Microarray meta-analysis of RNA-binding protein functions in alternative polyadenylation

PLoS ONE

Volumn 9, Issue 3, 2014, Pages

  Hu, Wenchao ^a   Liu, Yuting ^a,b   Yan, Jun ^a  

^a Chinese Academy of Sciences   (China)

^b BOSTON CHILDREN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MBNL1 PROTEIN; MESSENGER RNA; NOVA2 PROTEIN; RNA BINDING PROTEIN; UNCLASSIFIED DRUG; 3' UNTRANSLATED REGION;

3' UNTRANSLATED REGION; ALTERNATIVE POLYADENYLATION; ARTICLE; BRAIN; DEVELOPMENT; DIFFERENTIATION; DOG; EIF4E2 GENE; ELAVL1 GENE; GENE; GENE IDENTIFICATION; GENETIC DATABASE; HUMAN; IMMUNE RESPONSE; MAMMAL; MOUSE; NONHUMAN; POLYADENYLATION; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN MICROARRAY; RAT; RBM3 GENE; REGULATORY MECHANISM; RHESUS MONKEY; ANIMAL; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; GENETICS; INTERNET; METABOLISM;

3' UNTRANSLATED REGIONS; ANIMALS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; HUMANS; INTERNET; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYADENYLATION; RNA-BINDING PROTEINS;

EID: 84897971637     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0090774     Document Type: Article

References (48)

1. Yao P, Potdar AA, Arif A, Ray PS, Mukhopadhyay R, et al. (2012) Coding region polyadenylation generates a truncated tRNA synthetase that counters translation repression. Cell 149: 88-100.
2. Yan J, Marr TG (2005) Computational analysis of 3′-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat. Genome research 15: 369-375. (Pubitemid 40467778)
3. Martins R, Proença D, Silva B, Barbosa C, Silva AL, et al. (2012) Alternative polyadenylation and nonsense-mediated decay coordinately regulate the human HFE mRNA levels. PloS one 7: e35461-e35461.
4. Zhang H, Lee JY, Tian B (2005) Biased alternative polyadenylation in human tissues. Genome biology 6: R100-R100.
5. Derti A, Garrett-Engele P, Macisaac KD, Stevens RC, Sriram S, et al. (2012) A quantitative atlas of polyadenylation in five mammals. Genome research 22: 1173-1183.
6. Sandberg R, Neilson JR, Sarma A, Sharp Pa, Burge CB (2008) Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites. Science (New York, NY) 320: 1643-1647.
7. Ji Z, Luo W, Li W, Hoque M, Pan Z, et al. (2011) Transcriptional activity regulates alternative cleavage and polyadenylation. Molecular systems biology 7: 534-534.
8. Li Y, Sun Y, Fu Y, Li M, Huang G, et al. (2012) Dynamic landscape of tandem 3′ UTRs during zebrafish development. Genome research 22: 1899-1906.
9. Ulitsky I, Shkumatava A, Jan CH, Subtelny AO, Koppstein D, et al. (2012) Extensive alternative polyadenylation during zebrafish development. Genome research 22: 2054-2066.
10. Ji Z, Lee JY, Pan Z, Jiang B, Tian B (2009) Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proceedings of the National Academy of Sciences of the United States of America 106: 7028-7033.
11. Berg MG, Singh LN, Younis I, Liu Q, Pinto AM, et al. (2012) U1 snRNP determines mRNA length and regulates isoform expression. Cell 150: 53-64.
12. Katz Y, Wang ET, Airoldi EM, Burge CB (2010) Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature methods 7: 1009-1015.
13. Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, et al. (2008) HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature 456: 464-469. (Pubitemid 352759008)
14. Sanford JR, Wang X, Mort M, VanDuyn N (2009) Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome 19: 381-394.
15. Jenal M, Elkon R, Loayza-Puch F, van Haaften G, Kühn U, et al. (2012) The poly(A)-binding protein nuclear 1 suppresses alternative cleavage and polyadenylation sites. Cell 149: 538-553.
16. Bava F-A, Eliscovich C, Ferreira PG, Miñana B, Ben-Dov C, et al. (2013) CPEB1 coordinates alternative 3′-UTR formation with translational regulation. Nature 495: 121-125.
17. Hilgers V, Lemke SB, Levine M (2012) ELAV mediates 3′ UTR extension in the Drosophila nervous system. Genes & development 26: 2259-2264.
18. Castelo-Branco P, Furger A, Wollerton M, Smith C, Moreira A, et al. (2004) Polypyrimidine Tract Binding Protein Modulates Efficiency of Polyadenylation. Molecular and Cellular Biology 24: 4174-4183. (Pubitemid 41070991)
19. Mansfield KD, Keene JD (2011) Neuron-specific ELAV/Hu proteins suppress HuR mRNA during neuronal differentiation by alternative polyadenylation. Nucleic acids research 40: 2734-2746.
20. Avendaño-Vázquez SE, Dhir A, Bembich S, Buratti E, Proudfoot N, et al. (2012) Autoregulation of TDP-43 mRNA levels involves interplay between transcription, splicing, and alternative polyA site selection. Genes & development 26: 1679-1684.
21. Wang H, Liu Y, Briesemann M, Yan J (2010) Computational analysis of gene regulation in animal sleep deprivation. Physiological genomics 42: 427-436.
22. Lee JY, Yeh I, Park JY, Tian B (2007) PolyA-DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic acids research 35: D165-168. (Pubitemid 46056191)
23. Hinrichs aS, Karolchik D, Baertsch R, Barber GP, Bejerano G, et al. (2006) The UCSC Genome Browser Database: update 2006. Nucleic acids research 34: D590-598.
24. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biology 10: R25-R25.
25. Yang J-H, Li J-H, Shao P, Zhou H, Chen Y-Q, et al. (2011) starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic acids research 39: D202-209.
26. Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR (2011) RBPDB: a database of RNA-binding specificities. Nucleic acids research 39: D301-308.
27. Wang ET, Cody NaL, Jog S, Biancolella M, Wang TT, et al. (2012) Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins. Cell 150: 710-724.
28. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
29. Liu Y, Hu W, Murakawa Y, Yin J, Wang G, et al. (2013) Cold-induced RNA-binding proteins regulate circadian gene expression by controlling alternative polyadenylation. Scientific reports 3: 2054-2054.
30. Moher D, Liberati A, Tetzlaff J, Altman DG (2009) Preferred reporting items for systematic reviews and meta-analyses: the PRISMA statement. PLoS medicine 6: e1000097-e1000097.
31. Lutz CS, Moreira A (2011) Alternative mRNA polyadenylation in eukaryotes: an effective regulator of gene expression. Wiley interdisciplinary reviews RNA 2: 22-31.
32. Lebedeva S, Jens M, Theil K, Schwanhäusser B, Selbach M, et al. (2011) Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR. Molecular cell 43: 340-352.
33. Mukherjee N, Corcoran DL, Nusbaum JD, Reid DW, Georgiev S, et al. (2011) Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. Molecular cell 43: 327-339.
34. Uren PJ, Burns SC, Ruan J, Singh KK, Smith AD, et al. (2011) Genomic analyses of the RNA-binding protein Hu antigen R (HuR) identify a complex network of target genes and novel characteristics of its binding sites. The Journal of biological chemistry 286: 37063-37066.
35. Miura P, Shenker S, Andreu-Agullo C, Westholm JO, Lai EC (2013) Widespread and extensive lengthening of 3′ UTRs in the mammalian brain. Genome research.
36. Lianoglou S, Garg V, Yang JL, Leslie CS, Mayr C (2013) Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression. Genes & development 27: 2380-2396.
37. Martin G, Gruber AR, Keller W, Zavolan M (2012) Genome-wide analysis of pre-mRNA 3′ end processing reveals a decisive role of human cleavage factor I in the regulation of 3′ UTR length. Cell reports 1: 753-763.
38. Mercer TR, Wilhelm D, Dinger ME, Soldà G, Korbie DJ, et al. (2011) Expression of distinct RNAs from 3′ untranslated regions. Nucleic acids research 39: 2393-2403.
39. Takagaki Y, Seipelt RL, Peterson ML, Manley JL (1996) The polyadenylation factor CstF-64 regulates alternative processing of IgM heavy chain pre-mRNA during B cell differentiation. Cell 87: 941-952. (Pubitemid 26404292)
40. Elkon R, Ugalde AP, Agami R (2013) Alternative cleavage and polyadenylation: extent, regulation and function. Nature reviews Genetics 14: 496-506.
41. Gawande B, Robida MD, Rahn A, Singh R (2006) Drosophila Sex-lethal protein mediates polyadenylation switching in the female germline. The EMBO journal 25: 1263-1272.
42. Naipauer J, Gattelli A, Degese MS, Slomiansky V, Wertheimer E, et al. (2013) The use of alternative polyadenylation sites renders integrin b1 (Itgb1) mRNA isoforms with differential stability during mammary gland development. The Biochemical journal 454: 345-357.
43. Filteau M, Pavey Sa, St-Cyr J, Bernatchez L (2013) Gene coexpression networks reveal key drivers of phenotypic divergence in lake whitefish. Molecular biology and evolution 30: 1384-1396.
44. Oldham MC, Horvath S, Geschwind DH (2006) Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proceedings of the National Academy of Sciences of the United States of America 103: 17973-17978. (Pubitemid 44852270)
45. van Dam S, Cordeiro R, Craig T, van Dam J, Wood SH, et al. (2012) GeneFriends: an online co-expression analysis tool to identify novel gene targets for aging and complex diseases. BMC genomics 13: 535-535.
46. Wren JD (2009) A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide. Bioinformatics (Oxford, England) 25: 1694-1701.
47. Cowley M, Wood AJ, Böhm S, Schulz R, Oakey RJ (2012) Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus. Nucleic acids research 40: 8917-8926.
48. Spies N, Nielsen CB, Padgett RA, Burge CB (2009) Biased chromatin signatures around polyadenylation sites and exons. Molecular cell 36: 245-254.