Conservation of an RNA regulatory map between Drosophila and mammals

Genome Research

Volumn 21, Issue 2, 2011, Pages 193-202

  Brooks, Angela N ^a   Yang, Li ^b   Duff, Michael O ^b   Hansen, Kasper D ^a   Park, Jung W ^b   Dudoit, Sandrine ^a   Brenner, Steven E ^a,c   Graveley, Brenton R ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; NOVA1 PROTEIN; NOVA2 PROTEIN; PASILLA PROTEIN; RNA BINDING PROTEIN; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DROSOPHILA; EXON; GENE MAPPING; GENE SEQUENCE; GENE TARGETING; GENETIC CONSERVATION; NONHUMAN; ORTHOLOGY; PRIORITY JOURNAL; REGULATORY RNA SEQUENCE; RNA INTERFERENCE; RNA SEQUENCE; RNA SPLICING;

ALTERNATIVE SPLICING; ANIMALS; ANTIGENS, NEOPLASM; CELLS, CULTURED; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DROSOPHILA; DROSOPHILA PROTEINS; EXONS; GENE EXPRESSION PROFILING; INTRONS; MAMMALS; MOLECULAR SEQUENCE DATA; NERVE TISSUE PROTEINS; RIBONUCLEOPROTEINS; RNA INTERFERENCE; RNA PRECURSORS; RNA, MESSENGER; RNA-BINDING PROTEINS;

DROSOPHILA MELANOGASTER; HEXAPODA; MAMMALIA;

EID: 79551584794     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.108662.110     Document Type: Article

References (41)

1. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, et al. 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
2. Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, Blencowe BJ, Frey BJ. 2010. Deciphering the splicing code. Nature 465: 53-59.
3. Berriz GF, Beaver JE, Cenik C, Tasan M, Roth FP. 2009. Next generation software for functional trend analysis. Bioinformatics 25: 3043-3044.
4. Blanchette M, Labourier E, Green RE, Brenner SE, Rio DC. 2004. Genomewide analysis reveals an unexpected function for the Drosophila splicing factor U2AF50 in the nuclear export of intronless mRNAs. Mol Cell 14: 775-786.
5. Blanchette M, Green RE, Brenner SE, Rio DC. 2005. Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila. Genes Dev 19: 1306-1314.
6. Blanchette M, Green RE, MacArthur S, Brooks AN, Brenner SE, Eisen MB, Rio DC. 2009. Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNPA/B family members. Mol Cell 33: 438-449.
7. Celniker SE, Wheeler DA, Kronmiller B, Carlson JW, Halpern A, Patel S, Adams M, Champe M, Dugan SP, Frise E, et al. 2002. Finishing a wholegenome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biol 3: research0079. doi: 10.1186/gb-2002-3-12-research0079.
8. Chen M, Manley J. 2009. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat Rev Mol Cell Biol 10: 741-754.
9. Chiaromonte F, Yap VB, Miller W. 2002. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput 7: 115-126.
10. Jelen N, Ule J, Zivin M, Darnell RB. 2007. Evolution of Nova-dependent splicing regulation in the brain. PLoS Genet 3: 1838-1847.
11. Jensen KB, Musunuru K, Lewis HA, Burley SK, Darnell RB. 2000. The tetranucleotide UCAY directs the specific recognition of RNA by the Nova K-homology 3 domain. Proc Natl Acad Sci 97: 5740-5745.
12. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. 2003. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci 100: 11484-11489.
13. König J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J. 2010. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol 17: 909-915.
14. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25. doi: 10.1186/gb-2009-10-3-r25.
15. Lewis HA, Chen H, Edo C, Buckanovich RJ, Yang YY, Musunuru K, Zhong R, Darnell RB, Burley SK. 1999. Crystal structures of Nova-1 and Nova-2 K-homology RNA-binding domains. Structure 7: 191-203.
16. Lewis HA, Musunuru K, Jensen KB, Edo C, Chen H, Darnell RB, Burley SK. 2000. Sequence-specific RNA binding by a Nova KH domain: Implications for paraneoplastic disease and the fragile X syndrome. Cell 100: 323-332.
17. Li H, Coghlan A, Ruan J, Coin LJ, Hériché J-K, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, et al. 2006. TreeFam: A curated database of phylogenetic trees of animal gene families. Nucleic Acids Res 34: D572-D580. doi: 10.1093/nar/gkj118.
18. Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, Clark TA, Schweitzer AC, Blume JE, Wang X, et al. 2008. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature 456: 464-469.
19. McManus CJ, Coolon JD, Duff MO, Eipper-Mains J, Graveley BR, Wittkopp PJ. 2010. Regulatory divergence in Drosophila revealed by mRNA-seq. Genome Res 20: 816-825.
20. Meireles-Filho AC, Stark A. 2009. Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information. Curr Opin Genet Dev 19: 565-570.
21. Nilsen TW, Graveley BR. 2010. Expansion of the eukaryotic proteome by alternative splicing. Nature 463: 457-463.
22. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. 2008. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40: 1413-1415.
23. Park JW, Graveley BR. 2005. Use of RNA interference to dissect the roles of trans-acting factors in alternative pre-mRNA splicing. Methods 37: 341-344.
24. Park JW, Parisky K, Celotto AM, Reenan RA, Graveley BR. 2004. Identification of alternative splicing regulators by RNA interference in Drosophila. Proc Natl Acad Sci 101: 15974-15979.
25. Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, et al. 2010. The UCSC Genome Browser database: Update 2010. Nucleic Acids Res 38: D613-D619. doi: 10.1093/nar/gkp939.
26. Ruan J, Li H, Chen Z, Coghlan A, Coin LJM, Guo Y, Hériché J-K, Hu Y, Kristiansen K, Li R, et al. 2008. TreeFam: 2008 Update. Nucleic Acids Res 36: D735-D740. doi: 10.1093/nar/gkm1005.
27. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. 2003. Human-mouse alignments with BLASTZ. Genome Res 13: 103-107.
28. Seshaiah P, Miller B, Myat MM, Andrew DJ. 2001. Pasilla, the Drosophila homologue of the human Nova-1 and Nova-2 proteins, is required for normal secretion in the salivary gland. Dev Biol 239: 309-322.
29. Shomron N, Golan D, Hornstein E. 2009. An evolutionary perspective of animal microRNAs and their targets. J Biomed Biotechnol 2009: 594738. doi: 10.1155/2009/594738.
30. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034-1050.
31. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-515.
32. Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi-Sutherland D, Schroeder A, Seal R, et al. 2009. FlyBase: Enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res 37: D555-D559. doi: 10.1093/nar/gkn788.
33. Ule J, Ule A, Spencer J, Williams A, Hu JS, Cline M, Wang H, Clark T, Fraser C, Ruggiu M, et al. 2005. Nova regulates brain-specific splicing to shape the synapse. Nat Genet 37: 844-852.
34. Ule J, Stefani G, Mele A, Ruggiu M, Wang X, Taneri B, Gaasterland T, Blencowe BJ, Darnell RB. 2006. An RNA map predicting Nova-dependent splicing regulation. Nature 444: 580-586.
35. Wang Z, Burge CB. 2008. Splicing regulation: From a parts list of regulatory elements to an integrated splicing code. RNA 14: 802-813.
36. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476.
37. Wold B, Myers RM. 2008. Sequence census methods for functional genomics. Nat Methods 5: 19-21.
38. Xue Y, Zhou Y,Wu T, Zhu T, Ji X, Kwon YS, Zhang C, Yeo G, Black DL, 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.
39. Yeo GW, Coufal NG, Liang TY, Peng GE, Fu XD, Gage FH. 2009. An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat Struct Mol Biol 16: 130-137.
40. Zhang C, Zhang Z, Castle J, Sun S, Johnson J, Krainer A, Zhang M. 2008. Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes Dev 22: 2550-2563.
41. Zhang C, Frias MA, Mele A, Ruggiu M, Eom T, Marney CB,Wang H, Licatalosi DD, Fak JJ, Darnell RB. 2010. Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls. Science 329: 439-443.