메뉴 건너뛰기




Volumn 23, Issue 11, 2013, Pages 1256-1269

Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition

Author keywords

chromatin; epigenomics; histone acetylation; intragenic DNA methylation; MeCP2; splicing

Indexed keywords

MECP2 PROTEIN, HUMAN; METHYL CPG BINDING PROTEIN 2;

EID: 84887214395     PISSN: 10010602     EISSN: 17487838     Source Type: Journal    
DOI: 10.1038/cr.2013.110     Document Type: Article
Times cited : (448)

References (46)
  • 1
    • 79956294973 scopus 로고    scopus 로고
    • DNA methylation and demethylation in mammals
    • Chen ZX, Riggs AD. DNA methylation and demethylation in mammals. J Biol Chem 2011; 286:18347-18353.
    • (2011) J Biol Chem , vol.286 , pp. 18347-18353
    • Chen, Z.X.1    Riggs, A.D.2
  • 2
    • 0035839057 scopus 로고    scopus 로고
    • The role of DNA methylation in mammalian epigenetics
    • DOI 10.1126/science.1063852
    • Jones PA, Takai D. The role of DNA methylation in mammalian epigenetics. Science 2001; 293:1068-1070. (Pubitemid 32758075)
    • (2001) Science , vol.293 , Issue.5532 , pp. 1068-1070
    • Jones, P.A.1    Takai, D.2
  • 3
    • 32344450824 scopus 로고    scopus 로고
    • Genomic DNA methylation: The mark and its mediators
    • DOI 10.1016/j.tibs.2005.12.008, PII S096800040500352X
    • Klose RJ, Bird AP. Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 2006; 31:89-97. (Pubitemid 43221841)
    • (2006) Trends in Biochemical Sciences , vol.31 , Issue.2 , pp. 89-97
    • Klose, R.J.1    Bird, A.P.2
  • 4
    • 79959872458 scopus 로고    scopus 로고
    • Cell type-specifc DNA methylation at intragenic CpG islands in the immune system
    • Deaton AM, Webb S, Kerr AR, et al. Cell type-specifc DNA methylation at intragenic CpG islands in the immune system. Genome Res 2011; 21:1074-1086.
    • (2011) Genome Res , vol.21 , pp. 1074-1086
    • Deaton, A.M.1    Webb, S.2    Kerr, A.R.3
  • 5
    • 38949212693 scopus 로고    scopus 로고
    • A novel CpG island set identifes tissue-specifc methylation at developmental gene loci
    • Illingworth R, Kerr A, Desousa D, et al. A novel CpG island set identifes tissue-specifc methylation at developmental gene loci. PLoS Biol 2008; 6:e22.
    • (2008) PLoS Biol , vol.6
    • Illingworth, R.1    Kerr, A.2    Desousa, D.3
  • 6
    • 79955777417 scopus 로고    scopus 로고
    • Genome-wide survey reveals dynamic widespread tissue-specifc changes in DNA methyla-tion during development
    • Liang P, Song F, Ghosh S, et al. Genome-wide survey reveals dynamic widespread tissue-specifc changes in DNA methyla-tion during development. BMC Genomics 2011; 12:231.
    • (2011) BMC Genomics , vol.12 , pp. 231
    • Liang, P.1    Song, F.2    Ghosh, S.3
  • 7
    • 77954504873 scopus 로고    scopus 로고
    • Conserved role of intragenic DNA methylation in regulating alternative promoters
    • Maunakea AK, Nagarajan RP, Bilenky M, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 2010; 466:253-257.
    • (2010) Nature , vol.466 , pp. 253-257
    • Maunakea, A.K.1    Nagarajan, R.P.2    Bilenky, M.3
  • 8
    • 79955778919 scopus 로고    scopus 로고
    • Human epigenome data reveal increased CpG methylation in alternatively spliced sites and putative exonic splicing enhancers
    • Anastasiadou C, Malousi A, Maglaveras N, Kouidou S. Human epigenome data reveal increased CpG methylation in alternatively spliced sites and putative exonic splicing enhancers. DNA Cell Biol 2011; 30:267-275.
    • (2011) DNA Cell Biol , vol.30 , pp. 267-275
    • Anastasiadou, C.1    Malousi, A.2    Maglaveras, N.3    Kouidou, S.4
  • 9
    • 77954659099 scopus 로고    scopus 로고
    • Relationship between nucleosome positioning and DNA methylation
    • Chodavarapu RK, Feng S, Bernatavichute YV, et al. Relationship between nucleosome positioning and DNA methylation. Nature 2010; 466:388-392.
    • (2010) Nature , vol.466 , pp. 388-392
    • Chodavarapu, R.K.1    Feng, S.2    Bernatavichute, Y.V.3
  • 10
    • 77954171220 scopus 로고    scopus 로고
    • Contrasting chromatin organization of CpG islands and exons in the human genome
    • Choi JK. Contrasting chromatin organization of CpG islands and exons in the human genome. Genome Biol 2010; 11:R70.
    • (2010) Genome Biol , vol.11
    • Choi, J.K.1
  • 11
    • 77952734605 scopus 로고    scopus 로고
    • Conservation and divergence of methylation patterning in plants and animals
    • Feng S, Cokus SJ, Zhang X, et al. Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci USA 2010; 107:8689-8694.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 8689-8694
    • Feng, S.1    Cokus, S.J.2    Zhang, X.3
  • 12
    • 80455176999 scopus 로고    scopus 로고
    • CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
    • Shukla S, Kavak E, Gregory M, et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 2011; 479:74-79.
    • (2011) Nature , vol.479 , pp. 74-79
    • Shukla, S.1    Kavak, E.2    Gregory, M.3
  • 14
    • 7544231794 scopus 로고    scopus 로고
    • Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells
    • DOI 10.1038/nsmb840
    • Lorincz MC, Dickerson DR, Schmitt M, Groudine M. Intra-genic DNA methylation alters chromatin structure and elongation effciency in mammalian cells. Nat Struct Mol Biol 2004; 11:1068-1075. (Pubitemid 39453335)
    • (2004) Nature Structural and Molecular Biology , vol.11 , Issue.11 , pp. 1068-1075
    • Lorincz, M.C.1    Dickerson, D.R.2    Schmitt, M.3    Groudine, M.4
  • 15
    • 70450217879 scopus 로고    scopus 로고
    • Human DNA methy-lomes at base resolution show widespread epigenomic differences
    • Lister R, Pelizzola M, Dowen RH, et al. Human DNA methy-lomes at base resolution show widespread epigenomic differences. Nature 2009; 462:315-322.
    • (2009) Nature , vol.462 , pp. 315-322
    • Lister, R.1    Pelizzola, M.2    Dowen, R.H.3
  • 16
    • 77954393480 scopus 로고    scopus 로고
    • Demethylation by 5-aza-2′-deoxycytidine in colorectal cancer cells targets genomic DNA whilst promoter CpG island methylation persists
    • Mossman D, Kim KT, Scott RJ. Demethylation by 5-aza-2′- deoxycytidine in colorectal cancer cells targets genomic DNA whilst promoter CpG island methylation persists. BMC Cancer 2010; 10:366.
    • (2010) BMC Cancer , vol.10 , pp. 366
    • Mossman, D.1    Kim, K.T.2    Scott, R.J.3
  • 18
    • 33846038833 scopus 로고    scopus 로고
    • 5-Aza-2′-deoxycytidine-mediated reductions in G9A histone methyltransferase and histone H3 K9 di-methylation levels are linked to tumor suppressor gene reactivation
    • DOI 10.1038/sj.onc.1209763, PII 1209763
    • Wozniak RJ, Klimecki WT, Lau SS, Feinstein Y, Futscher BW. 5-Aza-2′-deoxycytidine-mediated reductions in G9A histone methyltransferase and histone H3 K9 di-methylation levels are linked to tumor suppressor gene reactivation. Oncogene 2007; 26:77-90. (Pubitemid 46067333)
    • (2007) Oncogene , vol.26 , Issue.1 , pp. 77-90
    • Wozniak, R.J.1    Klimecki, W.T.2    Lau, S.S.3    Feinstein, Y.4    Futscher, B.W.5
  • 19
    • 63149192174 scopus 로고    scopus 로고
    • Neu-ronal cell depolarization induces intragenic chromatin modif-cations affecting NCAM alternative splicing
    • Schor IE, Rascovan N, Pelisch F, Allo M, Kornblihtt AR. Neu-ronal cell depolarization induces intragenic chromatin modif-cations affecting NCAM alternative splicing. Proc Natl Acad Sci USA 2009; 106:4325-4330.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 4325-4330
    • Schor, I.E.1    Rascovan, N.2    Pelisch, F.3    Allo, M.4    Kornblihtt, A.R.5
  • 20
    • 0027495467 scopus 로고
    • Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2
    • Nan X, Meehan RR, Bird A. Dissection of the methyl-CpG binding domain from the chromosomal protein MeCP2. Nucleic Acids Res 1993; 21:4886-4892. (Pubitemid 23330162)
    • (1993) Nucleic Acids Research , vol.21 , Issue.21 , pp. 4886-4892
    • Nan, X.1    Meehan, R.R.2    Bird, A.3
  • 21
    • 79960724914 scopus 로고    scopus 로고
    • A brain-derived MeCP2 complex supports a role for MeCP2 in RNA processing
    • Long SW, Ooi JY, Yau PM, Jones PL. A brain-derived MeCP2 complex supports a role for MeCP2 in RNA processing. Biosci Rep 2011; 31:333-343.
    • (2011) Biosci Rep , vol.31 , pp. 333-343
    • Long, S.W.1    Ooi, J.Y.2    Yau, P.M.3    Jones, P.L.4
  • 23
    • 37649022627 scopus 로고    scopus 로고
    • Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes
    • Yasui DH, Peddada S, Bieda MC, et al. Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes. Proc Natl Acad Sci USA 2007; 104:19416-19421.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 19416-19421
    • Yasui, D.H.1    Peddada, S.2    Bieda, M.C.3
  • 24
    • 0032574977 scopus 로고    scopus 로고
    • Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex
    • DOI 10.1038/30764
    • Nan X, Ng HH, Johnson CA, et al. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 1998; 393:386-389. (Pubitemid 28269714)
    • (1998) Nature , vol.393 , Issue.6683 , pp. 386-389
    • Nan, X.1    Ng, H.-H.2    Johnson, C.A.3    Laherty, C.D.4    Turner, B.M.5    Eisenman, R.N.6    Bird, A.7
  • 25
    • 79952266577 scopus 로고    scopus 로고
    • Global impact of RNA poly-merase II elongation inhibition on alternative splicing regulation
    • Ip JY, Schmidt D, Pan Q, et al. Global impact of RNA poly-merase II elongation inhibition on alternative splicing regulation. Genome Res 2011; 21:390-401.
    • (2011) Genome Res , vol.21 , pp. 390-401
    • Ip, J.Y.1    Schmidt, D.2    Pan, Q.3
  • 27
    • 80052594686 scopus 로고    scopus 로고
    • Hu proteins regulate alternative splicing by inducing localized histone hyperacety-lation in an RNA-dependent manner
    • Zhou HL, Hinman MN, Barron VA, et al. Hu proteins regulate alternative splicing by inducing localized histone hyperacety-lation in an RNA-dependent manner. Proc Natl Acad Sci USA 2011; 108:E627-635.
    • (2011) Proc Natl Acad Sci USA , vol.108
    • Zhou, H.L.1    Hinman, M.N.2    Barron, V.A.3
  • 30
    • 57849109058 scopus 로고    scopus 로고
    • Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    • Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 2008; 322:1845-1848.
    • (2008) Science , vol.322 , pp. 1845-1848
    • Core, L.J.1    Waterfall, J.J.2    Lis, J.T.3
  • 31
    • 69949124307 scopus 로고    scopus 로고
    • Nucleosome positioning as a determinant of exon recognition
    • Tilgner H, Nikolaou C, Althammer S, et al. Nucleosome positioning as a determinant of exon recognition. Nat Struct Mol Biol 2009; 16:996-1001.
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 996-1001
    • Tilgner, H.1    Nikolaou, C.2    Althammer, S.3
  • 32
    • 84870552401 scopus 로고    scopus 로고
    • Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules
    • Kelly TK, Liu Y, Lay FD, Liang G, Berman BP, Jones PA. Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res 2012; 22:2497-2506.
    • (2012) Genome Res , vol.22 , pp. 2497-2506
    • Kelly, T.K.1    Liu, Y.2    Lay, F.D.3    Liang, G.4    Berman, B.P.5    Jones, P.A.6
  • 33
    • 0032830639 scopus 로고    scopus 로고
    • Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl- CpG-binding protein 2
    • DOI 10.1038/13810
    • Amir RE, Van den Veyver IB, Wan M, Tran CQ, Francke U, Zoghbi HY. Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat Genet 1999; 23:185-188. (Pubitemid 29455390)
    • (1999) Nature Genetics , vol.23 , Issue.2 , pp. 185-188
    • Amir, R.E.1    Van Den Veyver, I.B.2    Wan, M.3    Tran, C.Q.4    Francke, U.5    Zoghbi, H.Y.6
  • 34
    • 33645218385 scopus 로고    scopus 로고
    • Rett Syndrome: A Rosetta Stone for Understanding the Molecular Pathogenesis of Autism
    • DOI 10.1016/S0074-7742(05)71006-0, PII S0074774205710060, GABA in Autism and Related Disorders
    • LaSalle JM, Hogart A, Thatcher KN. Rett syndrome: a Rosetta stone for understanding the molecular pathogenesis of autism. Int Rev Neurobiol 2005; 71:131-165. (Pubitemid 43580937)
    • (2005) International Review of Neurobiology , vol.71 , pp. 131-165
    • LaSalle, J.M.1    Hogart, A.2    Thatcher, K.N.3
  • 35
    • 33646683567 scopus 로고    scopus 로고
    • MeCP2 dysfunction in Rett syndrome and related disorders
    • DOI 10.1016/j.gde.2006.04.009, PII S0959437X06000700
    • Moretti P, Zoghbi HY. MeCP2 dysfunction in Rett syndrome and related disorders. Curr Opin Genet Dev 2006; 16:276-281. (Pubitemid 43732423)
    • (2006) Current Opinion in Genetics and Development , vol.16 , Issue.3 , pp. 276-281
    • Moretti, P.1    Zoghbi, H.Y.2
  • 36
    • 65249109807 scopus 로고    scopus 로고
    • Variants within MECP2, a key transcription regulator, are associated with increased susceptibility to lupus and differential gene expression in patients with systemic lupus erythematosus
    • Webb R, Wren JD, Jeffries M, et al. Variants within MECP2, a key transcription regulator, are associated with increased susceptibility to lupus and differential gene expression in patients with systemic lupus erythematosus. Arthritis Rheum 2009; 60:1076-1084.
    • (2009) Arthritis Rheum , vol.60 , pp. 1076-1084
    • Webb, R.1    Wren, J.D.2    Jeffries, M.3
  • 37
    • 34247095504 scopus 로고    scopus 로고
    • Reduced MeCP2 expression is frequent in autism frontal cortex and correlates with aberrant MECP2 promoter methylation
    • Nagarajan RP, Hogart AR, Gwye Y, Martin MR, LaSalle JM. Reduced MeCP2 expression is frequent in autism frontal cortex and correlates with aberrant MECP2 promoter methylation. Epigenetics 2006; 1:e1-e11.
    • (2006) Epigenetics , vol.1
    • Nagarajan, R.P.1    Hogart, A.R.2    Gwye, Y.3    Martin, M.R.4    Lasalle, J.M.5
  • 38
    • 67650139492 scopus 로고    scopus 로고
    • MECP2 promoter methylation and X chromosome inactivation in autism
    • Nagarajan RP, Patzel KA, Martin M, et al. MECP2 promoter methylation and X chromosome inactivation in autism. Autism Res 2008; 1:169-178.
    • (2008) Autism Res , vol.1 , pp. 169-178
    • Nagarajan, R.P.1    Patzel, K.A.2    Martin, M.3
  • 39
    • 70350049103 scopus 로고    scopus 로고
    • Abnormal DNA methylation in CD4+ T cells from patients with systemic lupus erythemato-sus, systemic sclerosis, and dermatomyositis
    • Lei W, Luo Y, Lei W, et al. Abnormal DNA methylation in CD4+ T cells from patients with systemic lupus erythemato-sus, systemic sclerosis, and dermatomyositis. Scand J Rheu-matol 2009; 38:369-374.
    • (2009) Scand J Rheu-matol , vol.38 , pp. 369-374
    • Lei, W.1    Luo, Y.2    Lei, W.3
  • 42
    • 0035339188 scopus 로고    scopus 로고
    • MECP2 truncating mutations cause histone H4 hyperacetylation in Rett syndrome
    • Wan M, Zhao K, Lee SS, Francke U. MECP2 truncating mutations cause histone H4 hyperacetylation in Rett syndrome. Hum Mol Genet 2001; 10:1085-1092. (Pubitemid 32447786)
    • (2001) Human Molecular Genetics , vol.10 , Issue.10 , pp. 1085-1092
    • Wan, M.1    Zhao, K.2    Lee, S.S.J.3    Francke, U.4
  • 43
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009; 25:1105-1111.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 44
    • 57449100870 scopus 로고    scopus 로고
    • Design and analysis of ChIP-seq experiments for DNA-binding proteins
    • Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol 2008; 26:1351-1359.
    • (2008) Nat Biotechnol , vol.26 , pp. 1351-1359
    • Kharchenko, P.V.1    Tolstorukov, M.Y.2    Park, P.J.3
  • 45
    • 53849146020 scopus 로고    scopus 로고
    • Model-based analysis of ChIP-Seq (MACS)
    • Zhang Y, Liu T, Meyer CA, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008; 9:R137.
    • (2008) Genome Biol , vol.9
    • Zhang, Y.1    Liu, T.2    Meyer, C.A.3
  • 46
    • 79955400147 scopus 로고    scopus 로고
    • Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marks
    • Hahn MA, Wu X, Li AX, Hahn T, Pfeifer GP. Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marks. PLoS One 2011; 6:e18844.
    • (2011) PLoS One , vol.6
    • Hahn, M.A.1    Wu, X.2    Li, A.X.3    Hahn, T.4    Pfeifer, G.P.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.