Alternative splicing at GYNNGY 5' splice sites: More noise, less regulation

Nucleic Acids Research

Volumn 42, Issue 22, 2014, Pages 13969-13980

  Wang, Meng ^a,b   Zhang, Peiwei ^a,b   Shu, Yang ^a,b   Yuan, Fei ^a,b   Zhang, Yuchao ^a,b   Zhou, You ^a,b   Jiang, Min ^a,b   Zhu, Yufei ^a,b   Hu, Landian ^a,b   Kong, Xiangyin ^a,b   Zhang, Zhenguo ^c,d  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

^d UNIVERSITY OF ROCHESTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RNA SPLICING;

ALTERNATIVE RNA SPLICING; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DNA FLANKING REGION; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENETIC CONSERVATION; HUMAN; HUMAN TISSUE; INTRON; MOUSE; NOISE; NONHUMAN; NONSENSE MEDIATED MRNA DECAY; PRIORITY JOURNAL; TISSUE SPECIFICITY; ANIMAL; ANTIBODY SPECIFICITY; NUCLEOTIDE SEQUENCE; RHESUS MONKEY; RNA SPLICING;

EUKARYOTA; MUS;

ALTERNATIVE SPLICING; ANIMALS; BASE SEQUENCE; CONSERVED SEQUENCE; HUMANS; MACACA MULATTA; MICE; ORGAN SPECIFICITY; RNA SPLICE SITES;

EID: 84923152199     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1253     Document Type: Article

References (51)

1. Black, D. L. (2003) Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem., 72, 291-336.
2. Xing, Y. and Lee, C. (2007) Relating alternative splicing to proteome complexity and genome evolution. Adv. Exp. Med. Biol., 623, 36-49.
3. 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.
4. Nilsen, T. W. and Graveley, B. R. (2010) Expansion of the eukaryotic proteome by alternative splicing. Nature, 463, 457-463.
5. 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.
6. Ast, G. (2004) How did alternative splicing evolve? Nat. Rev. Genet., 5, 773-782.
7. Dou, Y, Fox-Walsh, K. L., Baldi, P. F. and Hertel, K. J. (2006) Genomic splice-site analysis reveals frequent alternative splicing close to the dominant splice site. RNA, 12, 2047-2056.
8. Sinha, R., Lenser, T., Jahn, N., Gausmann, U., Friedel, S., Szafranski, K., Huse, K., Rosenstiel, P., Hampe, J., Schuster, S. et al. (2010) TassDB2 - a comprehensive database of subtle alternative splicing events. BMC Bioinformatics, 11, 216.
9. Hiller, M., Huse, K., Szafranski, K., Jahn, N., Hampe, J., Schreiber, S., Backofen, R. and Platzer, M. (2004) Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity. Nat. Genet., 36, 1255-1257.
10. Pan, Q., Shai, O., Lee, L. J., Frey, B. J. and Blencowe, B. J. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet., 40, 1413-1415.
11. Filichkin, S. A., Priest, H. D., Givan, S. A., Shen, R., Bryant, D. W., Fox, S. E., Wong, W. K. and Mockler, T. C. (2010) Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res., 20, 45-58.
12. Roca, X., Krainer, A. R. and Eperon, I. C. (2013) Pick one, but be quick: 5' splice sites and the problems of too many choices. Genes Dev., 27, 129-144.
13. Koren, E., Lev-Maor, G and Ast, G (2007) The emergence of alternative 3' and 5' splice site exons from constitutive exons. PLoS Comput. Biol, 3, e95.
14. Hiller, M., Szafranski, K., Backofen, R. and Platzer, M. (2006) Alternative splicing at NAGNAG acceptors: simply noise or noise and more? PLoS Genet., 2, e207; author reply e208.
15. Chern, T. M., van Nimwegen, E., Kai, C, Kawai, J., Carninci, P, Hayashizaki, Y. and Zavolan, M. (2006) A simple physical model predicts small exon length variations. PLoS Genet., 2, e45.
16. Bradley, R. K., Merkin, J., Lambert, NJ. and Burge, C. B. (2012) Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution. PLoS Biol, 10, e1001229.
17. van Nimwegen, E. and Zavolan, M. (2006) Authors' Reply. PLoS Genet., 2, e208.
18. Hiller, M., Szafranski, K., Sinha, R., Huse, K., Nikolajewa, S., Rosenstiel, P, Schreiber, S., Backofen, R. and Platzer, M. (2008) Assessing the fraction of short-distance tandem splice sites under purifying selection. RNA, 14, 616-629.
19. Bortfeldt, R., Schindler, S., Szafranski, K., Schuster, S. and Holste, D. (2008) Comparative analysis of sequence features involved in the recognition of tandem splice sites. BMC Genom., 9, 202.
20. Pruitt, K. D., Brown, GR., Hiatt, S. M., Thibaud-Nissen, F, Astashyn, A., Ermolaeva, O., Farrell, CM., Hart, J., Landrum, M. J., McGarvey, K. M. et al (2014) RefSeq: an update on mammalian reference sequences. Nucleic Acids Res, 42, D756-D763.
21. Flicek, P, Ahmed, I., Amode, M. R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P, Coates, G, Fairley, S. et al (2013) Ensembl 2013. Nucleic Acids Res., 41, D48-D55.
22. Karolchik, D., Barber, GP, Casper, J., Clawson, H., Cline, M. S., Diekhans, M., Dreszer, T. R., Fujita, PA., Guruvadoo, L., Haeussler, M. et al (2014) The UCSC Genome Browser database: 2014 update. Nucleic Acids Res, 42, D764-D770.
23. Merkin, J., Russell, C, Chen, P and Burge, C. B. (2012) Evolutionary dynamics of gene and isoform regulation in mammalian tissues. Science, 338, 1593-1599.
24. Trapnell, C, Pachter, L. and Salzberg, S. L. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
25. Trapnell, C, Williams, B. A., Pertea, G, Mortazavi, A., Kwan, G, van Baren, M. J., Salzberg, S. L., Wold, B. J. and Pachter, L. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 28, 511-515.
26. R Core Team. (2014) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
27. Yeo, G. and Burge, CB. (2004) Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J. Comput. Biol, 11, 377-394.
28. Bailey, TL., Boden, M., Buske, FA., Frith, M., Grant, CE., Clementi, L., Ren, J., Li, W. W. and Noble, W. S. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res., 37, W202-W208.
29. Liao, B. Y, Scott, N. M. and Zhang, J. (2006) Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins. Mol Biol. Evol., 23, 2072-2080.
30. Barash, Y, Calarco, J. A., Gao, W., Pan, Q., Wang, X., Shai, O., Blencowe, B. J. and Frey, B. J. (2010) Deciphering the splicing code. Nature, 465, 53-59.
31. Graur, D., Zheng, Y, Price, N., Azevedo, R. B., Zufall, R. A. and Elhaik, E. (2013) On the immortality of television sets: 'function' in the human genome according to the evolution-free gospel of ENCODE. Genome Biol. Evol, 5, 578-590.
32. Aznarez, I., Barash, Y, Shai, O., He, D, Zielenski, J., Tsui, L. C, Parkinson, J., Frey, B. J., Rommens, J. M. and Blencowe, B. J. (2008) A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation. Genome Res., 18, 1247-1258.
33. Lareau, L. F., Brooks, A. N., Soergel, DA., Meng, Q. and Brenner, S. E. (2007) The coupling of alternative splicing and nonsense-mediated mRNA decay. Adv. Exp. Med. Biol, 623, 190-211.
34. Yang, X., Zhang, H. and Li, L. (2012) Alternative mRNA processing increases the complexity of microRNA-based gene regulation in Arabidopsis. Plant J., 70, 421-431.
35. Pickrell, J. K., Pai, A. A., Gilad, Y and Pritchard, J. K. (2010) Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet., 6, e1001236.
36. Zhang, Z., Xin, D., Wang, P, Zhou, L., Hu, L., Kong, X. and Hurst, L. D. (2009) Noisy splicing, more than expression regulation, explains why some exons are subject to nonsense-mediated mRNA decay. BMC Biol, 7, 23.
37. Hurst, L. D. (2009) Evolutionary genomics and the reach of selection. J. Biol, 8, 12.
38. Rao, C. V, Wolf, D. M. and Arkin, A. P (2002) Control, exploitation and tolerance of intracellular noise. Nature, 420, 231-237.
39. Hurst, L. D. (2013) Open questions: a logic (or lack thereof) of genome organization. BMC Biol, 11, 58.
40. Hiller, M. and Platzer, M. (2008) Widespread and subtle: alternative splicing at short-distance tandem sites. Trends Genet., 24, 246-255.
41. Hammes, A., Guo, J. K., Lutsch, G, Leheste, J. R., Landrock, D., Ziegler, U., Gubler, M. C. and Schedl, A. (2001) Two splice variants of the Wilms' tumor 1 gene have distinct functions during sex determination and nephron formation. Cell, 106, 319-329.
42. Burgar, H. R., Burns, H. D., Elsden, J. L., Lalioti, M. D. and Heath, J. K. (2002) Association of the signaling adaptor FRS2 with fibroblast growth factor receptor 1 (Fgfr1) is mediated by alternative splicing of the juxtamembrane domain. J. Biol. Chem., 277, 4018-4023.
43. Unoki, M., Shen, J. C., Zheng, Z. M. and Harris, C. C. (2006) Novel splice variants of ING4 and their possible roles in the regulation of cell growth and motility. J. Biol. Chem., 281, 34677-34686.
44. Trabzuni, D., Ramasamy, A., Imran, S., Walker, R., Smith, C., Weale, M. E., Hardy, J. and Ryten, M. (2013) Widespread sex differences in gene expression and splicing in the adult human brain. Nat. Commun., 4, 2771.
45. Mazin, P., Xiong, J., Liu, X., Yan, Z., Zhang, X., Li, M., He, L., Somel, M., Yuan, Y., Phoebe Chen, Y. P. et al. (2013) Widespread splicing changes in human brain development and aging. Mol. Syst. Biol., 9, 633.
46. Lappalainen, T., Sammeth, M., Friedlander, M. R., Hoen, P. A., Monlong, J., Rivas, M. A., Gonzalez-Porta, M., Kurbatova, N., Griebel, T., Ferreira, P. G. et al. (2013) Transcriptome and genome sequencing uncovers functional variation in humans. Nature, 501, 506-511.
47. Szafranski, K., Fritsch, C., Schumann, F., Siebel, L., Sinha, R., Hampe, J., Hiller, M., Englert, C., Huse, K. and Platzer, M. (2014) Physiological state co-regulates thousands of mammalian mRNA splicing events at tandem splice sites and alternative exons. Nucleic Acids Res., 42, 8895-8904.
48. Joyce-Brady, M., Jean, J. C. and Hughey, R. P. (2001) Gamma-glutamyltransferase and its isoform mediate an endoplasmic reticulum stress response. J. Biol. Chem., 276, 9468-9477.
49. Loeffen, J., Smeets, R., Smeitink, J., Triepels, R., Sengers, R., Trijbels, F. and van den Heuvel, L. (1999) The human NADH: ubiquinone oxidoreductase NDUFS5 (15 kDa) subunit: cDNA cloning, chromosomal localization, tissue distribution and the absence of mutations in isolated complex I-deficient patients. J. Inherit. Metab. Dis., 22, 19-28.
50. Lee, S., Liu, B., Lee, S., Huang, S. X., Shen, B. and Qian, S. B. (2012) Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proc. Natl. Acad. Sci. U. S. A., 109, E2424-E2432.
51. Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A. et al. (2013) Multiplex genome engineering using CRISPR/Cas systems. Science, 339, 819-823.