four states are
d OE-H4K20me3. Arrows indicate OR, V1R, and V2R clusters found on these
Each row represents one gene in 200 bp windows from �1 kb to +1 kb of the
at are positive for both modifications and are placed at the top of the heatmap.
enes that are positive for H3K9me3 and H4K20me3 in the MOE. Most of these
he heatmap.
Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc. 557
Figure 2. OR Clusters in the MOE Are Coated by Tissue-Specific Heterochromatic Blocks of H3K9me3 and H4K20me3
Ma2C analysis of our ChIP-on-chip data viewed on the UCSC genome browser.
(A) Part of the biggest OR cluster located on chromosome 2, which contains�240 genes and spans a 5 MB region. The thin blue (H3K9me3) or red (H4K20me3)
bars represent significant peaks (FDR% 5%) identified in the MOE byMA2C using standard parameters (window = 0.5 kb, min number of probes = 5, max gap =
0.25 kb); the thick blue or red bars represent the blocks identified with modified parameters (window = 10 kb, min number of probes = 20, max gap = 1 kb). In the
liver, there are only a few sporadic H3K9me3 peaks and blocks (purple).
558 Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc.
chromosome 7 have the lowest enrichment values among ORs.
Most of the non-OR genes that are enriched for H3K9me3 and
H4K20me3, represented by red lines in Figures 1B and 1C, are
also chemoreceptors, namely VRs and formyl-peptide receptors
(FPRs), which are also clustered in extremely AT-rich isochores
and likely follow the same regulatory logic as ORs (Figures S1B
and S1C) (Dulac and Axel, 1995; Liberles et al., 2009; Riviere
et al., 2009). Unlike chemoreceptors, the KRAB-ZFP genes are
heterochromatinized also in the liver and in other cell types
(Barski et al., 2007; O’Geen et al., 2007).
Heterochromatic Macrodomains Cover the OR Clustersin the MOETo identify significant sites of enrichment within OR clusters,
we used the Ma2C algorithm (Song et al., 2007). Using a sliding
window of 0.5 Kb and FDR % 5%, we observed that, in
the MOE, the peaks for the two histone modifications were
contained in broadly enriched genomic regions spreading
throughout the OR clusters in an almost continuous arrange-
ment (Figure 2A). Modification of the Ma2C parameters so
that local signal fluctuations would be averaged over a larger
sliding window of 10 Kb confirmed that H3K9me3 and
H4K20me3 form heterochromatic macrodomains (blocks) that
cover megabases of clustered OR genes in the MOE (Figure 2A).
Using this analysis, we found that 1376 ORs fall in H4K20me3
blocks and 1109 ORs fall in H3K9me3 blocks, out of a total
of 1441 annotated OR genes (Figure S1D) (p < 10�7). The
presence of heterochromatic macrodomains over OR clusters
was also confirmed by the application of an independent
algorithm that was developed and used for the detection of
long stretches of H3K9me2 in the liver, brain, and ES cells
(Figures S2A and S2B) (Wen et al., 2009). In contrast to our
findings in the MOE, there are only few H3K9me3 and
H4K20me3 peaks and blocks on the ORs in the liver (Figure 2A)
that do not overlap and are not confirmed by qPCR (see below).
As an independent estimate of the H3K9me3 and H4K20me3
enrichment on OR loci in the two tissues, we combined multiple
ChIPs and analyzed them by Southern blot. As a probe, we
used a �600 bp reverse transcriptase-polymerase chain
reaction (RT-PCR) product, generated by a degenerate primer
pair, which contains several hundred OR sequences (Buck
and Axel, 1991). As seen in Figure S2C, the OR hybridization
signal of the H3K9me3 and H4K20me3 ChIPs from the MOE
is significantly higher than the signal in the liver. We further
(B) Results fromH3K9me3 ChIP-qPCR analysis using native chromatin preparatio
the border of the OR cluster, which coincides with the border of the heterochroma
and H4K20me3, and its most distal intron, located 43 kb downstream, is free of
(C) Same as (B) but for H4K20me3.
(D) Part of an OR cluster on chromosome 11 is interrupted by a small group of non
the MOE, and genes marked by red rectangles do not have detectable transcrip
(E) Zoomed-in picture of the cluster, which shows that genes Btnl9 and Flt4, whi
each of these genes, one at the beginning (most proximal to the neighboring OR g
used in ChIP-qPCR.
(F) Results fromH3K9me3ChIP-qPCR analysis using native chromatin preparation
Flt4 genes were enriched. In contrast, the active genes Mgat1 and Mapk9, Zfp87
(G) Same as (F) but for H4K20me3.
All above experiments were performed in two biological replicates with similar re
also Figure S2.
validated our ChIP-on-chip and ChIP-Southern results by
ChIP-qPCR for multiple OR gene clusters in both tissues. Repre-
sentative data are shown in Figures 2B and 2C and Figures S2E
and S2F. Interestingly, the external borders of the heterochro-
matic blocks coating the OR clusters coincide with the borders
of the OR genomic loci (Figures 2A and 2D). The reported
binding of CTCF outside of OR clusters (Kim et al., 2007),
or other insulating elements (Dickson et al., 2010), might
contribute to the confinement of OR heterochromatin within
the OR clusters.
In few instances, embedding transcriptionally active non-OR
genes in an OR cluster interrupts the heterochromatin blocks
until the presence of another OR reconstitutes them (Fig-
ures 2D-2G). In contrast, genes that are not transcribed in the
MOE are partially covered by heterochromatin marks, suggest-
ing that, in the absence of a competing transcriptional state or
an insulating activity, the OR heterochromatin can extend to
the body of non-OR genes within an OR cluster.
Characterization of the OR HeterochromatinOur data demonstrate that OR clusters in the MOE fall in silent
domains marked by H3K9me3 and H4K20me3, whereas, in the
liver, they are enriched only for H3K9me2. To determine
whether there are functional differences stemming from these
chromatin modifications, we treated nuclei from MOE and liver
with DNase I and examined the accessibility of different loci
by qPCR analysis of the recovered DNA. As seen in Figure 3A
and Figures S3A and S3B, there is significant difference in
DNase I sensitivity of ORs between the two tissues. In MOE,
OR genes get hardly digested, even after 40 min of incubation
with DNase I, suggesting an inaccessible chromatin structure.
In contrast, transcriptionally active genes are rapidly digested,
and silent non-OR genes have intermediate accessibility prop-
erties. In liver, OR loci are indistinguishable from other genes
regarding their DNase I accessibility (Figure 3A). The DNase
I-qPCR data were also confirmed by a different method. DNA
with similar size distribution, extracted from DNase treated
nuclei from MOE and liver, was subjected to Southern blot anal-
ysis using the degenerate OR probe described earlier. As seen
in Figure S3C, hybridization signal intensity is stronger in the
MOE than in the liver, but most importantly, the signal in the
MOE is concentrated to the larger DNA fragments, providing
additional evidence that OR chromatin is less accessible in
the MOE. Hybridization of the same membrane with a ribosomal
ns fromMOE and liver. The Ptprj gene (marked by red rectangle in 2A) stands at
tic block. Its most proximal—to the OR cluster—intron is enriched for H3K9me3
these modifications. Zfp560 serves as positive control.
-OR. Genes that are marked by a green rectangle are transcriptionally active in
ts.
ch are transcriptionally inactive, are partly methylated. Two sets of primers for
ene) and one at the end of the gene (most distal from the neighboring OR), were
s from theMOE.ORgenes tested, aswell as Zfp354c, and part of theBtnl9 and
9, and the distal part of Btnl9 and Flt4 were devoid of modifications.
sults. Values are the mean of triplicate qPCR. Error bars indicate the SEM. See
Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc. 559
Figure 3. The ORs Acquire a Highly Compacted Chromatin Structure in the MOE
(A) DNase I accessibility assay with nuclei from both MOE and liver. Nuclei were treated with DNase I, DNA was isolated at various time points (2–40 min), and
equal amounts were used for qPCR. The amount of DNAmeasured at each interval was expressed as a fraction of the DNA present at 2 min of enzyme treatment
and was plotted over time. We assayed several ORs as well as genes that are active or inactive in theMOE or liver, and their mean is shown here (see Figures S3A
and S3B for detailed analysis of all genes). Representative data from one experiment are shown here.
(B)MNase-digested chromatinwas submitted to ultracentrifugation through asucrose gradient. The largest ormost compactedchromatin fragments are collected
in the fractions with the highest sucrose concentration. For a particular fragment size, the most compact chromatin is collected in more concentrated fractions.
(C) Fractions fromMOEand liver analyzed by agarose gel electrophoresis and Southern blot with a degenerateORprobe. Arrowsmark the low-molecular weight OR
sequences thatappear in thebottomfractionsof thechromatin fromtheMOE. Input lanes representDNAextracted fromchromatin thatwasnot loaded in thegradient.
(D) Selected fractions from the same experiment analyzed with the use of a ribosomal probe.
See also Figure S3.
560 Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc.
probe shows that the digestion differences do not reflect
universal differences between the two tissues.
To test directly the idea that OR heterochromatin has a more
compacted chromatin arrangement in the MOE, we examined
the buoyancy properties of OR chromatin (Ghirlando et al.,
2004; Gilbert et al., 2004). We performed limited MNase diges-
tion of MOE and liver chromatin followed by ultracentrifugation
in sucrose gradient (4%–60%) (Figure 3B). MNase digests
native chromatin independently of the compaction levels or
the transcriptional state of each locus (Weintraub and Grou-
dine, 1976). Thus, digestion with MNase produces chromatin
fragments of similar length distribution in the two tissues (Fig-
ure 3C). Chromatin fractions were collected from top to bottom,
and the DNA was analyzed by gel electrophoresis and Southern
blot. Figure 3C shows that the distribution of OR DNA is
dramatically different across fractions from the two tissues. In
the liver preparation, the strongest OR signal appears in the
second and third fractions. In contrast, in the MOE, there is
OR DNA in the first fractions but also a substantial signal in
the bottom five fractions (depicted by arrows). Importantly,
the signal in the fractions that correspond to the highest
sucrose concentration comes from OR DNA of lower molecular
weight, consistently with highly compacted chromatin.
Selected fractions from the same preparation analyzed by
a ribosomal probe verified the specificity of OR chromatin
compaction in the MOE (Figure 3D).
OR Silencing Is Independent of OR ExpressionThe MOE is a heterogeneous tissue composed of multiple cell
types (Duggan and Ngai, 2007) (Figure S4A). Although OSNs
comprise the majority of cells in our dissections, we sought to
confirm that our findingsdescribe thechromatin stateofORgenes
in the OR-expressing neurons. For this reason, we performed
a series of fluorescence-activated cell sorting (FACS) experiments
followed by ChIP-qPCR.
We isolated mature OSNs from OMP-IRES-GFP mice (Fig-
ure 4A), and as seen in Figure 4B, the OR genes tested have
high levels of enrichment for both H3K9me3 and H4K20me3 in
these cells. Although mature OSNs express ORs, each OR
gene is expressed in 0.1% of the cells; thus, it is not surprising
that we detect silencing marks on them. The confirmation,
however, that ORs are heterochromatinized in OSNs raises
questions of whether this silencing is induced by OR expression
as a consequence of the feedback signal. To address this, we
sorted sustentacular cells from the MOE with the use of SUS4
antibody (Chen et al., 2004). Sustentacular cells line the apical
surface of the epithelium (Figure 4C) and have common develop-
mental ancestors with the OSNs, but they do not express ORs
(Figure 4H). Figure 4D shows that, in sustentacular cells, the
levels of H3K9me3 and H4K20me3 on ORs are comparable to
the levels of these marks in mature OSNs, suggesting that
marking of OR genes with H3K9me3 and H4K20me3 occurs in
the absence of OR expression. In this scenario, it is possible
that trimethylation of lysines 9 and 20 takes place before OR
activation.
To explore this possibility, we performed ChIP-qPCR analysis
in progenitor cells, starting with the most multipotent cells of the
MOE, the horizontal basal cells (HBCs) (Leung et al., 2007), by
sorting ICAM-1+ cells (Carter et al., 2004) (Figure 4E). As seen
in Figure 4F, there is no enrichment for H3K9me3 and
H4K20me3 on OR genes, whereas the pericentromeric repeats
and the KRAB-ZFP genes (Zfp560) are already hypermethylated.
Interestingly, we detect high signal for H3K9me2 on ORs in the
HBCs (Figure S4B), showing that, in this multipotent state, ORs
are repressed via different mechanisms.
We also examined the chromatin state of OR genes in other
progenitor cells from the MOE that are negative for OMP,
ICAM-1, immature laminin receptor (iLR) (another marker for
multipotent basal cells [Jang et al., 2007]), and SUS4. As seen
in Figure 4G, in this population, the enrichment for H3K9me3
andH4K20me3 on the testedORs is as high as in theOMP+ cells.
This quadruple-negative population does not express ORs at
levels that are detectable by RT-PCR (Figure 4H). The above
data suggest that trimethylation of ORs occurs at a stage
preceding OR expression.
To examine a better-defined progenitor cell population, we
obtained a Neurogenin1-GFP (Ngn1-GFP) BAC transgenic
reporter mouse from GENSAT (Heintz, 2004). As expected,
GFP+ cells appear in the basal layer of the MOE in sections of
this strain (Figures 5A and 5B), consistent with the reported
expression of Ngn1 (Cau et al., 2002). RT-PCR analysis showed
that these cells represent a mixed population of progenitors and
immature neurons (Figure S5A). Immunofluorescence with
anti-MOR28, M50, and M71 antibodies (Barnea et al., 2004) in
sections of the transgenic mice verified the mutually exclusive
expression of ORs and Ngn1 (Figures 5A and 5B). However,
for a more sensitive and global view of the levels of OR transcrip-
tion in the Ngn1+ cells, we performed deep sequencing with
cDNA from Ngn1+ and OMP+ cells (see Table S1). We detected
transcripts for 1185 OR genes in the mature OSNs with an
average of 8-fold higher mRNA levels than in the Ngn1+ cells
(Figures 5C and 5D). Importantly, in the Ngn1+ cells, �95% of
OR genes have transcript levels similar to the transcript
levels of silent genes (data not shown). The low levels of OR
mRNA in these cells probably reflect a small percentage of
contaminating mature OSNs, detected by the extreme
sensitivity of RNaseq. In agreement, 25 genes that constitute
markers of mature OSNs (Sammeta et al., 2007) are also de-
tected in low levels in the Ngn1 sample, at a similar 7-fold
average reduction.
FACS and ChIP-qPCR analysis of the Ngn1+ cells revealed
high levels of enrichment for H3K9me3 and H4K20me3 on
ORs, demonstrating similar heterochromatic signature with the
mature OSNs (Figure 5E). Had only the few OR-expressing cells
contributed the H3K9me3 and H4K20me3 signal on OR genes,
the trimethylation signal would have also been 8-fold lower in
the Ngn1+ cells. Therefore, the ChIP-qPCR data from the
quadruple-negative cells and Ngn1+ cells are consistent with
H3K9me3 and H4K20me3 having been deposited on OR genes
before OR expression.
To test the consequences of the transition of di- to trimethyla-
tion in the chromatin structure of ORs, during MOE differentia-
tion, we performed the same DNase I-Southern blot analysis
described earlier, using FAC sorted ICAM1+, Ngn1+, and
OMP+ cells. Figure 5F demonstrates that the differentiation of
HBCs to Ngn1+ cells coincides with increased protection from
Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc. 561
Figure 4. ChIP-qPCR Assays for H3K9me3 and H4K20me3 in Sorted Cell Populations from the MOE
(A) Section of the MOE from an adult OMP-IRES-GFP mouse. Mature OSNs are GFP+.
(B) GFP+ cells (mature OSNs) were isolated with FACS from OMP-IRES-GFP mice and were used for ChIP-qPCR experiments. Golf, Tbp, and Omp are active
genes in these cells and are used as negative controls. Zfp560 and major satellite repeats are used as positive controls. Olfr690 is a type I OR.
(C) Immunostaining of MOE section with SUS4 antibody that specifically labels the sustentacular cells.
(D) ChIP-qPCR with isolated sustentacular cells. Cbr is an active gene and is used as a negative control.
562 Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc.
DNase I digestion, suggesting that this epigenetic transition
results in a less accessible OR chromatin structure retained in
mature OSNs.
An ‘‘Epigenetic’’ Switch Accompanies OR ChoiceTo test whether the active OR allele is free of H3K9me3/
H4K20me3, we enriched, by FACS, for neurons expressing
the olfactory receptor P2 from P2-IRES-GFP knocked in
mice. We isolated �40,000 GFP+ and GFP� neurons from
P2-IRES-GFP heterozygote mice and performed ChIP-qPCR
for H3K9me3 and H4K20me3. To monitor specifically the active
allele, we used a primer pair for GFP, which follows the epige-
netic properties of the P2 locus (data not shown), and a primer
pair specific for the wild-type P2 (p2WT) to monitor the inactive
allele (Figure 6A). As seen in Figures 6B, 6C, and 6F, the enrich-
ment for H3K9me3 and H4K20me3 is significantly reduced on
the active OR allele, compared to the enrichment of the inactive
allele or the enrichment of the same sequence in the GFP�
population. Olfr177, which is expressed in a different zone
than P2, is also highly enriched for H3K9me3 and H4K20me3,
suggesting that the primary function of this silencing mecha-
nism is not the restriction of OR expression within a zone.
Notably, the levels of H3K9me3 and H4K20me3 on the active
allele are reduced, but not eliminated. Control experiments in
which the GFP+ population was checked for purity indicated
that there was �30% contamination, a result that was
expected because we were sorting for an extremely rare pop-
ulation (�0.05% of total cells in the MOE). To obtain a pure
population, we performed a double FACS experiment; the
GFP+ cells were sorted again, resulting in a > 95% GFP+ pop-
ulation. For this experiment, we used MOR28-IRES-GFP
heterozygote knockin mice, which provide more GFP+ cells
than the P2-IRES-GFP mice. As seen in Figures 6D and 6E,
ChIP-qPCRs from this extremely pure population provide
strong evidence that H3K9me3 is absent from the transcription-
ally active MOR28 allele.
To further examine the epigenetic state of the active allele, we
performed ChIP-qPCR in P2-expressing neurons using an anti-
body against H3K4me3, which is found on active and poised
promoters (Guenther et al., 2007) and has a mutually exclusive
distribution with H3K9me3 and H4K20me3 (Regha et al.,
2007). In agreement with this incompatibility, H3K4me3 cannot
be detected on OR promoters using chromatin preparations
from the whole MOE (data not shown). As seen in Figure 6G,
only in the GFP+ population is there high enrichment for
H3K4me3 on the P2 promoter and CDS, supporting the idea
that activation of the P2 allele correlates with the removal of
H3K9me3 and H4K20me3. Although H3K4me3 is very abundant
throughout the active P2 allele, it is missing from the neighboring
P3 and P4 genes (Figure 6G and Figures S6A and S6B), despite
(E) Immunostaining of MOE section with an antibody against ICAM-1 (PE-ICAM-
(F) ChIP-qPCR experiments with isolated HBCs.
(G) ChIP-qPCR with immature neurons and progenitors from the MOE isolated b
(H) RNA isolated from combined OMP-GFP+, sustentacular, and basal cells or qua
ORs. Actin was used as endogenous control.
All above experiments were performed in at least two biological replicates with s
represent the SEM. See also Figure S4.
the sequence similarity between these genes and their expres-
sion in the same zone. Expression analysis of P2-GFP+ cells
confirmed the enrichment for P2-expressing neurons
(Figure S6C).
Heterochromatic Marks Induce Silencingand OR-like ExpressionOur data suggest that heterochromatinization of OR loci
prevents the simultaneous expression of every OR gene in every
OSN. To test whether this heterochromatic structure can influ-
ence gene expression, we examined a transgenic mouse, in
which an OMP promoter-driven LacZ transgene had been
inserted proximal to a singular OR gene (Olfr459). Unlike
numerous OMP-LacZ- or OMP-GFP-independent transgenes
that are expressed in the majority of olfactory neurons (Nguyen
et al., 2007; Walters et al., 1996), this transgene is silent in
99.9% of the neurons and has a sporadic and mostly zonal
expression reminiscent of that of the neighboring OR (Pyrski
et al., 2001).
We reasoned that this transgene is inserted within the hetero-
chromatic block flanking Olfr459. Unlike non-OR genes located
in OR clusters, which probably developed insulating mecha-
nisms that prevented heterochromatic silencing (e.g., Mgat1 in
Figure 2D), transgenes are influenced by the local chromatin
architecture. Mapping the exact insertion site of this transgene
revealed that it resides �55 kbs from Olfr459 (Figure 7A).
ChIP-qPCR experiments showed that the insertion site is heter-
ochromatinized in wild-type mice and remained so after the
transgenic insertion (Figures 7B and 7C). ChIP-qPCR on chro-
matin prepared from the transgenic mice confirms that this
reporter is marked by H3K9me3/H4K20me3 in an MOE-depen-
dent fashion, in contrast to the endogenous OMP promoter,
which is unmethylated (Figure 7C).
To examine whether the insertion of the OMP transgene within
OR-heterochromatin also results in monoallelic expression, we
compared the number of b-gal+ cells between homo- and
heterozygous mice. As seen in Figure 7D, OMP-LacZ homozy-
gotes have in average 1.8-fold more b-gal+ cells, consistent
with a monoallelic expression pattern that clearly does not
stem from the promoter properties of OMP. Finally, to test
whether this reporter is under the transcriptional control of the
OR locus, as indicated by the epigenetic influence of the locus,
we crossed this transgenic mouse with the Emx2 knockout
mice (Pellegrini et al., 1996). Emx2 is required for the expression
of Olfr459 and most OR genes, but it does not have significant
effects on OMP expression (McIntyre et al., 2008). Figure S7
shows that the reporter expression is abolished in the Emx2
KOmice, suggesting that this transgene conforms to the regula-
tory logic of the neighboring OR.
1) that specifically labels the HBCs.
y collecting OMP�, ICAM�, iLR�, and Sus4� cells (quadruple negative).
druple-negative cells was used in qRT-PCR reactions with primers for different
imilar results. Values shown here are the mean of triplicate qPCRs. Error bars
Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc. 563
DISCUSSION
OR choice is a seemingly stochastic process that culminates in
the expression of one out of �2800 OR alleles under poorly
understoodmolecular mechanisms. Here, we show that the hall-
marks of constitutive heterochromatin, H3K9me3 and
H4K20me3, are deposited on OR loci in the MOE. The extensive
marking of OR genes by these methyl groups results in the
generation of compacted heterochromatic macrodomains that
are likely incompatible with transcription. In agreement with an
instructive role of this chromatin structure in gene expression,
insertion of an OMP-LacZ transgene in OR heterochromatin
results in the transcriptional silencing of this reporter in
�99.9% of the OSNs, leading to an OR-like, sporadic, and likely
monoallelic expression.
The genome-wide ChIP-on-chip analysis presented here
provides a rare example for the involvement of H3K9 and
H4K20 trimethylation in transcriptional choices in addition to
their function in telomeric and pericentromeric silencing. Consis-
tent with a role in OR regulation, H3K9me3 and H4K20me3 mark
OR genes in the MOE in a developmentally regulated fashion.
They are added to the—already repressed via H3K9me2—OR
chromatin during the transition from HBCs to immature OSNs
and are possibly removed later from a single OR allele with
remarkable precision, as the neighboring ORs remain hetero-
chromatinized. Therefore, our data describe an unusual form of
silencing that combines characteristics of both constitutive and
facultative heterochromatin; OR heterochromatin has the same
molecular and biochemical characteristics as the pericentro-
meric and telomeric heterochromatin, but it is dynamic and it
depends on the identity of the cell and its differentiation state.
Different Repressive Methyl Marks Induce DistinctChromatin PropertiesThe finding that ORs are kept inactive in most tissues examined
via H3K9 dimethylation poses questions regarding the require-
ment for H3K9 and H4K20 trimethylation in the MOE. The obser-
vation that the additional lysine methylation events result in less
accessible chromatin structure, which likely prevents the binding
of OR-activating and OSN-specific transcription factors on
multiple OR alleles, offers a simple explanation. In other words,
this transition in methyl marks provides better protection from
the activating transcription factor millieux and more efficient
Figure 5. Expression and ChIP-qPCR Analysis of Ngn1+ Cells
(A and B) Sections of the MOE from an adult Ngn1-GFP mouse stained with an
immature neurons are the GFP+ cells (green).
(C) Expression levels of OR transcripts, as determined by Illumina mRNA-seq, are
mapped reads). RPKM increases with radius from the center of the figure, clam
a single OR. For each OR gene, red indicates the expression level in Ngn1+ neuron
by chromosome, indicated by the number or letter exterior to each wedge of the fi
two classes of ORs (classes I and II) are demarcated by background shading. S
(D) Boxplot representation of all OR gene expression in OMP+ and Ngn1+ cells, sh
expression was calculated in log2 (RPKM) units.
(E) ChIP-qPCR analysis for H3K9me3 and H4K20me3 with isolated Ngn1-GFP+ c
Values shown here are the mean of triplicate qPCRs. Error bars represent the SE
(F) ICAM-1+, Ngn1+, and OMP+ cells were sorted from theMOE of adult mice, and
electrophoresis and Southern blot with a degenerate OR or a ribosomal probe.
See also Figure S5.
repression, offering a unique and counterintuitive example in
developmental biology whereby genes are silenced in the exact
cell type that they are supposed to be expressed, assuring the
implementation of the ‘‘one receptor per neuron rule.’’ Indeed,
ChIP-qPCR from P2-expressing neurons shows that the primary
function of this silencingmechanism extends beyond the restric-
tion of OR expression within a zone because, in a P2-expressing
neuron, genes from the same or different zones have similar
trimethylation levels.
OR Silencing Precedes OR ChoiceOur data suggest a model for OR choice that incorporates our
biochemical findings with a feedback signal. According to this
model, all of the OR alleles become silenced before OR tran-
scription. At a later stage, a limited enzymatic activity removes
H3K9me3 and H4K20me3 from a stochastically chosen allele,
allowing its transcriptional activation. The synthesis of OR
protein elicits a feedback signal that prevents this enzyme/
selector from activating another allele and stabilizes the tran-
scription of the chosen allele. Thus, the feedback signal does
not silence the nonchosenOR alleles but prevents their desilenc-
ing. Consequently, an OR-generated feedback is not respon-
sible for creating the singularity in OR choice but, rather, for
preserving it for the life of the neuron.
Alternatively, at the moment of OR choice, OR genes could be
repressed only by H3K9me2, which is deposited on them at
earlier differentiation states. In this scenario, OR expression
could trigger the trimethylation of H3K9 and H4K20, resulting
in permanent OR silencing. However, our data are consistent
with the former model. We detect high levels of H3K9me3 and
H4K20me3 on sustentacular cells that do not express ORs and
do not experience such a feedback. Second, we isolated
progenitor cells and immature OSNs and progenitors with two
independent approaches, and in both cases, OR silencing was
detected before OR expression. In any case, the molecular logic
of OR choice is conceptually the same: in both models,
chromatin-mediated silencing precedes OR choice. Finally, it is
plausible that OR choice constitutes the ‘‘protection’’ of one
OR allele from either form of silencing. However, it is established
that OSNs can switch to different OR alleles (Shykind et al.,
2004), making such a model highly unlikely.
Our data cannot exclude the possibility that trimethylation of
H3K9 and H4K20 constitutes epi-phenomena causing neither
tibodies against ORs MOR28 and M50 (A) or M71 (B) (all in red). GBCs and
quantified by normalized RPKM (reads per kilobase of exon model per million
ped at a maximum of 1. Each radial bar represents the level of expression of
s, and blue indicates the expression level in OMP+ neurons. ORs are sorted first
gure, and then by increasing gene start position within each chromosome. The
ee Table S1 for detailed results.
owing that there is an �8-fold difference between the two cell types. Per gene
ells. Experiment was performed in two biological replicates with similar results.
M.
their nuclei were extracted, digestedwith DNase I, and analyzed by agarose gel
Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc. 565
the chromatin compaction nor the transcriptional silencing of OR
genes. However, there is significant support frommultiple model
organisms for a direct role of these epigenetic modifications in
chromatin structure and gene regulation (Fodor et al., 2010).
In conclusion, our experiments provide a molecular glimpse
into the monoallelic expression of olfactory receptors in the
mouse. In the other well-characterized stochastic regulatory
process inmammals, X inactivation, the choice is made between
two transcriptionally active X chromosomes; whereas one will
remain on, the other will be silenced as a consequence of the
choice (Royce-Tolland and Panning, 2008). In OR choice, the
logic is different. Silencing occurs before a choice is made,
and the choice itself could be mediated by derepression. Similar
logic applies to the immunoglobulin light chain rearrangement
and to var gene choice in Plasmodium falciparum (Goldmit
et al., 2005; Scherf et al., 2008). A common theme between
OR, kappa, and var gene choice is the high number of available
alleles (Goldmit and Bergman, 2004). If these genes were main-
tained in a poised and accessible state, then the concomitant
selection of multiple alleles would be unavoidable. Therefore,
the high number of OR alleles together with the need for a strictly
monogenic and monoallelic OR expression gave rise to an
unusual regulatory circuit. It remains to be seen whether the
regulatory principles proposed here apply to other neuronal
systems whereby neurons commit permanently to differentiation
processes regulated by stable transcriptional choices.
EXPERIMENTAL PROCEDURES
Animal Care
Micewere treated in compliance with the rules and regulations of IACUC under
a protocol approval number AN084169-01.
ChIP-qPCRs and ChIP-on-Chip Experiments
ChIP-qPCRs assays, sequential ChIPs, and ChIP-on-chip experiments were
performed according to standard protocols and are described in detail in
Extended Experimental Procedures.
Data Analysis
Quality control of the ChIP-on chip data was performed both by NimbleGen
(according to their protocols) and by our group. The log2 (ChIP/input) ratio
was normalized in a ‘‘weighted global’’ manner. For peak analysis, we used
the model-based analysis of two-color arrays (MA2C) (Song et al., 2007),
which is a variation of the general sliding window approach.We also confirmed
our results by a different algorithm (Wen et al., 2009). See Extended Experi-
Figure 6. The Active OR Allele Is Not Enriched for H3K9me3 or H4K20m
Heterozygote P2-IRES-GFP and MOR28-IRES-GFP mice were used to isolate G
with antibodies against H3K9me3 and H4K20me3 or against H3K4me3.
(A) The location of the primers used in this experiment is depicted here. Primers fo
the ORWT primers specifically amplified the inactive allele.
(B and C) GFP is hypomethylated on H3K9 (B) in the GFP+ cells, in which it is tra
inactive allele, amplified specifically by the p2WT primers, shows high enrichmen
negative controls and Zfp560 and repeats (major satellite) as positive controls.
(D and E) As above, but the GFP+ cells fromMOR28-IRES-GFP heterozygous mic
were then used for H3K9me3 ChIPs.
(F) Similar results were obtained for the H4K20me3 ChIPs with P2-GFP-sorted c
(G) We repeated the same ChIP-qPCR experiment with an antibody against H3K4
on the neighboring P3 gene or a distant OR (Olfr177) in the GFP+ cells. As expec
cells.
Values are the mean of triplicate qPCR. Error bars represent the SEM. See also
mental Procedures for more details. Raw and normalized Chip-on-chip data
can be accessed at GEO: GSE24420.
DNase I Accessibility Assay
Nuclei were isolated from MOE and liver and digested with DNase I for
2–40 min at 37�C; reactions were terminated with 0.5 M EDTA (pH 8.0).
Detailed protocol is found in the Extended Experimental Procedures.
Chromatin Fractionation
Nuclei were extracted and digested with diluted MNase to yield DNA frag-
ments with an average size larger than 20 Kbs. The fractionation was per-
formed as described before (Gilbert et al., 2004) with more details presented
in the Extended Experimental Procedures.
Fluorescence-Activated Cell Sorting of MOE Cell Populations
For FACS experiments, the olfactory epithelium of 6- to 10-week-old OMP-
IRES-GFP, Ngn1-GFP, or P2-IRES-GFP mice was dissected and cells were
dissociated using a papain dissociation kit (Worthington Biochemical,
Freehold, NJ) following the manufacturer’s instructions. See Extended
Experimental Procedures for more details.
Transgene Mapping and X-Galactosidase Staining
Mapping of the OMP-LacZ transgene and staining of neurons with X-galacto-
sidase were performed as per standard protocols. See Extended Experimental
Procedures for more details.
SUPPLEMENTAL INFORMATION
Supplemental Information includes Extended Experimental Procedures, seven
figures, and two tables and can be found with this article online at doi:10.1016/
j.cell.2011.03.040.
ACKNOWLEDGMENTS
We are grateful to Dr. Frank Margolis for the OMP-LacZmouse strain, Dr. John
Rubenstein for the Emx2 knockout mouse, Dr. James E. Schwob for the SUS4
antibody, Drs. Andrew Feinberg and Bo Wen for the primer sequences for the
positive controls for the H3K9me2 ChIPs, and Dr. Richard Axel for the P2-
IRES-GFP and OMP-IRES-GFP mice as well as for the helpful discussions
and support. We would also like to thank Drs. Hiten Madhani, Barbara
Panning, Nirao Shah, Dimitris Thanos, Tim Mcclintock, Kevin Monahan, and
Keith Yamamoto for critical reading of the manuscript. B.M.C., E.J.C., and
E.M.-P. are supported by fellowships from the National Science Foundation.
W.A. is supported by aRoyce Fellowship, G.B. is a PewScholar in the Biomed-
ical Sciences, and S.L. is funded by theMcKnight Endowment Fund for Neuro-
science, Rett Syndrome Research Trust, Hellman Family Foundation, NIDCD
(R03 DC010273), and Director’s New Innovator Award Program (1DP2
OD006667).
e3, but It Is Marked with H3K4me3
FP+ and GFP� cells by FACS. ChIP experiments were performed in these cells
r the GFP sequence were used to specifically monitor the active allele, whereas
nscribed, but not in the GFP� cells (C), in which this P2 allele is inactive. The
t for H3K9me3 in both GFP+ and GFP� populations. Omp and Tbp are used as
e were subject to a second round of FACS to yield a > 95%pure population and
ells.
me3. There is significant enrichment for H3K4me3 throughout the gene, but not
ted, there was no H3K4me3 on the P2 gene or any other OR gene in the GFP�
Figure S6.
Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc. 567
Figure 7. Tissue-Specific OR Modifications Are Associated with OR-like Transgene Expression
(A) Graphic representation of the Olfr459 locus and the OMP-LacZ insertion site located 55 kb away. Positions marked A, B, and C depict assayed regions in the
qPCR analysis below.
568 Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc.
Received: September 28, 2010
Revised: March 10, 2011
Accepted: March 17, 2011
Published online: April 28, 2011
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OMPare co-expressed during ontogeny and regeneration in olfactory receptor
neurons of OMP promoter-lacZ transgenic mice. Int. J. Dev. Neurosci. 14,
813–822.
Weintraub, H., and Groudine, M. (1976). Chromosomal subunits in active
genes have an altered conformation. Science 193, 848–856.
Wen, B., Wu, H., Shinkai, Y., Irizarry, R.A., and Feinberg, A.P. (2009). Large
histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated
from embryonic stem cells. Nat. Genet. 41, 246–250.
Supplemental Information
EXTENDED EXPERIMENTAL PROCEDURES
Chromatin Immunoprecipitation Assays, Sequential ChIPs, and Real-Time qPCRThe MOE and liver from 6- to 8-week-old C57BL/6 mice were dissected and native chromatin was prepared as described before
(Umlauf et al., 2004). Briefly, nuclei were extracted and digested with micrococcal nuclease (MNase, Sigma) to yield a population
of mono- to tetra- nucleosomes that was, subsequently, used in chromatin immunoprecipitation assays. The antibodies used
were specific to H3 monomethyl lysine-9 (ab8896), H3 dimethyl lysine-9 (ab1220), H3 trimethyl lysine-9 (ab8898), H3 trimethyl
lysine-4 (ab1012), H4 monomethyl lysine-20 (ab9051) and H4 trimethyl lysine-20 (ab9053) from Abcam, and H4 dimethyl lysine-20
(07-369), H3monomethyl lysine-27 (07-448), H3 dimethyl lysine-27 (07-421) and H3 trimethyl lysine-27 (07-449) fromUpstate. Immu-
noprecipitated DNA was isolated by phenol-chloroform extraction and ethanol precipitation and used in quantitative PCR reactions
on an ABI 7900 Real-Time PCRmachine. Primer sequences are provided in Table S2. Data were processedwith the ABI software and
the enrichment of ChIP sample over input was calculated by the 2-DCtmethod after correcting for the no antibody control. For sequen-
tial ChIP experiments, we followed the same protocol except that chromatin was eluted with 10mMDTT, diluted 20-fold and after the
addition of BSA, salmon sperm DNA and yeast tRNA, it was subjected to a second immunoprecipitation with a different antibody and
then eluted with standard elution buffer (0.1M NaHCO3, 1% SDS). The relative fold-enrichments were determined by the 2-DDCt
method, using Omp as the normalizer. All ChIP experiments were performed multiple times using different chromatin preparations.
ChIP-on-Chip Experiments and Data AnalysisChIP and input DNA samples were amplified using the WGA2 kit (Sigma). Labeling of DNA, hybridization on 2.1 Whole-Genome
Economy arrays and scanning were conducted at NimbleGen in Iceland for the MOE and at the UCSF Genomics Core Facility for
liver, according to NimbleGen standard protocols,. We performed duplicate or triplicate ChIP-on-chip experiments for the whole
genome for H3K9me3 and H4K20me3 in the MOE, and singletons for chromosomes 1-9 in the liver.
Quality control of the datawas performed both byNimbleGen (according to their protocols) and by us using the protocol advised by
the Epigenome Network of Excellence (Straub, 2009). The log2 (ChIP/input) ratio was normalized in a ‘weighted global’ manner. This
is similar to the usual global normalization (Wit andMcClure, 2004), except that it weights the data for each of the states (H3K9me3 in
OE, for example) equally, in spite of howmany replicates there are for a given state. Specifically, each sample of data is subtracted by
itsmedian and divided by itsmean absolute deviation (MAD) as usual. Then, the ‘weighted global’ median and ‘weighted global’ MAD
is calculated by first finding the average median and average MAD within each state, and then averaging these values across all four
states. Since we expect each state to have a similar distribution, this allows each state to weight the global distribution similarly, even
if certain states have more replicates than others. Using the normalized log-ratios, we generated positional heatmap representations
for the genes to visually summarize our findings. For each gene and state, we centered a 10Kb window at the translation start site.
Eachwindow consisted of 10 buckets of 1Kb each, and the normalized log ratio (IP/input) of each probewas added to the appropriate
bucket. All values in a bucket were averaged, including data from replicate experiments. Since thereweremultiple ‘states’ of the data,
the values for each of the four states – H3K9me3 in liver and OE tissue, and H4K20me3 in liver and OE tissue - were concatenated.
Once each gene was represented by its values (all four states with 10 buckets per modification), we created heatmaps of the data,
where the rowswere ordered by position in the genome.We also ranked the genes by histonemodification enrichment in theOEdata.
More specifically, we averaged the values in all 20 buckets for each gene (10 buckets of 200 base pairs each for each of the two
histone modifications), and then ranked all the genes in the mouse genome by these values in descending order. A corresponding
heatmap was created for this ranking. To quantify the significance of the OR genes showing stronger signal in this ranking than
random, we used the Mann-Whitney Rank-Sum test.
For peak analysis, two different pipelines of existing tools were used: one was for Large-Organized Chromatin K9 Modifications
(LOCKs) (Wen et al., 2009) and the other one was the Model-based Analysis of 2-Color arrays (MA2C) (Song et al., 2007). Both pipe-
lines are variations on the general sliding window approach, but we adjusted the parameters to, especially, search for large-scale
enrichment. In the LOCKs method, averaging was performed across 500 base pair windows, while the minimum block size was
10,000. In the MA2C pipeline, we used the default parameters for peak finding (window of 500bp, minimum number of probes in
a window 5 and maximum gap of 250 base pairs) and also the adjusted parameters for large domains (window of 10Kb, minimum
number of probes 20, max gap of 1Kb). An FDR % 5% was used in both cases.
DNase I Accessibility AssayNuclei were isolated fromMOE and liver and resuspended in assay buffer (0.32M sucrose, 50mMTris-HCl (pH 7.5), 4mMMgCl2 1mM
CaCl2, 0.1 mM PMSF), as described before (Umlauf et al., 2004); after digestion with 10U of DNase I (Ambion) per million nuclei for 2-
40min at 37�C, reactionswere terminatedwith 0.5MEDTA, pH 8.0. Because extraction of OR chromatin from theMOEwas inefficient
at the early time points, MOE nuclei were incubated overnight at 65�C at 6M Urea (a step that did not affect DNA extraction from the
liver, data not shown). Following proteinase K digestion, DNAwas purified by phenol-chloroform extraction and ethanol precipitation,
treatedwith RNase A and further purifiedwith the PCR-column purification kit (QIAGEN), before being quantified using the Nanodrop.
Equal amounts of DNA were used in qPCR. As a control, we also digested naked DNA (nuclei were treated with proteinase K, DNA
was purified and digested with DNase I) from the two tissues and there were no differences between them (data not shown).
Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc. S1
Fluorescence-Activated Cell Sorting of MOE Cell Populations and ChIP-qPCRs with Sorted CellsBecause of the expected low yields after sorting, we performed pilot experiments with dissociated cells to determine the lowest cell
number, as well as the MNase digestion conditions that would allow us to, reliably, detect histone modifications by ChIP-qPCR. We
found that we could use as few as 40,000 cells per IP by slightly modifying our native chromatin protocol. To test the specificity of the
FACS-ChIP protocol we used H3K4me3 IPs to test if the appropriate cellular markers are enriched for this mark according to their
expression pattern (data not shown).
For FACS experiments, the olfactory epithelium of 6 to 10-week-old OMP-IRES-GFP, Ngn1-IRES-GFP, P2-IRES-GFP or MOR28-
IRES-GFP mice was dissected and cells were dissociated using a papain dissociation kit (Worthington Biochemical, Freehold, NJ)
following the manufacturer’s instructions. For OMP and Ngn-1 FACS-ChIP experiments we dissected in average 10 olfactory
epithelia per experiments. For ICAM and SUS4 FACS-ChIP experiments we dissected on average 15 olfactory epithelia per exper-
iment. For P2-IRES-GFP we dissected on average 40 olfactory epithelia for heterozygote mice and 20 for homozygote P2-IRES-GFP
mice. For MOR28-IRES-GFP we dissected on average 20 olfactory epithelia. Cell sorting was performed on an AriaII (BD Biosci-
ences) cell sorter. For the Ngn1-IRES-GFP sorting we collected only the populations with the highest GFP signal, since our pilot
experiments showed that the population with lower GFP signal included OR expressing cells. To isolate various cell populations
from the MOE, dissociated cells were incubated with primary antibodies SUS4 for sustentacular cell labeling (a gift from Dr. JE
Schwob) or PE-ICAM for HBCs labeling, and subsequently with secondary antibodies conjugated to R-phycoerythrin (Jackson labo-
ratories) or Alexa 594 (Molecular Probes, Invitrogen). Data were analyzed using FLowJo. After FACS, the cells were visually inspected
under a microscope to confirm the purity of the sorted populations. Sorted cells were collected by centrifugation and nuclei were
extracted and digested with MNase under pre-optimized conditions. ChIP assays were performed as described above. All FACS-
ChIPs experiments were performed 2-4 times with similar results. All the knock-in and transgenic mice are backcrossed to
C57BL background and the antibody based sorting was performed using C57BL mice.
Expression Analysis of Sorted CellsSorted cells were spinned down and resuspended in Trizol. RNAwas extracted according tomanufacturer’s instructions and used for
reverse transcription (Superscript III by Invitrogen). cDNA was used for qPCR with primers for cell type-specific markers or various
OR genes. Results were normalized to actin.
Immunohistochemistry and Confocal MicroscopyTo visualize developmental markers, fresh frozen 12 mmMOEsectionswere prepared fromwild-type, OMP-ires-GFP, andNgn1-GFP
mice. Immunostaining was performed by briefly post-fixing in 4% PFA and incubating with anti-ICAM-1 and SUS4 antibodies
following standard procedures. Sections were imaged using a Nikon C1si confocal.
RNA-Seq and Data AnalysisRNA-seq libraries were prepared by the standard Illumina protocol from RNA extracted from FACS sorted OMP-GFP or Neurog1-
GFP positive neurons. An Illumina Genome Analyzer IIx was used to generate 35 bp single-end reads. These reads were then quality
filtered and aligned to the UCSC mm9 mouse reference genome with the short-read aligner Bowtie (Langmead et al., 2009). Reads
that could not be aligned or that aligned to more than one position in the genome were discarded. Gene expression was calculated
with a customPerl script as the per gene sumof the number of reads uniquely mapping to each exon of that gene, divided by the gene
length in kilobases and the number of millions of mapped reads in each library (Mortazavi et al., 2008).The figure was generated with
a custom script using the visualization library Protovis. The mature OSN markers that were used to estimate the fraction of mature
OSNs in the Neurogenin-1 sample were: Pde3c, Kcnc4, Clic3, Faim2, Pcdh10, Kcna6, Adcy3, Sema3e, Scn8a, Jakmip1, Pde7b,Mt3,
Epha5, Eomes, Lect, S100a5, Nap1l5, Omp, Crocc, Stom, Cidea, Pde1c, Cnga2, Olfm1, GnaI.
Transgene Mapping and X-Galactosidase StainingGenomic DNA from OMP-LacZ positive animals was digested with XbaI, diluted, and self-ligated. Inverse PCR was performed using
primers directed against the SV40 polyadenylation sequence in the transgene, and the resulting amplicon was cloned using the
TOPO-TA system (Invitrogen). Multiple inserts were sequenced and mapped to the mm8 reference sequence. The exact location
of the insertion is 30 end: chr6:41758578 (mm8). Lateral whole mounts of the nasal cavities were fixed for 30 min with 4% PFA
and stained for 1 hr with 1 mg/ml X-gal in X-gal staining solution (35 mM potassium ferricyanide, 35 mM potassium ferrocyanide,
2 mMMgCl2,, 0.02% NP-40, 0.01% sodium deoxycholate). Counts of OMP-LacZ+ cells were collected in two regions of each whole
mount and normalized to region area using ImageJ.
SUPPLEMENTAL REFERENCES
Langmead, B., Trapnell, C., Pop,M., and Salzberg, S.L. (2009). Ultrafast andmemory-efficient alignment of short DNA sequences to the human genome. Genome
Biol. 10, R25.
Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., and Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5,
621–628.
S2 Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc.
Straub, T. (2009). Epigenome NoE - protocol: Basic Analysis of NimbleGen ChIP-on-chip Data using Bioconductor/R. http://www.epigenome-noe.net/WWW/
researchtools/protocol.php?protid=43.
Wit, E., and McClure, J. (2004). Statistics for Microarrays: Design, Analysis, and Inference (West Sussex: John Wiley & Sons, Ltd.).
Umlauf, D., Goto, Y., and Feil, R. (2004). Site-specific analysis of histone methylation and acetylation. Methods Mol. Biol. 287, 99–120.
Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc. S3
A
0
2
4
6
8
tK9/tK9 tK9/tK20
fold
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Sequential ChIPs in MOE
Olfr177Olfr389Zfp560Zfp319Omp
B
AT content:
AT
+1Kb
+1Kb
- 1Kb
-1Kb H3K9me3 H4K20me3
C
AT
+1Kb
+1Kb
- 1Kb
-1Kb H3K9me3 H4K20me3
Gene Family Positive Total P valueFunction/
Description qPCROlfr* 1106 1441 0.E+00 Olfactory GPCR High levels
Zfp 82 325 2.E-24Zinc Finger
Transcription High levels
V2r / Vmn2r 71 118 7.E-61Vomeronasal
GPCR Low Levels
V1r / Vmn1r 67 212 1.E-30Vomeronasal
GPCR Low Levels
Pcdha,b,g 35 59 2.E-41Protocadherin
Adhesion High levels
Klra 16 21 6.E-27NK Cell Immune
Receptor Not detected
Defa 14 14 6.E-28Defensin Immune
PeptideMup 10 13 1.E-17 Urine Secreted Not detected
Ssx 8 9 4.E-15KRAB
Transcription
Zscan 7 13 2.E-08Zinc Finger
TranscriptionEsp 6 7 7.E-12 Exocrine SecretedPrame 6 11 1.E-07 UnknownMrg 6 20 1.E-03 Nociception GPCRTdpoz* 5 8 2.E-02 Unknown Not detected
Cts 5 23 4.E-02CathepsinMigration
Amy 4 5 3.E-08 Amylase Digestion
Obox 4 5 3.E-08Homeobox
Transcription
Fpr 4 6 8.E-07Vomeronasal
GPCRMs4 4 15 4.E-02 UnknownMisc / Unknown Family 456Total Positive Genes 1916Total Genes 20427Overall Proportion 0.094
D
Figure S1. Genome-wide Mapping of H3K9me3 and H4K20me3 in the MOE, Related to Figure 1
(A) Sequential ChIPs confirm that H3K9me3 and H4K20me3 are present at the same time on the same loci. Chromatin immunoprecipitated with an antibody
against H3K9me3 was eluted and submitted to a second round of immunoprecipitation with the same antibody (tK9/tK9, as a control) or an antibody against
H4K20me3 (tK9/tK20). Real-time PCR ratios reflect the relative enrichment of indicated loci overOmp, which is used as a negative control. Representative results
of two experiments are shown.
(B) Ranked heatmap illustrating 1000 randomly selected genes (�1 in 15 genes) in descending order for H3K9me3 and H4K20me3 enrichment. An additional
heatmap on the side demonstrates the average AT content of each represented gene (30%–70%).
(C) As above but the ranked heatmap illustrates the top 1,000 genes positive for H3K9me3 and H4K20me3 in descending order of enrichment.
S4 Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc.
(D) Table presenting the genes that are enriched for both H3K9me3 and H4K20me3 based on the MA2C analysis with a sliding window of 10Kb. Blocks in mm8
built were intersected with murine genes using RefGene mm9 records lifted over to mm8. Gene families with an asterisk were completed by manual annotation;
others were simply summarized by RefGene name2 prefix. Genes were called ‘‘positive,’’ if they were at least 50% covered by both H3K9me3 and H4K20me3.
Included in the table are families with at least four positive members and with p value for enrichment of the family, relative to the whole positive set, less than .05
(chi square test). The column on the right depicts whether the ChIP-on-chip results were confirmed by ChIP-qPCR or not.
Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc. S5
cluster 9.1 cluster 9.2cluster 2.2cluster 2.1
A B
MOE MOELiver Liver
Inpu
t
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Inpu
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3meK
9
3meK
9
3meK
20
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20
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ChIP-Southern with a pan-OR CDS probe
Inpu
t
Inpu
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Inpu
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9
3meK
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3meK
20
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MOE MOELiver Liver
ChIP-Southern with a ribosomal probe
C D
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1
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H3K9me3 ChIPs in MOE
0
0.5
1
1.5
2
2.5
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inpu
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H3K9me3 ChIPs in LiverE F
Figure S2. Distribution of H3K9me3 and H4K20me3 on the ORs in MOE and Liver, Related to Figure 2
(A and B) Analysis of the Chip-on-chip data with two independent, computer algorithms yield similar results. Two examples, from chromosomes 2 (A) and 9 (B),
are shown here. The blue (H3K9me3) and red (H4K20me3) bars represent the blocks identified by MA2C (Song et al., 2007), while the green ones represent large
domains (called LOCKs by the authors) identified by amethod described in (Wen et al., 2009) (see Supplemental Experimental Procedures). Note the presence of
blocks, apart from the OR clusters, only in a small group of Zfps (*) and in gene-poor areas (**) with high AT-content. Images generated on UCSC browser.
(C) DNA from several ChIPs for H3K9me3, H4K20me3 and H3K9me2 from MOE and liver were pooled together and analyzed by agarose gel electrophoresis
followed by Southern blot with a pan-OR probe. The ORs appear to be more highly enriched for H3K9me3 and H4K20me3 in the MOE than in the liver confirming
our ChIP-qPCR and ChIP-on-chip data. In liver, the ORs are highly enriched for H3K9me2.
(D) Probing of the same membrane with a ribosomal probe to serve as a control.
(E and F) ChIP-qPCR analysis of H3K9me3 in MOE and liver. There are 9 out of the �240 annotated ORs in the big cluster of chr.2 falling into liver trimK9 blocks
(Figure 2A). We designed primers for 7 of them (Olfr1260-Olfr1506 in plot) and performed ChIP-qPCR. Comparing to Zfp560 (which has the same levels of
enrichment in OE and liver) they have negligible levels of trimK9 in the liver, but they are significantly enriched in theMOE (Olfr 1260, 1261 and 1262 are also shown
in the qPCR plots in Figure 2B-C). Values are the mean of triplicate qPCR. Error bars represent SEM.
S6 Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc.
MOE Liver
PanOR probe Ribosomal probe
MOE MOELiver LiverDNase I treatment
(min)
0
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albumintransferrinprotamineCycATuba1aGapdhOlfr51Olfr672Olfr1030Olfr18Olfr1507Olfr1402
0
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DNase I in Liver OmpZfp319G9aalbuminTbptransferrinOlfr51Olfr672Olfr1030Olfr18Olfr1507Olfr1402
DNase I in MOEA
B
C
Figure S3. DNase I Accessibility Assay in MOE and Liver, Related to Figure 3
(A) DNase I accessibility assay for several ORs and control genes in theMOE.We used cyclophilin A (CycA), tubulin a1a (Tuba1a) andGapdh as examples of active
genes and albumin, transferrin and protamine as inactive genes. All OR primers amplify part of the CDS and all control primers amplify part of the promoter.
(B) DNase I accessibility assay for several ORs and control genes in the liver.Olfactory marker protein (Omp) and Zfp319were used as examples of inactive genes
in this tissue, while the histonemethyltransferaseG9a, the TATA-binding protein (Tbp) transferrin and albumin as examples of active genes. All OR primers amplify
part of the CDS and all control primers amplify part of the promoter.
(C) Nuclei from MOE and liver were digested with 10 or 0.1 units of DNase I/million respectively for different time intervals and the extracted DNA was ran on an
agarose gel. Fractions that appeared to have the same digestion pattern in both tissues were selected for Southern blot analysis with a panOR or a ribosomal
probe.
Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc. S7
0
1
2
3
4
5
fract
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inpu
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H3K9me2 ChIPs in HBCs (Icam1+) B
HBC (ICAM-1)
Sustentacular (SUS4)
mature OSN (OMP-IRES-GFP)
immature OSN (Ngn-1-IRES-GFP and quadruple neg.)
GBC(Ngn-1-IRES-GFP and quadruple neg.)
A
Figure S4. ChIP-qPCRs and Expression Analysis of Sorted Cells from the MOE, Related to Figure 4
(A) Cartoon depicting the cell lineage relationships in the MOE. Basal stem cells (HBCs and GBCs) give rise to OSNs and non-neuronal supporting cells (sus-
tentacular).
(B) ChIP-qPCR experiments with DNA immunoprecipitated by an antibody against H3K9me2 in HBCs. All OR loci tested with qPCR were enriched for this
modification. Primers for Wnt2 and intergenic region (on chromosome 7) were used as positive control (Wen et al., 2009).Omp and Icam are devoid of H3K9me2.
Interestingly Zfp560, which is enriched for H3K9me3 in these cells, is negative for H3K9me2. Values are the mean of triplicate qPCR. Error bars represent SEM.
S8 Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc.
0
0.3
0.6
0.9
1.2
Omp GAP43 Ngn1 Mash1 ICAM Cbr2 Reg3g
expression profile of sorted cells
Basal/Sus
Ngn1+
Omp+
Figure S5. Expression Profiling of the Sorted Populations from the MOE, Related to Figure 5
mRNA analysis of the different cell populations from the MOE confirms that each isolated population expresses predominantly the respective cell type marker.
Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc. S9
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A p3 p4 p2
p2upst p2prom.4.3 kb 3.8 kb
20 kb
p4prom.3.7 kb
37 kb
p3prom.5.1 kb
0
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Expression profile of p2-GFP+ cells
C
Figure S6. ChIP-qPCR and Expression Analysis of P2-GFP+ Neurons, Related to Figure 6
(A) Graphic representation of the P2 locus on chromosome 7 with the P3 (Olfr713), P4 (Olfr714) and P2 (Olfr17) genes. The arrows mark the location where the
indicated primers bind; their distance from the translation start site is also shown. Picture not to scale.
(B) Immunoprecipitated DNAwith an antibody against H3K4me3, aswell as input, fromP2-GFP+ cells, was amplified using theWGA4 kit (Sigma). Equal amount of
IP DNA and input were used for qPCRwith primers located in the promoter of P2, P3 and P4 genes, as well as that of a distant OR (Olfr177 on chr.16). H3K4me3 is
detected only in the promoter and the CDS of the active P2 gene, while just 500bp upstream of the promoter (p2upstr. primers), there is no detectable signal. Tbp
and Omp are active genes in these cells and were used as positive controls.
(C) RNA was isolated from P2-GFP+ cells and was used in RT-PCR. As expected, only the P2 gene is expressed in these cells confirming the significant
enrichment for P2 expressing neurons of this isolated population. Actin was used as an endogenous control. Error bars represent SEM.
S10 Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc.
Emx2+/-; OMP-LacZ+/+ Emx2-/-; OMP-LacZ+/+
BA
Figure S7. The OMP-lacZ Locus Is under the Control of the Transcription Factor Emx2, Related to Figure 7
(A) X-gal staining of lateral whole mounts of the nasal cavities from homozygote OMP-LacZ mouse crossed to a hemizygote Emx2.
(B) X-gal staining of lateral whole mounts of the nasal cavities from homozygote OMP-LacZ mouse crossed to an Emx2 knock out mouse. The absence of lacZ
positive neurons suggests that the transgene is under the control of the Emx2 transcriptional factor like the nearby Olfr459 gene.
Cell 145, 555–570, May 13, 2011 ª2011 Elsevier Inc. S11