DNA methylation regulates tissue-specific expression of Shank3

Silvana Beri,*,1 Noemi Tonna,�,1 Giorgia Menozzi,* Maria Clara Bonaglia,* Carlo Sala� andRoberto Giorda*

*‘‘E. Medea’’ Scientific Institute, Bosisio Parini, LC, Italy�CNR Institute of Neuroscience and Department of Pharmacology,

University of Milano, Milano, Italy

Abstract

Tissue-specific gene expression can be controlled by

epigenetic modifications such as DNA methylation. SHANK3,

together with its homologues SHANK1 and SHANK2, has a

central functional and structural role in excitatory synapses

and is involved in the human chromosome 22q13 deletion

syndrome. In this report, we show by DNA methylation ana-

lysis in lymphocytes, brain cortex, cerebellum and heart that

the three SHANK genes possess several methylated CpG

boxes, but only SHANK3 CpG islands are highly methylated in

tissues where protein expression is low or absent and un-

methylated where expression is present. SHANK3 protein

expression is significantly reduced in hippocampal neurons

after treatment with methionine, while HeLa cells become able

to express SHANK3 after treatment with 5-Aza-2¢-deoxycyti-

dine. Altogether, these data suggest the existence of a spe-

cific epigenetic control mechanism regulating SHANK3, but

not SHANK1 and SHANK2, expression.

Keywords: CpG island, DNA methylation, epigenetic control

of gene expression, SHANK3, tissue-specific expression.

J. Neurochem. (2007) 101, 1380–1391.

Epigenetic modifications such as DNA methylation andhistone modification are essential for genome reprogrammingduring development, tissue-specific gene expression andlarge-scale gene silencing. The bulk of DNA methylationinvolves transfer of a methyl group to cytosine in a CpGdinucleotide by DNA methyltransferases. Regions whereCpG dinucleotides are at least five times more abundant thanthe genome average are labelled CpG islands (Bird et al.1985; Gardiner-Garden and Frommer 1987). CpG islands arefound in 50% of human genes, where they usually encom-pass promoters or exons (Gardiner-Garden and Frommer1987; Larsen et al. 1992; Takai and Jones 2002). Someislands, associated with imprinted genes (Surani 1998), geneson the inactive X chromosome in females or tissue-specificgenes (Surani 1998; De Smet et al. 1999) can be differen-tially methylated.

Recently, a CpG island in the SHANK3 gene has beenidentified in a whole-genome screen of tissue-specificdifferential methylation (Ching et al. 2005).

The three Shank genes, also known as proline-richsynapse-associated protein (ProSAP), somatostatin receptorinteracting protein, cortactin-binding protein, Synamon andSpank encode structural proteins of the neuronal post-synaptic density (PSD) (Du et al. 1998; Boeckers et al.1999b; Lim et al. 1999; Naisbitt et al. 1999; Ching et al.2005).

Over-expression of Shank1 in hippocampal neuronsaccelerates the maturation of filopodial-like protrusions inmature spines and promotes the enlargement of maturespines (which acquire the classical mushroom shape) withoutincreasing their number. (Sala et al. 2001, 2003, 2005). Wehave also recently shown that Shank3 over-expression incerebellar granule cells induces dendritic spine and synapseformation by recruiting different subtypes of glutamatereceptors, whereas the inhibition of Shank3 expression inhippocampal neurons reduces the number of dendritic spines(Roussignol et al. 2005). The SHANK3/PROSAP2 proteincould form a platform for the construction of the PSDcomplex by forming large sheets composed of helical fibersstacked side by side which assembly is regulated by Zn2+

(Baron et al. 2006).

Received June 13, 2006; revised manuscript received November 21,2006; accepted December 10, 2006.Address correspondence and reprint requests to Roberto Giorda, ‘‘E.

Medea’’ Scientific Institute, via don Monza 20, Bosisio Parini, LC23842, Italy. E-mail: roberto.giorda@bp.lnf.it1SB and NT should be considered joint first authors.Abbreviations used: 5-AdC, 5-aza-2¢-deoxycytidine; CCC, chromo-

some conformation capture; ProSAP, proline-rich synapse-associatedprotein; EBV, Epstein–Barr virus; GFP, green fluorescent protein; PSD,post-synaptic density; PBL, peripheral blood lymphocyte; DIV, daysin vitro; RT-Q-PCR, real-time quantitative PCR.

Journal of Neurochemistry, 2007, 101, 1380–1391 doi:10.1111/j.1471-4159.2007.04539.x

1380 Journal Compilation � 2007 International Society for Neurochemistry, J. Neurochem. (2007) 101, 1380–1391� 2007 The Authors

These in vitro studies may indicate that haploinsufficiencyof the SHANK3/PROSAP2 gene is the cause of the majorneurological features associated with the chromosomal22q13 deletion syndrome. Specific involvement ofSHANK3/PROSAP2 in the syndrome was first reported byBonaglia et al. (2001), strongly supported by the observationthat all cases analysed showed a deletion of SHANK3(Wilson et al. 2003), and recently strengthened by theidentification of a recurrent breakpoint within the SHANK3gene (Bonaglia et al. 2006).

In this study, we have analysed the tissue-specificmethylation of human SHANK genes CpG islands andselected mouse Shank3 islands. We show that the threeSHANK genes possess several CpG boxes but only Shank3undergoes tissue-specific methylation at most of its CpGislands. The gene is highly methylated in tissues whereits expression is low or absent. We also demonstrate in a cellculture model that agents that either reduce or increasegenomic DNA methylation modulate Shank3 expressionat the protein level. The fact that SHANK3, but not SHANK1and SHANK2, expression might be regulated by epigeneticmechanisms such as DNA methylation is very intriguing andsuggests that SHANK3 may be involved in the pathogenesisof some disorders of DNA methylation.

Materials and methods

Nucleic acids extraction, modification, amplification, cloning

and sequencing

Genomic DNA was extracted from tissues and cell lines with

standard protocols. We obtained brain, cerebellum and heart

samples from the Telethon Bank (Milan, Italy) of DNA, Nerve

and Muscle Tissues. We treated total genomic DNA with sodium

bisulphite (Grunau et al. 2001) and carried out amplifications

essentially as in Kubota et al. 1997; PCR products from all CpG

boxes were cloned in pCR4/TOPO using the TOPO TA cloning

kit (Invitrogen, Milan, Italy) and 12 clones were sequenced for

each fragment on an ABI 3100AV automated DNA sequencer

(Applied Biosystems, Milan, Italy). All PCR products were also

tested by restriction mapping of the amplified fragments with

TaqI, as after the bisulphite reaction unmethylated DNA remains

intact following TaqI digestion, whereas methylated DNA is

cleaved. Selected CpG boxes were also tested by methylation-

specific PCR (Kubota et al. 1997). The sequences of all primers

used as well as the annotated sequences of all regions analysed,

showing the position of primers, CpG dinucleotides and CpG

islands, are available on request.

Total RNA was extracted with Eurozol (Euroclone, Milan, Italy)

following manufacturer’s protocols; cDNA synthesis was performed

with Ready-To-Go You-Prime First strand beads (Amersham, Milan,

Italy) and random hexamers; cDNA amplifications were performed

as in Bonaglia et al. (2001); PCR products were analysed on 2%

agarose Tris/acetate/EDTA gels. Glyceraldehyde 3 Phosphate

Dehydrogenase amplification primers and protocol are from

Clontech-Takara Bio Europe (Saint-Germain-en-Laye, France).

Quantitative expression analysis

Total RNAwas extracted from 5 · 105–2 · 106 rat neurons or HeLa

cells using the Rneasy Mini Kit (Qiagen) according to the

manufacturer’s protocol; cDNA was synthesized using the Super

Script III First-Strand Synthesis System (Invitrogen). Expression of

human and rat Shank genes was assessed by Real-Time Quantitative

PCR (RT-Q-PCR) on a 7900HT Sequence Detection System

(Applied Biosystems) using the following TaqMan Gene Expression

Assays (Applied Biosystems) and manufacturer’s protocols: human

SHANK1 (Hs00211718_m1), SHANK2 (Hs00324404_m1),

SHANK3 (Hs01393537_m1), GAPDH (Hs99999905_m1); rat

Shank1 (Rn00582088_m1), Shank2 (Rn00591649_m1), Shank3(Rn00572344_m1), Gapdh (Rn99999916_s1). Validation experi-

ments demonstrated that amplification efficiencies of the control and

all target amplicons were approximately equal (not shown);

accordingly, relative quantification of DNA amount was obtained

using the Comparative Cycle Threshold method (described in

Applied Biosystems User Bulletin No. 2, December 11, 1997; ABI

PRISM 7700 Sequence Detection System).

Cell culture experiments

Neuroblastoma cell lines were grown in Dulbecco’s modified

Eagle’s medium with 10% foetal calf serum. Epstein–Barr

virus (EBV) lines were grown in Roswell Park Memorial Institute

(RPMI) with 20% foetal calf serum.

Hippocampal neurons and HeLa cell cultures were grown in

humidified incubator at 37�C in 5% CO2. The hippocampal neurons

cultures were prepared from embryonic day 18 (E18–E19) rat

hippocampus (Charles River, Calco, LC, Italy) as previously

described (Brewer et al. 1993). Dissociated neurons were plated at

medium density (150–200 cells/mm2) on 6-well plates (Iwaki,

Barlow Scientific Inc., Olympia, MA, USA) for biochemistry

experiments and at low density (40–50 cells/mm2) on coverslips.

At days in vitro (DIV) 5–10 cultures were incubated with

methionine (Sigma, Milano, Italy) at a final concentration of

2 mmol/L at 37�C for 24 and 72 h. HeLa were plated at 2 · 105

cells/33-mm dish and treated for 24 or 72 h with 5-Aza-2¢-deoxycytidine (5-AdC) (Sigma).

Cell extracts were prepared in lysis buffer (Laemmli Buffer,

62 mmol/L Tris–HCl, pH 6.8, 2% sodium dodecyl sulfate, 5%

mercaptoethanol, 10% glycerol and 0.001% bromophenol blue) and

loaded on 7.5% sodium dodecyl sulfate–polyacrylamide gel

electrophoresis gels.

For western blot, primary antibodies [mouse anti b-Tubulin1 : 1000 (Sigma), mouse anti Actin 1 : 1000 (Sigma), Rabbit anti

Shank 1 : 500 (Chemicon, Europe Ltd., Chandlers Ford, UK), Rabbit

anti Shank 3856 1 : 500 (gift from M. Sheng, MIT, Cambridge, MA,

USA), Rabbit anti ProSAP1/Shank2 1 : 1000, Rabbit anti Shank3/

ProSAP2 1 : 1500 (gifts from T. Boeckers, Ulm University,

Germany), Rabbit anti Shank3-pep 1 : 500 (made in collaboration

with Biotest Ltd, Czech Republic) and Rabbit anti PSD-95 1 : 500

(gift from E. Kim, Korea Advanced Institute of Science and

Technology (KAIST), Daejeon, South Korea)] were applied for 3 h

in blocking buffer (20 mmol/LTris, pH 7.4, 150 mmol/L NaCl, 0.1%

Tween 20 and 3% dried non-fat milk); secondary antibodies

(Horseradish Peroxidase (HRP)-conjugated anti-mouse or anti-rabbit)

(Amersham) were used at a 1 : 2000 dilution. The signal was detected

using an Enhanced Chemiluminescence (ECL) detection system

DNA methylation regulates SHANK3 expression 1381

� 2007 The AuthorsJournal Compilation � 2007 International Society for Neurochemistry, J. Neurochem. (2007) 101, 1380–1391

(Perkin Elmer Life Sciences, Emeryville, CA, USA) and quantified by

means of ImageQuant software (Bio-Rad, Segrate, MI, Italy). Rabbit

ProSAP1/Shank2 and ProSAP2/Shank3 were a generous gift form

Tobias M Boeckers, Ulm University, Germany. The Shank3-pep

antibody was raised against the peptide ARDPERGSLASPAFSPRS-

PAWI corresponding to residues 214–235 of the Shank3 human

sequence (National Center for Biotechnology Information accession

number Q9BYB0).

For dendritic spines quantification, neurons were infected at DIV

3 with a lentivirus expressing Enhanced Green Fluorescent Protein

or transfected with a Green Fluorescent Protein (GFP)-expressing

cDNA (pEGFP) before methionine treatment. Images of transfected

neurons were acquired with a MRC1024 confocal microscope (Bio-

Rad) and spines quantified as described in Sala et al. (2001). ThecDNAs expressing HA-Shank3 and the Shank3 siRNA (Roussignol

et al. 2005) were cotransfected with GFP at DIV 14, treated at DIV

16, fixed and stained with Shank3-pep antibodies at DIV19.

Chromosome conformation capture

We carried out chromosome conformation capture (CCC) assays

essentially as described by Tolhuis et al. (2002) and Horike et al.(2005). We selected EcoRI and HindIII-restriction enzymes because

they generated fragments containing single CpG islands and

designed specific primers accordingly. The sequences of all primers

used are available on request. We tested amplification of all PCR

primer combinations using HindIII- and EcoRI-digested, ligated

fragments of Bacterial Artificial Chromosome clone CTA-799 F10

containing the human SHANK3 gene. As a negative control, we

determined that none of the primer combinations amplified genomic

DNA similarly digested and ligated.

In silico analysis

The University of California, Santa Cruz (UCSC) Human Genome

Browser (May 2004 assembly) (http://genome.ucsc.edu/cgi-bin/

hgGateway) maps and sequence were used as references, except

for a portion of the SHANK3 gene on chromosome 22 overlapping

with the CpG 2 island where the published sequence was not correct

(Bonaglia et al. 2001; Wilson et al. 2003). The corrected sequence

has been submitted to Genbank (Accession number DQ173561).

Multiple alignment was performed using the clustalw algorithm with

standard parameters.

Given the length of the SHANK2 gene, it has been necessary to

split the whole sequence into overlapping segments that have been

subsequently merged. Clustalw output files were analysed in order

to extract the sub alignment scores for exons and CpG islands: for

each position, perfect identity in every species was assigned 1 and

non-identity as 0. Subscores were calculated as the mean over the

length of sub alignments. Details of the analysis in Table format are

available on request.

Results

Methylation analysis

The structure of all human SHANK genes was identified bycomparison with full-length human, mouse and rat mRNAs.As the precise location of the first exons was not known in allcases, we decided to label as Promoter-associated (P) the

CpG island closest to the first known exon. Seven CpGislands were identified in the human SHANK1 and SHANK2genes, five in SHANK3. All SHANK3 islands, and severalislands in SHANK1 and 2, were associated to one or moreexons and, at least in SHANK3, each island was associatedwith exons coding for distinct functional domains(see Fig. 1). We numbered the SHANK3 islands CpGPromoter-associated (P, split in PC and PB) and 2–5; wetried to keep the same numbers for islands associated toexons involved in the same functional domain in the othertwo genes. SHANK2 has two major isoforms: one containingankyrin repeat domains is expressed in liver epithelia(McWilliams et al. 2004) and we tentatively assigned to itthe P1 CpG island; the second isoform starts at an alternativefirst exon associated with the P2 island (Du et al. 1998;Boeckers et al. 1999a).

Bisulphite cloning and sequencing showed that SHANK3CpG islands 2–5 were extensively methylated in peripheralblood lymphocytes (PBLs), whereas methylation wasreduced or absent in brain, cerebellum and heart (Fig. 1);the CpG 2 island showed the most dramatic differences, withall CpG dinucleotides being unmethylated in cerebellum andin the majority of brain and heart clones (Fig. 2); the CpG 4island was completely unmethylated in cerebellum, partlymethylated in brain and heart (Fig. 2). The CpG 3 and CpG 5islands were partly methylated in cerebellum, almost com-pletely methylated in brain and heart; the CpG P island wascompletely unmethylated in all tissues. As we had evidenceof an effect of some amplified CpG island fragments onpCR4 cloning orientation and efficiency, we sought to verifyour results by restriction mapping. TaqI restriction analysis ofbisulphite-treated amplified CpG islands confirmed thesequencing results (Fig. 2b).

Analysis of the majority of the CpG islands in SHANK1and SHANK2 showed extensive variability in methylationbut no tissue-specificity (Figs 1 and 2). Promoter-associatedCpG islands were always completely unmethylated.

In order to exclude artifacts related to primer position andsequence, we also set up methylation-specific PCRs (Kubotaet al. 1997) of SHANK1/SHANK2 CpG 4 and SHANK3 CpG2–4 islands and obtained similar results (Fig. 2c).

We then tested SHANK3 expression and CpG methylationin four human neuroblastoma lines (Lan-5, SY5Y, IMR-32and GI-LI-N) and an EBV-transformed human lymphoblas-toid line (Fig. 3). Three of the neuroblastomas expressSHANK3 (Fig. 3a), although only the CpG 2 island iscompletely unmethylated in all lines (Figs 3b and c). Allislands in the EBV-transformed line, like all other EBV andPBL lines we tested (not shown), are fully methylated andSHANK3 is not expressed.

Tissue-specific methylation analysis in mouse Shank3CpG 2 (Fig. 4) and CpG 4 islands (not shown) demonstrateda close correspondence with the human results. We alsofound that strong tissue-specific methylation was already in

1382 S. Beri et al.

Journal Compilation � 2007 International Society for Neurochemistry, J. Neurochem. (2007) 101, 1380–1391� 2007 The Authors

place in mouse embryo (E15 Brain) and newborn (P1 brain,heart and liver) tissues (Figs 4b and c and data not shown).

Comparative in silico analysis of the human, mouse andrat SHANK genes (not shown) did not reveal any SHANK3-specific feature. Average sequence identity is the same, andthis is true also for exons and CpG islands. Promoter-associated islands show the highest conservation.

Changes in CpG methylation influence SHANK3

expression

Previous reports demonstrated the possibility to regulate thelevel of DNA methylation in cultured cells by eitherincreasing methionine concentration in the medium (Nohet al. 2005) or by treating the cells with de-methylatingagents such as 5-AdC (Zhang et al. 2004). If tissue-specificexpression of the Shank3 gene is regulated by methylation, itshould be possible to verify whether induced DNA hyper-

methylation or hypomethylation change Shank3 proteinexpression. This was tested by western Blot looking at theexpression of Shank3 after increasing or reducing DNAmethylation, respectively, in hippocampal and HeLa cellcultures. We first characterized the specificity of the Shankantibodies previously described in (Boeckers et al. 1999a;Bockers et al. 2001; Redecker et al. 2001), we also produceda Shank3-specific antibody. As shown in SupplementaryFig. S1a, the Shank1 antibody recognizes Shank1 but notShank3 proteins expressed by COS-7 cells transfected witheither Shank1A or Shank3 cDNA, while the pan-Shankantibody recognizes both proteins. As expected, the pan-Shank antibody recognizes all three GFP Shank proteins,while the ProSAP1/Shank2 antibody recognizes only GFPShank2 protein and both ProSAP2/Shank3 and Shank3-peprecognize only the GFP Shank3 protein (SupplementaryFig. S1b).

Fig. 1 Tissue-specific methylation of human SHANK genes CpG

islands. The intron/exon organization of SHANK1, SHANK2 and

SHANK3 and the location of exons coding for the ankyrin repeats

domain (ANK, orange), Src homology domain 3 (SH3, dark blue),

post-synaptic density (PSD95)/Dlg/ZO-1 domain (PDZ, light blue),

proline-rich (purple) and sterile a-motif (SAM, pink) domains are

shown. CpG islands are drawn in green; the methylation status of each

island in peripheral blood lymphocyte (PBL), brain, cerebellum and

heart is indicated by dots; white dots indicate complete non-methyla-

tion, red/white dots indicate partial methylation and red dots indicate

complete methylation.

DNA methylation regulates SHANK3 expression 1383

� 2007 The AuthorsJournal Compilation � 2007 International Society for Neurochemistry, J. Neurochem. (2007) 101, 1380–1391

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1384 S. Beri et al.

Journal Compilation � 2007 International Society for Neurochemistry, J. Neurochem. (2007) 101, 1380–1391� 2007 The Authors

Expression of Shank proteins was tested in hippocampalcultures treated for 24 and 72 h with 2 mmol/L methionine.In untreated neurons, Shank proteins are highly expressedbut the two major bands recognized by the pan-Shankantibodies are reduced in intensity after treatment withmethionine for 24 and 72 h, respectively, to 65.0 ± 10.9(mean ± SE) and 40.5 ± 13.2% of the intensity measuredin untreated cells (Figs 5a and b). Similarly, the bandsrecognized by the ProSAP2/Shank3 and Shank3-pep anti-bodies are reduced in intensity after methionine treatment.The quantification in Fig. 5b shows a reduction, respect-ively, for ProSAP2/Shank3 and Shank3-pep to 56.3 ± 8.1%and 56.2 ± 10.4% at 24 h and 24.6 ± 6.2% and 31.4 ±4.2% at 72 h of the intensity measured in untreated cells.No change in expression has been found for Shank1,Shank2, PSD-95, b-tubulin and actin. RT-Q-PCR analysisshowed that SHANK3 expression consistently decreased(0.9 ± 0.25 at 24 h and 0.69 ± 0.07 at 72 h, assuming

expression in untreated cells equal to one) followingmethionine treatment, while SHANK1 and SHANK2 showedonly inconsistent variations (Fig. 5c). Methylation analysisof CpG islands in parallel hippocampal cultures treated withmethionine showed partial methylation in untreated andtreated samples (not shown); there was no statisticallysignificant difference in the relative amount of methylated/unmethylated CpG boxes of SHANK3 between untreatedand methionine-treated samples. This could be due to therelatively low amount of DNA we can collect from thehippocampal neurons cultures and to the presence of gliacells in addition to neurons in our cultures. Methioninetreatment-induced methylation in neurons may not beevident on the background of the other cell types in theculture. Expression of Shank proteins was tested in HeLacells treated for 24 and 72 h with 3 lmol/L 5-AdC. Asexpected, untreated HeLa cells do not express Shank orPSD-95, another major neuronal PSD protein (Fig. 5d).

(a)

(c)

(b)

Fig. 3 SHANK3 expression and methyla-

tion in human cell lines. Neuroblastoma

lines LAN-5, SY5Y, IMR-32, GI-LI-N and an

Epstein–Barr virus (EBV) -transformed

lymphoblastoid line (EBV) were used. (a).

Expression of SHANK3 was assessed by

PCR amplification of a portion of the tran-

script (exons 21/22) from random-primed

cDNA; Glyceraldehyde 3 Phosphate Dehy-

drogenase was amplified as a control.

Molecular weight marker for Glycer-

aldehyde 3 Phosphate Dehydrogenase is

Marker X (Roche). (b) methylation-specific

restriction analysis of SHANK3 CpG 2

island; (c) methylation-specific PCR of

human SHANK3 CpG 2 island. The size of

all fragments is shown. Molecular weight

marker (M) is Marker V (Roche).

DNA methylation regulates SHANK3 expression 1385

� 2007 The AuthorsJournal Compilation � 2007 International Society for Neurochemistry, J. Neurochem. (2007) 101, 1380–1391

After 24 and 72 h of 5-AdC treatment, some protein bandswith a molecular weight similar to Shank proteins inneuronal extracts become clearly visible on Western blotusing pan-Shank but not Shank1 or PSD-95 antibodies(Fig. 5d). Quantitative expression analysis showed thatSHANK3 mRNA was present in untreated cells and itsexpression significantly increased (1.37 ± 0.067 at 24 and3.0 ± 0.3 at 72 h) after 5-AdC treatment (Fig. 5e).SHANK1 and SHANK2 were never expressed. At thesame time, SHANK3 CpG islands 3–5, completely methy-lated in untreated HeLa cells, became gradually non-methylated following treatment at increasing times(Fig. 5f). We have previously shown that inhibition ofShank3 expression by siRNA in hippocampal neuronsreduces dendritic spine number (Roussignol et al. 2005),thus not surprisingly we measured a reduction in spinenumber from 4.3 ± 0.8 spines for 10-lm dendrite inuntreated neurons to 2.7 ± 0.4 in neurons treated for 72 h

with 2 mmol/L methionine (Fig. 6b). Spine width was alsostatistically reduced in neurons treated with methionine,suggesting that the remaining spines are smaller. Interest-ingly, dendritic spines modifications induced by methionineare very similar to the effect induced by the transfection ofspecific Shank3 siRNA (that were previously used inRoussignol et al. 2005) [Figs 6a(III1–3)] and can berescued by the over-expression of a cDNA coding forHA-Shank3 [Figs 6aIV(1–3)]. Also, methionine treatmentdoes not further modify spines morphology of neuronstransfected with a Shank3-specific siRNA [Figs 6aV(1–3)].Using our Shank3pep-specific antibodies, we were alsoable to show that Shank3 staining is dramatically reducedin neurons treated with methionine or transfected withShank3 siRNA [Figs 6aII(1–3) and III(1–3)]. Altogether,these data suggest a role for DNA methylation inregulating Shank3, but not Shank1 and Shank2, proteinexpression.

(a)

(b)

(c)

Fig. 4 Methylation analysis of mouse Shank3 CpG 2 island. (a) Bi-

sulfite sequencing in peripheral blood lymphocyte (PBL), brain, cere-

bellum, liver and heart from adult animals; (b) methylation-specific

restriction analysis; bisulfite-treated, amplified samples from adult

brain (B), cerebellum (C), heart (H), liver (L), PBL (P), brain from E10

embryo (E10), brain, heart, liver from newborn (P1) mice were cut with

TaqI and analysed on a 2% agarose Tris/acetate/EDTA gel; uncut

amplified DNA (U) was included as a control; (c) methylation-specific

PCR of mouse Shank3 CpG 2 island; primer pairs specific for

methylated (m) or unmethylated (u) CpG islands were used. Molecular

weight marker (M) is Marker V (Roche).

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Journal Compilation � 2007 International Society for Neurochemistry, J. Neurochem. (2007) 101, 1380–1391� 2007 The Authors

Chromosome conformation at the SHANK3 locus differs

in expressing and non-expressing human cell lines

As chromatin conformation has been shown to play a role ineukaryotic transcription regulation (Tolhuis et al. 2002) andmay be mediated by epigenetic modifications (Horike et al.2005), we applied CCC methodology (Dekker et al. 2002) tothe human SHANK3 locus to investigate long-range interac-tions in the region (see Fig. 7a for a schematic outline of theCCC analysis).

We analysed chromatin conformation in human brain,cerebellum, two neuroblastoma lines (IMR-32 and SY5Y)and one EBV-transformed lymphoblastoid line (Fig. 7b).All experiments were conducted on at least two-independ-ent samples, and each amplification was replicated at leastthree times. All PCR bands were isolated and sequenced to

confirm their identity. In brain, SY5Y (not shown) and theEBV line, we found no interactions between any of theSHANK3 regions analysed, while in cerebellum and IMR-32 a number of specific PCR products were present.Although these results show the existence of two differentchromatin conformations in human tissues and cell lines,we could not demonstrate any clear-cut association betweenchanges in chromatin conformation and SHANK3 expres-sion levels or CpG island methylation. In 5-AdC-treatedHeLa cells, where Shank3 protein expression is associatedto decreased CpG island methylation, we detected nochanges in chromosome conformation (not shown). Thus,there may be no straightforward relationship between CpGisland methylation/ SHANK3 expression and chromatinconformation.

Fig. 5 Changes in CpG methylation influence SHANK3 expression.

(a) Shank expression was tested in hippocampal neurons cultures

after treatment with 2mmol/L methionine for 24 and 72 h. In neurons,

Shank proteins are highly expressed, but at least two bands (including

the major one) recognized by the pan-Shank antibodies are reduced in

intensity. Also, the bands recognized by the proline-rich synapse-

associated protein (ProSAP2)/Shank3 and Shank3-pep antibodies are

reduced in intensity after treatment with 2mmol/L methionine for 24

and 72 h. No change in expression was found for Shank1, Shank2,

post-synaptic density (PSD-95), b-tubulin and actin. (b) Western blots

obtained from at least four independent experiments were quantified

and values were expressed as percentage of untreated neurons

(±SE). (c) RT-Q-PCR analysis of Shank expression in hippocampal

neurons after treatment with 2mmol/L methionine for 24 and 72 h

consistently showed a decrease of Shank3 mRNA, while Shank1 and

Shank2 expression did not show consistent variations. (d) Expression

of Shank proteins was tested in HeLa cells treated for 24 and 72 h with

3 lmol/L 5-Aza-2¢-deoxycytidine (5-AdC) as indicated above the pa-

nel. Untreated HeLa cells do not express Shank and PSD-95 proteins.

After 24 and 72 h of 5-AdC treatment, some protein bands with a MW

similar to Shank proteins in neuronal extracts become clearly visible

using pan-Shank but not Shank1 or PSD-95 antibodies. b-tubulin and

actin antibodies were used as loading control. (e) RT-Q-PCR analysis

reveals that untreated HeLa cells transcribe SHANK3; SHANK1 and

SHANK2 are not expressed (not shown); after 24 and 72 h of 5-AdC

treatment SHANK3 transcription increases significantly; RQ, Relative

Quantitation. (f) Methylation analysis of SHANK3 CpG islands in 5-

AdC-treated HeLa cells. Bisulfite-treated genomic DNA from untreated

cells (NT) and cells treated for 24 or 72 h with 3 mmol/L 5-AdC was

tested by methylation-specific restriction analysis (CpG islands 3–5);

uncut amplified DNA (U) was included as a control. All SHANK3 CpG

islands were also tested by direct bisulfite sequencing (not shown).

DNA methylation regulates SHANK3 expression 1387

� 2007 The AuthorsJournal Compilation � 2007 International Society for Neurochemistry, J. Neurochem. (2007) 101, 1380–1391

Discussion

Tissue-specific methylation has long been assumed to be oneof the main mechanisms used to regulate gene expression.The location of most of the cis-acting elements and themeans by which methylation might modulate expressionlevels are not known. About 60% of human genes, includingall housekeeping genes and up to 40% of tissue-specificgenes, are associated with CpG islands (Larsen et al. 1992).The islands generally cover all or part of the promoter andmay extend to the first exon and beyond. They usually existin an unmethylated state (Antequera and Bird 1993),although examples of differential methylation are known(De Smet et al. 1999; Lunyak et al. 2002; Song et al. 2005).Recently, several methods have been developed (Gitan et al.2002; Novik et al. 2002; Matsuyama et al. 2003; Shi et al.2003) allowing differential methylation analysis across awhole genome. One such screening (Ching et al. 2005)identified evolutionarily conserved tissue-specific methyla-tion of an intragenic CpG island at the SHANK3 locus. Ourdata confirm these results, as the CpG island described byChing et al. corresponds to SHANK3 CpG 4 in our setup. We

also describe tissue-specific differential methylation at addi-tional CpG islands in SHANK3 and demonstrate that, whiletissue-specific methylation is conserved in mouse and rat(Ching et al. 2005), it is not present in other members of thehuman SHANK family of genes. The fact that all promoter-associated CpG islands are unmethylated is in completeagreement with the literature data and supports the hypothesisthat an unmethylated promoter may be a prerequisite for latertranscriptional potential (Robinson et al. 2004). The mech-anism by which methylation of intragenic sequences mightmodulate gene expression is not yet known, although a recentreport suggests that methylation may alter chromatin struc-ture and impair transcription efficiency (Lorincz et al. 2004).

While it is very easy to differentiate the CpG methylationpatterns in PBLs from all other tissues, there are no clear-cut distinctions between brain, cerebellum and heart (andliver in the mouse) although differences in methylationlevels are apparent in many instances. On one hand, as allthese tissue express SHANK3 at some level, their methy-lation pattern may be similar. We should also consider thepossibility that in our experiments the tissue-specificdifferences in CpG methylation could be masked by the

I1 I2 I3

II1 II2 II3

III1 III2 III3

IV1 IV2 IV3

V1 V2 V3

(a)

(b)

Fig. 6 Effect of Shank3 expression on dendritic spines. (a) The

panels show confocal images of selected dendrites obtained from

hippocampal neurons trasfected with GFP alone [NT, panels I(1–3)

and II(1–3)], GFP plus Shank3 siRNA [Sh3si, III(1–3) and V(1–3)],

GFP plus HAShank3 [Sh3, IV(1–3)] expressing cDNAs and treated

with [II(1–3), IV(1–3) and V(1–3)] or without [I(1–3) and III(1–3)]

2mmol/L methionine for 72 h (meth, as indicated on the left). Neurons

were transfected at days in vitro (DIV) 14, treated with methionine at

DIV 16, fixed at DIV 19 and stained for GFP [I(1), II(1), III(1), IV(1) and

V(1)] and Shank3-pep antibodies [I(2), II(2), III(2), IV(2) and V(2)];

merge panels are shown in the right column [I(3), II(3), III(3), IV(3) and

V(3)]. Scale bar: 5 lm. (b) Dendritic spine length, width and number

were measured in transfected neurons treated or not with 2mmol/L

methionine for 72 h. Spine width and number were statistically re-

duced in neurons treated with methionine or transfected with Shank3

siRNA or both. Values are means (±SE) obtained from at least 15

neurons for each experimental condition; *p<0.05.

1388 S. Beri et al.

Journal Compilation � 2007 International Society for Neurochemistry, J. Neurochem. (2007) 101, 1380–1391� 2007 The Authors

presence of many different cell populations in each of ourtissue samples.

However, the observation that high-dose methioninetreatment induces a reduction of Shank3 expression incultured neurons and a consequent reduction in dendriticspines number suggests that at least in cultured hippocampalprimary neurons DNA methylation regulates Shank3 expres-sion. Uchino et al. (2006) have demonstrated that Shank3expression in mouse brain undergoes a twofold increase fromE15 to P15 at least, then it becomes lower again in 8-week-old animals. We did not find any dramatic difference inShank3 methylation levels between mouse E15, newborn andadult brain, possibly because, as we noted earlier, wholeorgan methylation analysis is hampered by the presence ofmultiple cell types. Our results also suggest that mechanismscontrolling differential tissue-specific methylation are presentearly during development.

We were not able to detect any distinctive features of theCpG-rich sequences undergoing tissue-specific methylation,and indeed there may be no easy-to-read genomic signaturefor such sites. Further genome-wide screenings may be ableto assemble a set of sequences large enough to allow asuccessful in silico analysis, although the limited number of

sites discovered in the first screen (Ching et al. 2005) couldhint to the existence of only few differentially methylatedregions.

The fact that SHANK3, but not SHANK1 and SHANK2,possesses several such regions is very intriguing and suggeststhat some of the mechanisms used to regulate its expressionmay be specific. Haploinsufficiency of the gene, alreadyknown for its structural role in PSD organization anddendritic spine morphogenesis (Roussignol et al. 2005), hasbeen associated with the human 22q13 deletion syndrome(Bonaglia et al. 2001; Wilson et al. 2003). Some of thetypical features of the syndrome (global developmentaldelay, often not readily apparent in the first year of life,severely delayed or absent speech, poor social behavioursalong the autistic spectrum) (Phelan et al. 2001; Havenset al. 2004) are strongly reminiscent of other neurodevelop-mental disorders such as Rett syndrome, caused by MECP2mutations, and Angelman syndrome, caused by maternal15q11-q13 or UBE3A deficiency. MECP2 associates withhistone H3 Lys9 methyltransferase (Fuks et al. 2003) andwith the DNA methyltransferase Dnmt1 (Kimura and Shiota2003), linking DNA methylation and histone methylation.MECP2 deficiency causes modifications of chromatin

(a)

(b)

Fig. 7 SHANK3 chromosome conforma-

tion capture (CCC) analysis.(a) Schematic

representation of SHANK3 CCC strategy.

Intron/exon structure of the gene and loca-

tion of CpG islands and repeated se-

quences are shown; the location of HindIII

and EcoRI restriction sites and fragments

and all CCC primers are also shown. (b)

CCC analysis of the human SHANK3 gene.

Only amplifications generating tissue-spe-

cific products are shown. All fragments

were sequenced to confirm that the expec-

ted product was generated. Purified ge-

nomic DNA (ligation control) and cloned

Bacterial Artificial Chromosome DNA con-

taining the SHANK3 gene (Bacterial Artifi-

cial Chromosome control) after HindIII or

EcoRI digestion and ligation were used as

templates for PCR amplification using all

available combinations of primers; No PCR

product could be formed from distant se-

quences using purified genomic DNA,

whereas all primer combinations tested

could be amplified from the Bacterial Artifi-

cial Chromosome DNA owing to high molar

concentration of fragments. All experiments

were conducted on at least two independ-

ent samples, and each amplification was

replicated at least three times. Molecular

weight marker (M) is Marker V (Roche).

DNA methylation regulates SHANK3 expression 1389

� 2007 The AuthorsJournal Compilation � 2007 International Society for Neurochemistry, J. Neurochem. (2007) 101, 1380–1391

looping at the Dlx5-Dlx6 locus in mice (Horike et al. 2005),epigenetic aberrations at the PWS/AS imprinting centreaffecting UBE3A expression (Makedonski et al. 2005),deficiency in homologous pairing of the 15q11-13 imprinteddomains in brain (Thatcher et al. 2005), reduced expressionof UBE3A and GABRB3 (Samaco et al. 2005). As thepresence of several differentially methylated regions shouldmake the SHANK3 gene an obvious target, it will beimportant to test whether MECP2 binds to any of the CpGislands and whether its deficiency will affect SHANK3methylation, expression and chromosomal conformation.

Acknowledgements

The ‘‘Telethon Bank of DNA, Nerve and Muscle Tissues’’ (No.

GTF02008), located at the Department of Neurological Sciences,

I.R.C.C.S. Ospedale Maggiore Policlinico, Mangiagalli and Regina

Elena Foundation, Milan, Italy, was the source of the human tissue

samples used in this study. Human neuroblastoma lines were kindly

provided by M. Ponzoni, G. Gaslini Children’s Hospital, Genova.

We thank U. Pozzoli and M. Sironi for helpful discussion and

critical reading of the manuscript. CS is supported by the Giovanni

Armenise-Harvard Foundation Career Development Program and by

European Community (LSHM-CT-2004-511995, SYNSCAFF). The

financial support of Telethon – Italy (Grant No. GGP06208) is

gratefully acknowledged.

Supplementary material

The following supplementary material is available for this article

online:

Fig. S1 Antibody specificity was tested in COS7 cells transfected

with Shank1 and Shank3 or GFP Shank1, GFP Shank2 and GFP

Shank3 as indicated above the panels. (a) The Shank1 antibody

recognizes Shank1 but not Shank3 protein, while the pan-Shank

antibody recognizes both proteins. b-tubulin antibodies were used asloading control. (b) The pan-Shank antibody recognizes all three

GFP Shank proteins, while the ProSAP1/Shank2 antibody recogni-

zes only GFP Shank2 protein and both ProSAP2/Shank3 and

Shank3-pep recognize only the GFP Shank3 protein.

This material is available as part of the online article from http://

www.blackwell-synergy.com.

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