메뉴 건너뛰기




Volumn 41, Issue 18, 2013, Pages 8503-8514

Integrative analysis of tissue-specific methylation and alternative splicing identifies conserved transcription factor binding motifs

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE; GENOMIC DNA; TRANSCRIPTION FACTOR;

EID: 84885909715     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt652     Document Type: Article
Times cited : (44)

References (49)
  • 1
    • 0023216891 scopus 로고
    • CpG islands in vertebrate genomes
    • Gardiner-Garden, M. and Frommer, M. (1987) CpG islands in vertebrate genomes. J. Mol. Biol., 196, 261-282.
    • (1987) J. Mol. Biol , vol.196 , pp. 261-282
    • Gardiner-Garden, M.1    Frommer, M.2
  • 3
    • 79959872458 scopus 로고    scopus 로고
    • Cell type-specific DNA methylation at intragenic CpG islands in the immune system
    • Deaton, A.M., Webb, S., Kerr, A.R., Illingworth, R.S., Guy, J., Andrews, R. and Bird, A. (2011) Cell type-specific DNA methylation at intragenic CpG islands in the immune system. Genome Res., 21, 1074-1086.
    • (2011) Genome Res , vol.21 , pp. 1074-1086
    • Deaton, A.M.1    Webb, S.2    Kerr, A.R.3    Illingworth, R.S.4    Guy, J.5    Andrews, R.6    Bird, A.7
  • 7
    • 59149084538 scopus 로고    scopus 로고
    • The human colon cancer methylome shows similar hypoand hypermethylation at conserved tissue-specific CpG island shores
    • Irizarry, R.A., Ladd-Acosta, C., Wen, B., Wu, Z., Montano, C., Onyango, P., Cui, H., Gabo, K., Rongione, M., Webster, M. et al. (2009) The human colon cancer methylome shows similar hypoand hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet., 41, 178-186.
    • (2009) Nat. Genet , vol.41 , pp. 178-186
    • Irizarry, R.A.1    Ladd-Acosta, C.2    Wen, B.3    Wu, Z.4    Montano, C.5    Onyango, P.6    Cui, H.7    Gabo, K.8    Rongione, M.9    Webster, M.10
  • 8
    • 70649095120 scopus 로고    scopus 로고
    • Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells embryonic stem cells and fibroblasts
    • Doi, A., Park, I.H., Wen, B., Murakami, P., Aryee, M.J., Irizarry, R., Herb, B., Ladd-Acosta, C., Rho, J., Loewer, S. et al. (2009) Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat. Genet., 41, 1350-1353.
    • (2009) Nat. Genet , vol.41 , pp. 1350-1353
    • Doi, A.1    Park, I.H.2    Wen, B.3    Murakami, P.4    Aryee, M.J.5    Irizarry, R.6    Herb, B.7    Ladd-Acosta, C.8    Rho, J.9    Loewer, S.10
  • 9
    • 79952727299 scopus 로고    scopus 로고
    • Hypermethylation of CpG islands and shores around specific microRNAs and mirtrons is associated with the phenotype and presence of bladder cancer
    • Dudziec, E., Miah, S., Choudhry, H.M., Owen, H.C., Blizard, S., Glover, M., Hamdy, F.C. and Catto, J.W. (2011) Hypermethylation of CpG islands and shores around specific microRNAs and mirtrons is associated with the phenotype and presence of bladder cancer. Clin. Cancer Res., 17, 1287-1296.
    • (2011) Clin. Cancer Res , vol.17 , pp. 1287-1296
    • Dudziec, E.1    Miah, S.2    Choudhry, H.M.3    Owen, H.C.4    Blizard, S.5    Glover, M.6    Hamdy, F.C.7    Catto, J.W.8
  • 16
    • 78650429329 scopus 로고    scopus 로고
    • Tissue-specific expression of IL-15RA alternative splicing transcripts and its regulation by DNA methylation
    • Diniz, S.N., Pendeloski, K.P., Morgun, A., Chepelev, I., Gerbase-DeLima, M. and Shulzhenko, N. (2010) Tissue-specific expression of IL-15RA alternative splicing transcripts and its regulation by DNA methylation. Eur. Cytokine Netw., 21, 308-318.
    • (2010) Eur. Cytokine Netw , vol.21 , pp. 308-318
    • Diniz, S.N.1    Pendeloski, K.P.2    Morgun, A.3    Chepelev, I.4    Gerbase-Delima, M.5    Shulzhenko, N.6
  • 17
    • 84878623709 scopus 로고    scopus 로고
    • A novel methyl-binding domain protein enrichment method for identifying genome-wide tissue-specific DNA methylation from nanogram DNA samples
    • Oliver, V.F., Wan, J., Agarwal, S., Zack, D.J., Qian, J. and Merbs, S.L. (2013) A novel methyl-binding domain protein enrichment method for identifying genome-wide tissue-specific DNA methylation from nanogram DNA samples. Epigenetics Chromatin, 6, 17.
    • (2013) Epigenetics Chromatin , vol.6 , pp. 17
    • Oliver, V.F.1    Wan, J.2    Agarwal, S.3    Zack, D.J.4    Qian, J.5    Merbs, S.L.6
  • 18
    • 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. and Kouidou, S. (2011) Human epigenome data reveal increased CpG methylation in alternatively spliced sites and putative exonic splicing enhancers. DNA Cell Biol., 30, 267-275.
    • (2011) DNA Cell Biol , vol.30 , pp. 267-275
    • Anastasiadou, C.1    Malousi, A.2    Maglaveras, N.3    Kouidou, S.4
  • 19
    • 70349333201 scopus 로고    scopus 로고
    • Nucleosomes are well positioned in exons and carry characteristic histone modifications
    • Andersson, R., Enroth, S., Rada-Iglesias, A., Wadelius, C. and Komorowski, J. (2009) Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res., 19, 1732-1741.
    • (2009) Genome Res , vol.19 , pp. 1732-1741
    • Andersson, R.1    Enroth, S.2    Rada-Iglesias, A.3    Wadelius, C.4    Komorowski, J.5
  • 21
    • 76249090741 scopus 로고    scopus 로고
    • Nucleosome deposition and DNA methylation at coding region boundaries
    • Choi, J.K., Bae, J.B., Lyu, J., Kim, T.Y. and Kim, Y.J. (2009) Nucleosome deposition and DNA methylation at coding region boundaries. Genome Biol., 10, R89.
    • (2009) Genome Biol , vol.10
    • Choi, J.K.1    Bae, J.B.2    Lyu, J.3    Kim, T.Y.4    Kim, Y.J.5
  • 22
    • 84877108379 scopus 로고    scopus 로고
    • DNAmethylation effect on co-transcriptional splicing is dependent on GC-architecture of the exon-intron structure
    • Gelfman, S., Cohen, N., Yearim, A. and Ast, G. (2013) DNAmethylation effect on co-transcriptional splicing is dependent on GC-architecture of the exon-intron structure. Genome Res., 23, 789-799.
    • (2013) Genome Res , vol.23 , pp. 789-799
    • Gelfman, S.1    Cohen, N.2    Yearim, A.3    Ast, G.4
  • 23
  • 24
    • 69949132191 scopus 로고    scopus 로고
    • Chromatin organization marks exon-intron structure
    • Schwartz, S., Meshorer, E. and Ast, G. (2009) Chromatin organization marks exon-intron structure. Nat. Struct. Mol. Biol., 16, 990-995.
    • (2009) Nat. Struct. Mol. Biol , vol.16 , pp. 990-995
    • Schwartz, S.1    Meshorer, E.2    Ast, G.3
  • 25
    • 84858976475 scopus 로고    scopus 로고
    • Epigenetic features are significantly associated with alternative splicing
    • Zhou, Y., Lu, Y. and Tian, W. (2012) Epigenetic features are significantly associated with alternative splicing. BMC Genomics, 13, 123.
    • (2012) BMC Genomics , vol.13 , pp. 123
    • Zhou, Y.1    Lu, Y.2    Tian, W.3
  • 27
    • 0034713275 scopus 로고    scopus 로고
    • CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus
    • Hark, A.T., Schoenherr, C.J., Katz, D.J., Ingram, R.S., Levorse, J.M. and Tilghman, S.M. (2000) CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus. Nature, 405, 486-489.
    • (2000) Nature , vol.405 , pp. 486-489
    • Hark, A.T.1    Schoenherr, C.J.2    Katz, D.J.3    Ingram, R.S.4    Levorse, J.M.5    Tilghman, S.M.6
  • 34
    • 84867611767 scopus 로고    scopus 로고
    • Use of laser capture microdissection for analysis of retinal mRNA/miRNA expression and DNA methylation
    • Hackler, L. Jr, Masuda, T., Oliver, V.F., Merbs, S.L. and Zack, D.J. (2012) Use of laser capture microdissection for analysis of retinal mRNA/miRNA expression and DNA methylation. Methods Mol. Biol., 884, 289-304.
    • (2012) Methods Mol. Biol , vol.884 , pp. 289-304
    • Hackler Jr., L.1    Masuda, T.2    Oliver, V.F.3    Merbs, S.L.4    Zack, D.J.5
  • 36
    • 33750882505 scopus 로고    scopus 로고
    • Compact universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
    • Berger, M.F., Philippakis, A.A., Qureshi, A.M., He, F.S., Estep, P.W. III and Bulyk, M.L. (2006) Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat. Biotech., 24, 1429-1435.
    • (2006) Nat. Biotech , vol.24 , pp. 1429-1435
    • Berger, M.F.1    Philippakis, A.A.2    Qureshi, A.M.3    He, F.S.4    Estep Iii., P.W.5    Bulyk, M.L.6
  • 39
    • 0032532734 scopus 로고    scopus 로고
    • WT1 interacts with the splicing factor U2AF65 in an isoform-dependent manner and can be incorporated into spliceosomes
    • Davies, R.C., Calvio, C., Bratt, E., Larsson, S.H., Lamond, A.I. and Hastie, N.D. (1998) WT1 interacts with the splicing factor U2AF65 in an isoform-dependent manner and can be incorporated into spliceosomes. Genes Dev., 12, 3217-3225.
    • (1998) Genes Dev , vol.12 , pp. 3217-3225
    • Davies, R.C.1    Calvio, C.2    Bratt, E.3    Larsson, S.H.4    Lamond, A.I.5    Hastie, N.D.6
  • 43
    • 77952355762 scopus 로고    scopus 로고
    • Genome-wide evolutionary analysis of eukaryotic DNA methylation
    • Zemach, A., McDaniel, I.E., Silva, P. and Zilberman, D. (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science, 328, 916-919.
    • (2010) Science , vol.328 , pp. 916-919
    • Zemach, A.1    McDaniel, I.E.2    Silva, P.3    Zilberman, D.4
  • 44
    • 84867539515 scopus 로고    scopus 로고
    • Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus
    • Cowley, M., Wood, A.J., Bohm, S., Schulz, R. and Oakey, R.J. (2012) Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus. Nucleic Acids Res., 40, 8917-8926.
    • (2012) Nucleic Acids Res , vol.40 , pp. 8917-8926
    • Cowley, M.1    Wood, A.J.2    Bohm, S.3    Schulz, R.4    Oakey, R.J.5
  • 46
    • 84864689380 scopus 로고    scopus 로고
    • DNA hypermethylation of alternatively spliced and repeat sequences in humans
    • Malousi, A. and Kouidou, S. (2012) DNA hypermethylation of alternatively spliced and repeat sequences in humans. Mol. Genet. Genomics, 287, 631-642.
    • (2012) Mol. Genet. Genomics , vol.287 , pp. 631-642
    • Malousi, A.1    Kouidou, S.2
  • 48
    • 70349125488 scopus 로고    scopus 로고
    • Co-transcriptional splicing of constitutive and alternative exons
    • Pandya-Jones, A. and Black, D.L. (2009) Co-transcriptional splicing of constitutive and alternative exons. RNA, 15, 1896-1908.
    • (2009) RNA , vol.15 , pp. 1896-1908
    • Pandya-Jones, A.1    Black, D.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.