Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors

Nucleic Acids Research

Volumn 42, Issue 5, 2014, Pages 2856-2869

  Ye, Zhenqing ^a   Chen, Zhong ^b   Lan, Xun ^c   Hara, Stephen ^c   Sunkel, Benjamin ^b   Huang, Tim H M ^a   Elnitski, Laura ^d   Wang, Qianben ^b   Jin, Victor X ^a  

^a UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT SAN ANTONIO   (United States)

^b OHIO STATE UNIVERSITY   (United States)

^c OHIO STATE UNIVERSITY   (United States)

^d NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA BINDING PROTEIN; SERINE ARGININE RICH PROTEIN; SERINE ARGININE RICH PROTEIN SC35; TRANSCRIPTION FACTOR; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CHROMATIN ASSEMBLY AND DISASSEMBLY; COMPUTER ANALYSIS; CORRELATION ANALYSIS; DNA BINDING; DONOR SITE; EPIGENETICS; EXON SKIPPING; GENETIC PROCEDURES; GRAPH BASED EXON SKIPPING SCANNER; HISTONE MODIFICATION; HUMAN; INTRON; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN MOTIF; REAL TIME POLYMERASE CHAIN REACTION; RNA PROCESSING; RNA SEQUENCE; RNA SPLICING; RNA TRANSCRIPTION; SPLICEOSOME; TRANSCRIPTION ELONGATION; TRANSCRIPTION REGULATION;

ALTERNATIVE SPLICING; BINDING SITES; CELL LINE; COMPUTATIONAL BIOLOGY; EPIGENESIS, GENETIC; EXONS; HISTONES; HUMANS; K562 CELLS; NUCLEOTIDE MOTIFS; RNA SPLICE SITES; RNA, MESSENGER; RNA-BINDING PROTEINS; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 84898977299     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1338     Document Type: Article

References (36)

1. Pan, Q., Shai, O., Lee, L.J., Frey, B.J. and Blemcowe, B.J. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-Throughput sequencing. Nat. Genet., 40, 1413-1415.
2. Wang, E.T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S.F., Schroth, G.P. and Burge, C.B. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature, 456, 470-476. (Pubitemid 352759009
3. Matlin, A.J., Clark, F. and Smith, C.W.J. (2005) Understanding alternative splicing: Towards a cellular code. Nat. Rev. Mol. Cell Biol., 6, 386-398.
4. Tazi, J., Bakkour, N. and Stamm, S. (2009) Alternative splicing and disease. Biochim. Biophys. Acta., 1792, 14-26.
5. Black, D.L. (2003) Mechanisms of alternative pre-messenger RNA splicing. Ann. Rev. Biochem., 72, 291-336.
6. Christofk, H.R., Vander Heiden, M.G., Wu, N., Asara, J.M. and Cantley, L.C. (2008) Pyruvate kinase M2 is a phosphotyrosinebinding protein. Nature, 452, 181-186.
7. Cooper, T.A., Wan, L. and Dreyfuss, G. (2009) RNA and disease. Cell, 136, 777-793.
8. Garber, M., Grabherr, M.G., Guttman, M. and Trapnell, C. (2011) Computational methods for transcriptome annotation and quantification using RNA-seq. Nat. Methods, 8, 469-477.
9. Trapnell, C., Pachter, L. and Salzberg, S. (2009) TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
10. Wu, J., Akerman, M., Sun, S., McCombie, W.R., Krainer, A.R. and Zhang, M.Q. (2011) SpliceTrap: A method to quantify alternative splicing under single cellular conditions. Bioinformatics, 27, 3010-3016.
11. Katz, Y., Wang, E.T., Airoldi, E.M. and Burge, C.B. (2010) Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat. Methods, 7, 1009-1015.
12. The ENCODE Project Consortium. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
13. Yeo, G. and Burge, C.B. (2004) Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J. Comput. Biol., 11, 377-394.
14. Paz, I., Akerman, M., Dror, I., Kosti, I. and Mandel-Gutfreund, Y. (2010) SFmap: A web server for motif analysis and prediction of splicing factor binding sites. Nucleic Acids Res., 38, W281-W285.
15. Akerman, M., David-Eden, H., Pinter, R.Y. and Mandel-Gutfreund, Y. (2009) A computational approach for genome-wide mapping of splicing factor binding sites. Genome. Biol., 10, R30.
16. Chen, Z., Zhang, C., Wu, D., Chen, H., Rorick, A., Zhang, X. and Wang, Q. (2011) Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth. EMBO J., 30, 2405-2419.
17. Trapnell, C., Williams, B.A., Pertea, G., Mortazavi, A.M., Kwan, G., van Baren, M.J., Salzberg, S.L., Wold, B. and Pachter, L. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotech., 28, 511-515.
18. Chen, M. and Manley, J.L. (2009) Mechanisms of alternative splicing regulation: Insights from molecular and genomics approaches. Nat. Rev. Mol. Cell Biol., 10, 741-754.
19. Spellman, R. and Smith, C.W. (2006) Novel modes of splicing repression by PTB. Trends Biochem. Sci., 31, 73-76.
20. Xue, Y., Zhou, Y., Wu, T., Zhu, T., Ji, X., Kwon, Y.S., Zhang, C., Yeo, G., Black, D.L., Sun, H. et al. (2009) Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping. Mol. Cell, 36, 996-1006.
21. Sharma, S., Maris, C., Allain, F.H. and Black, D.L. (2011) U1 snRNA directly interacts with polypyrimidine tract-binding protein during splicing repression. Mol. Cell, 41, 579-588.
22. Lin, S., Coutinho-Mansfield, G., Wang, D., Pandit, S. and Fu, X.D. (2008) The splicing factor SC35 has an active role in transcriptional elongation. Nat. Struct. Mol. Biol., 15, 819-826.
23. Tripathi, K. and Parnaik, V.K. (2008) Differential dynamics of splicing factor SC35 during the cell cycle. J. Biosci., 33, 345-354.
24. Kornblihtt, A.R., de la Mata, M., Fededa, J.P., Munoz, M.J. and Nogues, G. (2004) Multiple links between transcription and splicing. RNA, 10, 1489-1498. (Pubitemid 39288183
25. Kim, H.D. and O'Shea, E.K. (2008) A quantitative model of transcription factor-Activated gene expression. Nat. Struct. Mol. Biol., 15, 1192-1198.
26. Shukla, S., Kavak, E., Gregory, M., Imashimizu, M., Shutinoski, B., Kashlev, M., Oberdoerffer, P., Sandberg, R. and Oberdoerffer, S. (2011) CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature, 479, 74-79.
27. Luco, R.F., Pan, Q., Tominaga, K., Blencowe, B.J., Pereira-Smith, O.M. and Misteli, T. (2010) Regulation of alternative splicing by histone modifications. Science, 327, 996-1000.
28. Luco, R.F., Allo, M., Schor, I.E., Kornblihtt, A.R. and Misteli, T. (2011) Epigenetics in alternative pre-mRNA splicing. Cell, 144, 16-26.
29. de la Mata, M., Alonso, C.R., Kadener, S., Fededa, J.P., Blaustein, M., Pelisch, F., Cramer, P., Bentley, D. and Kornblihtt, A.R. (2003) A slow RNA polymerase II affects alternative splicing in vivo. Mol. Cell, 12, 525-532.
30. Schwartz, S., Meshorer, E. and Ast, G. (2009) Chromatin organization marks exon-intro structure. Nat. Struct. Mol. Biol., 16, 990-995.
31. Wahl, M.C., Will, C.L. and Luhrmann, R. (2009) The spliceosome: Design principles of a dynamic RNP machine. Cell, 136, 701-718.
32. Sharma, S., Kohlstaedt, L.A., Damianov, A., Rio, D.C. and Black, D.L. (2008) Polypyrimidine tract binding protein controls the transition from exon definition to an intron defined spliceosome. Nat. Struct. Mol. Biol., 15, 183-191.
33. Zhou, Z., Licklider, L.J., Gygi, S.P. and Reed, R. (2002) Comprehensive proteomic analysis of the human spliceosome. Nature, 419, 182-185. (Pubitemid 35025448
34. Guillouf, C., Gallais, I. and Moreau-Gachelin, F. (2006) SPI-1/PU. oncoprotein affects splicing decisions in a promoter-binding dependent manner. J. Biol. Chem., 281, 19145-19155.
35. Gupta, P., Gurudutta, G.U., Verma, Y.K., Kishore, V., Gulati, S., Sharma, R.K. et al. (2006) PU.1: An ETS family transcription factor that regulates leukemogenesis besides normal hematopoiesis. Stem. Cells Dev., 15, 609-617.
36. Jung, I., Kim, S.K., Kim, M., Han, Y.M., Sung Kim, Y.S., Kim, D. and Lee, D. (2012) H2B monoubiquitylation is a 50-enriched active transcription mark and correlates with exon-intron structure in human cells. Genome Res., 22, 1026-1035.