Evolution of a tissue-specific splicing network

Genes and Development

Volumn 25, Issue 6, 2011, Pages 608-620

  Taliaferro, J Matthew ^a   Alvarez, Nehemiah ^b,c   Green, Richard E ^d   Blanchette, Marco ^b,c   Rio, Donald C ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b STOWERS INSTITUTE FOR MEDICAL RESEARCH   (United States)

^c UNIVERSITY OF KANSAS SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Alternative splicing; Splicing evolution; Splicing regulation; U2AF

Indexed keywords

HETERODIMER;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DROSOPHILA; GENE DUPLICATION; HUMAN; NONHUMAN; PRIORITY JOURNAL; RNA SEQUENCE; RNA SPLICING; RNA TRANSCRIPTION; TESTIS;

ANIMALS; CELL LINE; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE EXPRESSION REGULATION; MALE; NUCLEAR PROTEINS; ORGAN SPECIFICITY; PHYLOGENY; PROTEIN SPLICING; RIBONUCLEOPROTEINS; TESTIS;

EUKARYOTA; METAZOA;

EID: 79952592130     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.2009011     Document Type: Article

References (57)

1. Akerman M, David-Eden H, Pinter RY, Mandel-Gutfreund Y. 2009. A computational approach for genome-wide mapping of splicing factor binding sites. Genome Biol 10: R30. doi: 10.1186/gb-2009-10-3-r30.
2. Al-Shahrour F, Minguez P, Tarraga J, Montaner D, Alloza E, Vaquerizas JM, Conde L, Blaschke C, Vera J, Dopazo J. 2006. BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res 34: W472-W476. doi: 10.1093/nar/gkl172. (Pubitemid 44529816)
3. Amarasinghe AK, MacDiarmid R, Adams MD, Rio DC. 2001. An in vitro-selected RNA-binding site for the KH domain protein PSI acts as a splicing inhibitor element. RNA 7: 1239-1253. (Pubitemid 32831353)
4. Baek D, Green P. 2005. Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing. Proc Natl Acad Sci 102: 12813-12818. (Pubitemid 41279448)
5. Bai Y, Casola C, Betran E. 2008. Evolutionary origin of regulatory regions of retrogenes in Drosophila. BMC Genomics 9: 241.
6. Bai Y, Casola C, Betran E. 2009. Quality of regulatory elements in Drosophila retrogenes. Genomics 93: 83-89.
7. Bailey TL, Elkan C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28-36.
8. Baker BS, Gorman M, Marin I. 1994. Dosage compensation in Drosophila. Annu Rev Genet 28: 491-521.
9. Ben-Dov C, Hartmann B, Lundgren J, Valcarcel J. 2008. Genome-wide analysis of alternative pre-mRNA splicing. J Biol Chem 283: 1229-1233.
10. Betran E, Thornton K, Long M. 2002. Retroposed new genes out of the X in Drosophila. Genome Res 12: 1854-1859. (Pubitemid 35469934)
11. Black DL. 2003. Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem 72: 291-336. (Pubitemid 36930448)
12. 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. (Pubitemid 41003020)
13. 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 hnRNP A/B family members. Mol Cell 33: 438-449.
14. Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR. 2011. Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res 21: 193-202.
15. Buckanovich RJ, Posner JB, Darnell RB. 1993. Nova, the paraneoplastic Ri antigen, is homologous to an RNA-binding protein and is specifically expressed in the developing motor system. Neuron 11: 657-672. (Pubitemid 23321775)
16. Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, et al. 2009. Unlocking the secrets of the genome. Nature 459: 927-930.
17. Chintapalli VR, Wang J, Dow JA. 2007. Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nat Genet 39: 715-720. (Pubitemid 46848596)
18. Dreyfuss G, Matunis MJ, Pinol-Roma S, Burd CG. 1993. hnRNP proteins and the biogenesis of mRNA. Annu Rev Biochem 62: 289-321. (Pubitemid 23237873)
19. Elliott DJ, Grellscheid SN. 2006. Alternative RNA splicing regulation in the testis. Reproduction 132: 811-819. (Pubitemid 46040651)
20. Gan Q, Chepelev I, Wei G, Tarayrah L, Cui K, Zhao K, Chen X. 2010. Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq. Cell Res 20: 763-783.
21. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al. 2004. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80. doi: 10.1186/gb-2004-5-10-r80.
22. Kanaar R, Roche SE, Beall EL, Green MR, Rio DC. 1993. The conserved pre-mRNA splicing factor U2AF from Drosophila: requirement for viability. Science 262: 569-573. (Pubitemid 23350670)
23. Kent OA, Reayi A, Foong L, Chilibeck KA, MacMillan AM. 2003. Structuring of the 39 splice site by U2AF65. J Biol Chem 278: 50572-50577.
24. Kielkopf CL, Rodionova NA, Green MR, Burley SK. 2001. A novel peptide recognition mode revealed by the X-ray structure of a core U2AF35/U2AF65 heterodimer. Cell 106: 595-605. (Pubitemid 32879321)
25. Kikuchi T, Ichikawa M, Arai J, Tateiwa H, Fu L, Higuchi K, Yoshimura N. 2000. Molecular cloning and characterization of a new neuron-specific homologue of rat polypyrimidine tract binding protein. J Biochem 128: 811-821.
26. Liang G, Lin JC, Wei V, Yoo C, Cheng JC, Nguyen CT, Weisenberger DJ, Egger G, Takai D, Gonzales FA, et al. 2004. Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome. Proc Natl Acad Sci 101: 7357-7362. (Pubitemid 38638037)
27. Markovtsov V, Nikolic JM, Goldman JA, Turck CW, Chou MY, Black DL. 2000. Cooperative assembly of an hnRNP complex induced by a tissue-specific homolog of polypyrimidine tract binding protein. Mol Cell Biol 20: 7463-7479.
28. Martinez-Contreras R, Cloutier P, Shkreta L, Fisette JF, Revil T, Chabot B. 2007. hnRNP proteins and splicing control. Adv Exp Med Biol 623: 123-147.
29. Merendino L, Guth S, Bilbao D, Martinez C, Valcarcel J. 1999. Inhibition of msl-2 splicing by Sex-lethal reveals interaction between U2AF35 and the 39 splice site AG. Nature 402: 838-841.
30. Nelson KK, Green MR. 1988. Splice site selection and ribonucleoprotein complex assembly during in vitro pre-mRNA splicing. Genes Dev 2: 319-329.
31. Nilsen TW, Graveley BR. 2010. Expansion of the eukaryotic proteome by alternative splicing. Nature 463: 457-463.
32. Oliver B. 2002. Genetic control of germline sexual dimorphism in Drosophila. Int Rev Cytol 219: 1-60. (Pubitemid 34925066)
33. Padgett RA, Hardy SF, Sharp PA. 1983. Splicing of adenovirus RNA in a cell free transcription system. Proc Natl Acad Sci 80: 5230-5234. (Pubitemid 13050211)
34. Parisi M, Nuttall R, Naiman D, Bouffard G, Malley J, Andrews J, Eastman S, Oliver B. 2003. Paucity of genes on the Drosophila X chromosome showing male-biased expression. Science 299: 697-700. (Pubitemid 36159482)
35. 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. (Pubitemid 39507912)
36. Pinol-Roma S, Swanson MS, Matunis MJ, Dreyfuss G. 1990. Purification and characterization of proteins of heterogeneous nuclear ribonucleoprotein complexes by affinity chromatography. Methods Enzymol 181: 326-331. (Pubitemid 20219705)
37. Proschel M, Zhang Z, Parsch J. 2006. Widespread adaptive evolution of Drosophila genes with sex-biased expression. Genetics 174: 893-900. (Pubitemid 44656476)
38. Rudner DZ, Breger KS, Kanaar R, Adams MD, Rio DC. 1998a. RNA binding activity of heterodimeric splicing factor U2AF: at least one RS domain is required for high-affinity binding. Mol Cell Biol 18: 4004-4011. (Pubitemid 28287924)
39. Rudner DZ, Kanaar R, Breger KS, Rio DC. 1998b. Interaction between subunits of heterodimeric splicing factor U2AF is essential in vivo. Mol Cell Biol 18: 1765-1773. (Pubitemid 28152625)
40. Ruskin B, Zamore PD, Green MR. 1988. A factor, U2AF, is required for U2 snRNP binding and splicing complex assembly. Cell 52: 207-219. (Pubitemid 18042857)
41. Selenko P, Gregorovic G, Sprangers R, Stier G, Rhani Z, Kramer A, Sattler M. 2003. Structural basis for the molecular recognition between human splicing factors U2AF(65) and SF1/mBBP. Mol Cell 11: 965-976. (Pubitemid 36566318)
42. Shepard PJ, Hertel KJ. 2009. The SR protein family. Genome Biol 10: 242.
43. Sickmier EA, Frato KE, Shen H, Paranawithana SR, Green MR, Kielkopf CL. 2006. Structural basis for polypyrimidine tract recognition by the essential pre-mRNA splicing factor U2AF65. Mol Cell 23: 49-59. (Pubitemid 43963446)
44. Singh R, Valcarcel J, Green MR. 1995. Distinct binding specificities and functions of higher eukaryotic polypyrimidine tract-binding proteins. Science 268: 1173-1176.
45. Singh R, Banerjee H, Green MR. 2000. Differential recognition of the polypyrimidine-tract by the general splicing factor U2AF65 and the splicing repressor sex-lethal. RNA 6: 901-911. (Pubitemid 30396030)
46. Smyth GK. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article 3. doi: 10.2202/1544-6115.1027.
47. Sridharan V, Heimiller J, Singh R. 2011. Genomic mRNA profiling reveals compensatory mechanisms for the requirement of the essential splicing factor U2AF. Mol Cell Biol 31: 652-661.
48. Tamura K, Subramanian S, Kumar S. 2004. Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol 21: 36-44. (Pubitemid 38233516)
49. Venables JP, Eperon I. 1999. The roles of RNA-binding proteins in spermatogenesis and male infertility. Curr Opin Genet Dev 9: 346-354. (Pubitemid 29286476)
50. Wang Z, Burge CB. 2008. Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA 14: 802-813. (Pubitemid 351574901)
51. Wu S, Romfo CM, Nilsen TW, Green MR. 1999. Functional recognition of the 3′ splice site AG by the splicing factor U2AF35. Nature 402: 832-835.
52. Xiao X, Wang Z, Jang M, Nutiu R, Wang ET, Burge CB. 2009. Splice site strength-dependent activity and genetic buffering by poly-G runs. Nat Struct Mol Biol 16: 1094-1100.
53. Yeo G, Burge CB. 2004. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 11: 377-394. (Pubitemid 38901668)
54. Yu Y, Maroney PA, Denker JA, Zhang XH, Dybkov O, Luhrmann R, Jankowsky E, Chasin LA, Nilsen TW. 2008. Dynamic regulation of alternative splicing by silencers that modulate 5′ splice site competition. Cell 135: 1224-1236.
55. Zamore PD, Green MR. 1989. Identification, purification, and biochemical characterization of U2 small nuclear ribonucleoprotein auxiliary factor. Proc Natl Acad Sci 86: 9243-9247. (Pubitemid 20010401)
56. Zamore PD, Patton JG, Green MR. 1992. Cloning and domain analysis of the mammalian splicing factor U2AF. Nature 355: 609-614.
57. Zorio DA, Blumenthal T. 1999. Both subunits of U2AF recognize the 39 splice site in Caenorhabditis elegans. Nature 402: 835-838.