When epigenetics meets alternative splicing: The roles of DNA methylation and GC architecture

Epigenomics

Volumn 5, Issue 4, 2013, Pages 351-353

  Gelfman, Sahar ^a   Ast, Gil ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

DNA methylation; GC content; splicing

Indexed keywords

DINUCLEOTIDE; MESSENGER RNA; MESSENGER RNA PRECURSOR; RNA; RNA POLYMERASE II;

ALTERNATIVE RNA SPLICING; CHROMATIN; CHROMATIN STRUCTURE; CODING; DNA BASE COMPOSITION; DNA METHYLATION; EPIGENETICS; EXON; GENE STRUCTURE; GENOME; HISTONE MODIFICATION; INTRON; INTRON RETENTION; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PURIFYING SELECTION; REVIEW; RNA PROCESSING; SPLICEOSOME;

ALTERNATIVE SPLICING; ANIMALS; BASE COMPOSITION; DNA METHYLATION; EPIGENESIS, GENETIC; EXONS; HUMANS;

EID: 84881113432     PISSN: 17501911     EISSN: 1750192X     Source Type: Journal    
DOI: 10.2217/epi.13.32     Document Type: Review

References (18)

1. Kornblihtt AR, Schor IE, Allo M, Blencowe BJ. When chromatin meets splicing. Nat. Struct. Mol. Biol. 16(9), 902-903 (2009
2. Schwartz S, Meshorer E, Ast G. Chromatin organization marks exon-intron structure. Nat. Struct. Mol. Biol. 16(9), 990-995 (2009
3. Spies N, Nielsen CB, Padgett RA, Burge CB. Biased chromatin signatures around polyadenylation sites and exons. Mol. Cell 36(2), 245-254 (2009
4. Tilgner H, Nikolaou C, Althammer S et al. Nucleosome positioning as a determinant of exon recognition. Nat. Struct. Mol. Biol. 16(9), 996-1001 (2009
5. Brenet F, Moh M, Funk P et al. DNA methylation of the first exon is tightly linked to transcriptional silencing. PLoS One 6(1), e14524 (2011
6. Lister R, Pelizzola M, Dowen RH et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462(7271), 315-322 (2009
7. Amit M, Donyo M, Hollander D et al. Differential GC Content between exons and introns establishes distinct strategies of splice-site recognition. Cell Rep. 1(5), 543-556 (2012
8. Gelfman S, Burstein D, Penn O et al. Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons. Genome Res. 22(1), 35-50 (2012
9. Batsche E, Yaniv M, Muchardt C. The human SWI/SNF subunit Brm is a regulator of alternative splicing. Nat. Struct. Mol. Biol. 13(1), 22-29 (2006
10. de la Mata M, Alonso CR, Kadener S et al. A slow RNA polymerase II affects alternative splicing in vivo. Mol. Cell 12(2), 525-532 (2003
11. Hodges C, Bintu L, Lubkowska L, Kashlev M, Bustamante C Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. Science 325(5940), 626-628 (2009
12. Luco RF, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith OM, Misteli T. Regulation of alternative splicing by histone modifications. Science 327(5968), 996-1000 (2010
13. Barbosa-Morais NL, Irimia M, Pan Q et al. The evolutionary landscape of alternative splicing in vertebrate species. Science 338(6114), 1587-1593 (2012
14. Merkin J, Russell C, Chen P, Burge CB. Evolutionary dynamics of gene and isoform regulation in mammalian tissues. Science 338(6114), 1593-1599 (2012
15. Gelfman S, Cohen N, Yearim A, Ast G. DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure. Genome Res. 23(5), 789-799 (2013
16. Shukla S, Kavak E, Gregory M et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 479(7371), 74-79 (2011
17. Choy JS, Wei S, Lee JY, Tan S, Chu S, Lee TH. DNA methylation increases nucleosome compaction and rigidity. J. Am. Chem. Soc. 132(6), 1782-1783 (2010
18. Sarraf SA, Stancheva I. Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly. Mol. Cell 15(4), 595-605 (2004