Dynamic expression of 3' UTRs revealed by Poisson hidden Markov modeling of RNA-Seq: Implications in gene expression profiling

Gene

Volumn 527, Issue 2, 2013, Pages 616-623

  Lu, Jun ^a,b,c   Bushel, Pierre R ^a  

^a NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^b GENERAL DYNAMICS   (United States)

^c Omicsoft Corp   (United States)

Author keywords

Alternative polyadenylation; Microarray; Untranslated region

Indexed keywords

MESSENGER RNA; RNA;

3' UNTRANSLATED REGION; ANIMAL CELL; ANIMAL TISSUE; ARTICLE; BRAIN CORTEX; CELLULAR DISTRIBUTION; GENE EXPRESSION; GENE EXPRESSION PROFILING; HIDDEN MARKOV MODEL; LIVER; MOUSE; NONHUMAN; POLYADENYLATION; PRIORITY JOURNAL; RNA SEQUENCE; SENSITIVITY AND SPECIFICITY;

3′ UNTRANSLATED REGIONS; 3′ UTRS; ALTERNATIVE POLYADENYLATION; APA; BASE-PAIRS; BAYESIAN INFORMATION CRITERION; BIC; BP; CDFS; CHIP DESIGN FILES; EM; EST; EXPECTATION AND MAXIMIZATION; EXPRESSED SEQUENCE TAG; GENE EXPRESSION OMNIBUS; GEO; IN VITRO TRANSCRIPTION; IVT; MICROARRAY; MICRORNA; MIRNA; PAS-SEQ; PHMM; POISSON HIDDEN MARKOV MODEL; POLYADENYLATION SITE SEQUENCING; RACE; RAPID AMPLIFICATION OF CDNA ENDS; RNA-SEQ; RNA-SEQUENCING; SEQUENCE READ ARCHIVE; SRA; SUPPORT VECTOR MACHINE; SVM; UNTRANSLATED REGION;

3' UNTRANSLATED REGIONS; GENE EXPRESSION PROFILING; MARKOV CHAINS; POISSON DISTRIBUTION; SEQUENCE ANALYSIS, RNA;

EID: 84881541534     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2013.06.052     Document Type: Article

References (51)

1. Asmann Y.W., et al. 3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer. BMC Genomics 2009, 10:531.
2. Brawand D., et al. The evolution of gene expression levels in mammalian organs. Nature 2011, 478:343-348.
3. Bullard J.H., Purdom E., Hansen K.D., Dudoit S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 2010, 11:94.
4. Conne B., Stutz A., Vassalli J.D. The 3' untranslated region of messenger RNA: A molecular 'hotspot' for pathology?. Nat. Med. 2000, 6:637-641.
5. Dai M., et al. Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res. 2005, 33:e175.
6. Day N., Hemmaplardh A., Thurman R.E., Stamatoyannopoulos J.A., Noble W.S. Unsupervised segmentation of continuous genomic data. Bioinformatics 2007, 23:1424-1426.
7. Derti A., et al. A quantitative atlas of polyadenylation in five mammals. Genome Res. 2012, 22:1173-1183.
8. Di Giammartino D.C., Nishida K., Manley J.L. Mechanisms and consequences of alternative polyadenylation. Mol. Cell 2011, 43:853-866.
9. D'Mello V., Lee J.Y., MacDonald C.C., Tian B. Alternative mRNA polyadenylation can potentially affect detection of gene expression by affymetrix genechip arrays. Appl. Bioinformatics 2006, 5:249-253.
10. Dreszer T.R., et al. The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res. 2012, 40:D918-D923.
11. Edgar R., Domrachev M., Lash A.E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002, 30:207-210.
12. Ernst J., et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 2011, 473:43-49.
13. Foat B.C., Houshmandi S.S., Olivas W.M., Bussemaker H.J. Profiling condition-specific, genome-wide regulation of mRNA stability in yeast. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:17675-17680.
14. Fu Y., et al. Differential genome-wide profiling of tandem 3' UTRs among human breast cancer and normal cells by high-throughput sequencing. Genome Res. 2011, 21:741-747.
15. Gautier L., Cope L., Bolstad B.M., Irizarry R.A. affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004, 20:307-315.
16. Gentleman R.C., et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5:R80.
17. Harris L.W., Lockstone H.E., Khaitovich P., Weickert C.S., Webster M.J., Bahn S. Gene expression in the prefrontal cortex during adolescence: implications for the onset of schizophrenia. BMC Med. Genomics 2009, 2:28.
18. Ji Z., Tian B. Reprogramming of 3' untranslated regions of mRNAs by alternative polyadenylation in generation of pluripotent stem cells from different cell types. PLoS One 2009, 4:e8419.
19. Ji Z., Lee J.Y., Pan Z., Jiang B., Tian B. Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:7028-7033.
20. Karolchik D., et al. The UCSC Genome Browser Database. Nucleic Acids Res. 2003, 31:51-54.
21. Katz Y., Wang E.T., Airoldi E.M., Burge C.B. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat. Methods 2010, 7:1009-1015.
22. Kuhn R.M., et al. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 2009, 37:D755-D761.
23. Langmead B., Trapnell C., Pop M., Salzberg S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10:R25.
24. Lee J.Y., Yeh I., Park J.Y., Tian B. PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic Acids Res. 2007, 35:D165-D168.
25. Lewis B.P., Shih I.H., Jones-Rhoades M.W., Bartel D.P., Burge C.B. Prediction of mammalian microRNA targets. Cell 2003, 115:787-798.
26. Lutz C.S. Alternative polyadenylation: a twist on mRNA 3' end formation. ACS Chem. Biol. 2008, 3:609-617.
27. MacDonald C.C., McMahon K.W. Tissue-specific mechanisms of alternative polyadenylation: testis, brain, and beyond. Wiley Interdiscip. Rev. RNA 2010, 1:494-501.
28. MacIsaac J.L., Bogutz A.B., Morrissy A.S., Lefebvre L. Tissue-specific alternative polyadenylation at the imprinted gene Mest regulates allelic usage at Copg2. Nucleic Acids Res. 2012, 40:1523-1535.
29. Mahmud M.P., Schliep A. Fast MCMC sampling for hidden Markov Models to determine copy number variations. BMC Bioinformatics 2011, 12:428.
30. Mayr C., Bartel D.P. Widespread shortening of 3' UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 2009, 138:673-684.
31. Mercer T.R., et al. Expression of distinct RNAs from 3' untranslated regions. Nucleic Acids Res. 2012, 39:2393-2403.
32. Metzker M.L. Sequencing technologies - the next generation. Nat. Rev. Genet. 2010, 11:31-46.
33. Morgan M., Pagès H. Rsamtools: Import aligned BAM file format sequences into R/Bioconductor http://bioconductor.org/packages/release/bioc/html/Rsamtools.html.
34. Neilson J.R., Sandberg R. Heterogeneity in mammalian RNA 3' end formation. Exp. Cell Res. 2010, 316:1357-1364.
35. Pruitt K.D., Tatusova T., Maglott D.R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007, 35:D61-D65.
36. R Development core team R: A Language and Environment for Statistical Computing 2012, R Foundation for Statistical Computing, (http://www.R-project.org).
37. Ramskold D., Wang E.T., Burge C.B., Sandberg R. An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput. Biol. 2009, 5:e1000598.
38. Sandberg R., Neilson J.R., Sarma A., Sharp P.A., Burge C.B. Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science 2008, 320:1643-1647.
39. Sayers E.W., et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2012, 40:D13-D25.
40. Shepard P.J., Choi E.A., Lu J., Flanagan L.A., Hertel K.J., Shi Y. Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. RNA 2011, 17:761-772.
41. Smibert P., et al. Global patterns of tissue-specific alternative polyadenylation in Drosophila. Cell Rep. 2012, 1:277-289.
42. Storey J.D. A direct approach to false discovery rates. J. R. Stat. Soc. B Stat. Methodol. 2002, 64:479-498.
43. Storey J.D. The positive false discovery rate: A Bayesian interpretation and the q-value. Ann. Stat. 2003, 31:2013-2035.
44. Thierry-Mieg D., Thierry-Mieg J. AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol. 2006, 7(Suppl. 1):S12.1-S12.14.
45. Tian B., Hu J., Zhang H., Lutz C.S. A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res. 2005, 33:201-212.
46. Trapnell C., Pachter L., Salzberg S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111.
47. Trapnell C., et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 2010, 28:511-515.
48. von Roretz C., Gallouzi I.E. Decoding ARE-mediated decay: is microRNA part of the equation?. J. Cell Biol. 2008, 181:189-194.
49. Wang Z., Gerstein M., Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10:57-63.
50. Winter J., Kunath M., Roepcke S., Krause S., Schneider R., Schweiger S. Alternative polyadenylation signals and promoters act in concert to control tissue-specific expression of the Opitz Syndrome gene MID1. BMC Mol. Biol. 2007, 8:105.
51. Zhang H., Lee J.Y., Tian B. Biased alternative polyadenylation in human tissues. Genome Biol. 2005, 6:R100.