Single Nucleotide Polymorphisms Can Create Alternative Polyadenylation Signals and Affect Gene Expression through Loss of MicroRNA-Regulation

PLoS Computational Biology

Volumn 8, Issue 8, 2012, Pages

  Thomas, Laurent F ^a,b   Sætrom, Pål ^a,b  

^a NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

^b Interagon AS   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION REGULATION; NUCLEOTIDES; RNA;

GENES EXPRESSION; HUMAN CELLS; HUMAN DISEASE; MESSENGER RNA; POLYADENYLATION; POLYADENYLATION SIGNALS; PROTEIN-CODING GENES; REGULATORY PROCESS; SINGLE NUCLEOTIDE POLYMORPHISMS; UNTRANSLATED REGIONS;

GENE EXPRESSION;

MESSENGER RNA; MICRORNA;

3' UNTRANSLATED REGION; ALLELIC IMBALANCE; ALTERNATIVE POLYADENYLATION; ARTICLE; EXPRESSED SEQUENCE TAG; GENE CONTROL; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC RISK; GENOTYPE; HETEROZYGOTE; HOMOZYGOTE; MICROARRAY ANALYSIS; POLYADENYLATION; RNA SEQUENCE; SEQUENCE DATABASE; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84866084186     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002621     Document Type: Article

References (37)

1. Tian B, Hu J, Zhang H, Lutz C, (2005) A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res 33: 201-212.
2. Colgan D, Manley J, (1997) Mechanism and regulation of mRNA polyadenylation. Genes Dev 11: 2755-2766.
3. Legendre M, Ritchie W, Lopez F, Gautheret D, (2006) Differential repression of alternative tran-scripts: A screen for miRNA targets. PLoS Comput Biol 2: 333-342.
4. Mayr C, Bartel DP, (2009) Widespread Shortening of 3′ UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells. Cell 138: 673-684.
5. 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 320: 1643-1647.
6. Singh P, Alley TL, Wright SM, Kamdar S, Schott W, et al. (2009) Global Changes in Processing of mRNA 3′ Untranslated Regions Characterize Clinically Distinct Cancer Subtypes. Cancer Res 69: 9422-9430.
7. Danckwardt S, Hentze MW, Kulozik AE, (2008) 3′ end mRNA processing: molecular mechanisms and implications for health and disease. EMBO J 27: 482-498.
8. Uitte De Willige S, Rietveld IM, De Visser MCH, Vos HL, Bertina RM, (2007) Polymorphism 10034c>t is located in a region regulating polyadenylation of fgg transcripts and inuences the fibrinogen γ′/γa mrna ratio. J Thromb Haemost 5: 1243-1249.
9. Wiestner A, Tehrani M, Chiorazzi M, Wright G, Gibellini F, et al. (2007) Point mutations and genomic deletions in CCND1 create stable truncated cyclin D1 mRNAs that are associated with increased proliferation rate and shorter survival. Blood 109: 4599-4606.
10. Mu XJ, Lu ZJ, Kong Y, Lam HYK, Gerstein MB, (2011) Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project. Nucleic Acids Res 39: 7058-7076.
11. Int HapMap Consortium (2007) Frazer KA, Ballinger DG, Cox DR, Hinds DA, et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-U3.
12. Zhang H, Hu J, Reccel M, Tian B, (2005) PolyA DB: a database for mammalian mRNA polyadeny-lation. Nucleic Acids Res 33: D116-D120.
13. Lee JY, Yeh I, Park JY, Tian B, (2007) PolyA DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic Acids Res 35: D165-D168.
14. Sherry S, Ward M, Kholodov M, Baker J, Phan L, et al. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29: 308-311.
15. Heap GA, Yang JHM, Downes K, Healy BC, Hunt KA, et al. (2010) Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing. Hum Mol Genet 19: 122-134.
16. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, et al. (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129: 1401-1414.
17. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, et al. (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315: 848-853.
18. Wang L, Oberg AL, Asmann YW, Sicotte H, McDonnell SK, et al. (2009) Genome-Wide Tran-scriptional Profiling Reveals MicroRNA-Correlated Genes and Biological Processes in Human Lym-phoblastoid Cell Lines. PLoS One 4: e5878.
19. Nunes NM, Li W, Tian B, Furger A, (2010) A functional human Poly(A) site requires only a potent DSE and an A-rich upstream sequence. EMBO J 29: 1523-1536.
20. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A 106: 9362-9367.
21. Hindorff LA, Junkins HA, Hall PN, Mehta JP, Manolio TA A Catalog of Published Genome-Wide Association Studies. Available: www.genome.gov/gwastudies. Accessed Apr. 18, 2011.
22. Thomas LF, Saito T, Sætrom P, (2011) Inferring causative variants in microRNA target sites. Nucleic Acids Res 39: e109.
23. Hill WG, Robertson A, (1968) Linkage disequilibrium in finite populations. Theor Appl Genet 38: 226-231.
24. Wang Z, Gerstein M, Snyder M, (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
25. Int Human Genome Sequencing Conso (2001) Lander E, Linton L, Birren B, Nusbaum C, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
26. Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, et al. (2010) The ucsc genome browser database: update 2011. Nucl Acids Res 39: D876-82.
27. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476.
28. Griffths-Jones S, Saini HK, van Dongen S, Enright AJ, (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36: D154-D158.
29. Smith AD, Xuan Z, Zhang MQ, (2008) Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics 9: 128.
30. Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM, (2010) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 38: 1767-1771.
31. Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-effcient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
32. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
33. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-U174.
34. Saito T, Sætrom P, (2010) A two-step site and mRNA-level model for predicting microRNA targets. BMC Bioinformatics 11: 612.
35. R Development Core Team (2011) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. Available: http://www.R-project.org.
36. Gentleman RC, Carey VJ, Bates DM, et al. (2004) Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol 5: R80.
37. Pages H, Carlson M, Falcon S, LiN AnnotationDbi: Annotation Database Interface. R package version 1.8.2.