miRNA-mediated relationships between Cis-SNP genotypes and transcript intensities in lymphocyte cell lines

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Zhang, Wensheng ^a   Edwards, Andrea ^a   Zhu, Dongxiao ^b   Flemington, Erik K ^c   Deininger, Prescott ^c   Zhang, Kun ^a  

^a XAVIER UNIVERSITY OF LOUISIANA   (United States)

^b Wayne State University   (United States)

^c TULANE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; MESSENGER RNA;

3' UNTRANSLATED REGION; ALG8 GENE; ARTICLE; BINDING SITE; CONTROLLED STUDY; COPY NUMBER VARIATION; DGKE GENE; EXON; GENE EXPRESSION REGULATION; GENE LINKAGE DISEQUILIBRIUM; GENE PRODUCT; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOTYPE; GLYCOSYLATION; GNA12 GENE; HOMOZYGOSITY; HUMAN; HUMAN CELL; KLF11 GENE; LRPAP1 GENE; LYMPHOCYTE; MMAB GENE; NUCLEOTIDE SEQUENCE; PROTEIN MODIFICATION; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTION REGULATION; BIOLOGY; CELL LINE; GENETIC PREDISPOSITION; GENETICS; METABOLISM; PHYSIOLOGY;

METAZOA;

3' UNTRANSLATED REGIONS; BINDING SITES; CELL LINE; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION; GENETIC PREDISPOSITION TO DISEASE; GENOTYPE; HUMANS; LINKAGE DISEQUILIBRIUM; LYMPHOCYTES; MICRORNAS; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA, MESSENGER;

EID: 84863116007     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0031429     Document Type: Article

References (61)

1. Filipowicz W, Bhattacharyya SN, Sonenberg N, (2008) Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 9: 102-114.
2. Bartel DP, (2009) MicroRNAs: target recognition and regulatory functions. Cell 136: 215-233.
3. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, et al. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27: 91-105.
4. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ, (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36: D154-158.
5. Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG, (2009) The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res 37: D155-158.
6. Stark A, Brennecke J, Bushati N, Russell RB, Cohen SM, (2005) Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3′UTR evolution. Cell 123: 1133-1146.
7. UCSC Genome Browser website. Available: http://genome.ucsc.edu/. Accessed 2011 Dec 22.
8. Huang RS, Duan S, Bleibel WK, Kistner EO, Zhang W, et al. (2007) A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity. Proc Natl Acad Sci U S A 104: 9758-9763.
9. Stranger BE, Forrest MS, Clark AG, Minichiello MJ, Deutsch S, et al. (2005) Genome-wide associations of gene expression variation in humans. PLoS Genet 1: e78.
10. Li Y, Rowland C, Schrodi S, Laird W, Tacey K, et al. (2006) A case-control association study of the 12 single-nucleotide polymorphisms implicated in Parkinson disease by a recent genome scan. Am J Hum Genet 78: 1090-1092 author reply 1092-1094.
11. Gan SQ, Du Z, Liu SR, Yang YL, Shen M, et al. (2008) Association of SNP haplotypes at the myostatin gene with muscular hypertrophy in sheep. Asian- Australasian Journal of Animal Sciences 21: 928-935.
12. Simko I, Pechenick DA, McHale LK, Truco MJ, Ochoa OE, et al. (2009) Association mapping and marker-assisted selection of the lettuce dieback resistance gene Tvr1. BMC Plant Biol 9: 135.
13. Fraser HB, Xie X, (2009) Common polymorphic transcript variation in human disease. Genome Res 19: 567-575.
14. Smith WJ, Li Y, Ingham A, Collis E, McWilliam SM, et al. (2010) A genomics-informed, SNP association study reveals FBLN1 and FABP4 as contributing to resistance to fleece rot in Australian Merino sheep. BMC Vet Res 6: 27.
15. Shu Y, Li Y, Zhu Z, Bai X, Cai H, et al. (2010) SNPs discovery and CAPS marker conversion in soybean. Mol Biol Rep.
16. Zhang W, Duan S, Bleibel WK, Wisel SA, Huang RS, et al. (2009) Identification of common genetic variants that account for transcript isoform variation between human populations. Hum Genet 125: 81-93.
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. Myles S, Davison D, Barrett J, Stoneking M, Timpson N, (2008) Worldwide population differentiation at disease-associated SNPs. BMC Med Genomics 1: 22.
19. Amato R, Pinelli M, Monticelli A, Marino D, Miele G, et al. (2009) Genome-wide scan for signatures of human population differentiation and their relationship with natural selection, functional pathways and diseases. PLoS One 4: e7927.
20. Nica AC, Montgomery SB, Dimas AS, Stranger BE, Beazley C, et al. (2010) Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet 6: e1000895.
21. Brown EM, Barrat BJ, (2007) The HapMap-A haplotype map of human genome. Bioinformatics for geneticists: a bioinformatics primer for the analysis of genetic data. 2 ed West Sussex John Wiley & Sons, Ltd pp. 35-54.
22. Plagnol V, Smyth DJ, Todd JA, Clayton DG, (2009) Statistical independence of the colocalized association signals for type 1 diabetes and RPS26 gene expression on chromosome 12q13. Biostatistics 10: 327-334.
23. Yamaguchi-Kabata Y, Shimada MK, Hayakawa Y, Minoshima S, Chakraborty R, et al. (2008) Distribution and effects of nonsense polymorphisms in human genes. PLoS One 3: e3393.
24. The GPC (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
25. Kim J, Bartel DP, (2009) Allelic imbalance sequencing reveals that single-nucleotide polymorphisms frequently alter microRNA-directed repression. Nat Biotechnol 27: 472-477.
26. Brown EM, Barrat BJ, eds. (2007) The HapMap- A Haplotype Map of Human Genome. 2 ed Wiley pp. 35-58.
27. Sethupathy P, Collins FS, (2008) MicroRNA target site polymorphisms and human disease. Trends Genet 24: 489-497.
28. Bao L, Zhou M, Wu L, Lu L, Goldowitz D, et al. (2007) PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. Nucleic Acids Res 35: D51-54.
29. Saunders MA, Liang H, Li WH, (2007) Human polymorphism at microRNAs and microRNA target sites. Proc Natl Acad Sci U S A 104: 3300-3305.
30. Huang DW, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protoc 4: 44-57.
31. DAVID website. Available: http://david.abcc.ncifcrf.gov/. Accessed 2010 Dec 15.
32. TargetScan website. Available: http://www.targetscan.org/. Accessed 2010 Jul 20.
33. Lall S, Grun D, Krek A, Chen K, Wang YL, et al. (2006) A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol 16: 460-471.
34. Betel D, Wilson M, Gabow A, Marks DS, Sander C, (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res 36: D149-153.
35. Friedman RC, Farh KK, Burge CB, Bartel DP, (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19: 92-105.
36. Gamazon ER, Im HK, Duan S, Lussier YA, Cox NJ, et al. (2010) Exprtarget: an integrative approach to predicting human microRNA targets. PLoS One 5: e13534.
37. Sturm M, Hackenberg M, Langenberger D, Frishman D, (2010) TargetSpy: a supervised machine learning approach for microRNA target prediction. BMC Bioinformatics 11: 292.
38. HapMap website. Available: http://hapmap.ncbi.nlm.nih.gov/. Accessed 2010 Jul 25.
39. Wang L, Oberg AL, Asmann YW, Sicotte H, McDonnell SK, et al. (2009) Genome-wide transcriptional profiling reveals microRNA-correlated genes and biological processes in human lymphoblastoid cell lines. PLoS One 4: e5878.
40. Jiang Q, Wang Y, Hao Y, Juan L, Teng M, et al. (2009) miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 37: D98-104.
41. Wang D, Qiu C, Zhang H, Wang J, Cui Q, et al. (2010) Human microRNA oncogenes and tumor suppressors show significantly different biological patterns: from functions to targets. PLoS One 5.
42. Imai S, Kai M, Yasuda S, Kanoh H, Sakane F, (2005) Identification and characterization of a novel human type II diacylglycerol kinase, DGK kappa. J Biol Chem 280: 39870-39881.
43. Borel C, Antonarakis SE, (2008) Functional genetic variation of human miRNAs and phenotypic consequences. Mamm Genome 19: 503-509.
44. He H, Jazdzewski K, Li W, Liyanarachchi S, Nagy R, et al. (2005) The role of microRNA genes in papillary thyroid carcinoma. Proc Natl Acad Sci U S A 102: 19075-19080.
45. Mishra PJ, Humeniuk R, Longo-Sorbello GS, Banerjee D, Bertino JR, (2007) A miR-24 microRNA binding-site polymorphism in dihydrofolate reductase gene leads to methotrexate resistance. Proc Natl Acad Sci U S A 104: 13513-13518.
46. Wang G, van der Walt JM, Mayhew G, Li YJ, Zuchner S, et al. (2008) Variation in the miRNA-433 binding site of FGF20 confers risk for Parkinson disease by overexpression of alpha-synuclein. Am J Hum Genet 82: 283-289.
47. Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, et al. (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464: 773-777.
48. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, et al. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464: 768-772.
49. Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, et al. (2004) Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 74: 106-120.
50. Hawley ME, Kidd KK, (1995) HAPLO: a program using the EM algorithm to estimate the frequencies of multi-site haplotypes. J Hered 86: 409-411.
51. Hill WG, (1974) Estimation of linkage disequilibrium in randomly mating populations. Heredity 33: 229-239.
52. Hartl DL, Clark AG, (1989) Principles of population genetics Sunderland, Mass. Sinauer Associates.
53. Bansal A, Vignal C, McGinnis R, (2007) Tools for statistical genetics. In: Barnes MR, editors. Bioinformatics for geneticists: a bioinformatics primer for the analysis of genetic data. 2 ed West Sussex John Wiley & Sons, Ltd.
54. dbSNP website. Available: http://www.ncbi.nlm.nih.gov/projects/SNP/. Accessed 2010 Sep 20.
55. Bolstad BM, Irizarry RA, Astrand M, Speed TP, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
56. Benjamini Y, Hochberg Y, (1995) Controlling the false discover rate - A practical and powerful approach to multiple testing. J ROY STAT SOC B MET 75: 289-300.
57. Diana website. Available: http://diana.cslab.ece.ntua.gr/?sec=home. Accessed 2010 Aug 1.
58. Biostrings website. Available: http://www.bioconductor.org/packages/2.2/bioc/html/Biostrings.html. Accessed 2010 Mar 10.
59. Pritchard JK, Przeworski M, (2001) Linkage disequilibrium in humans: models and data. Am J Hum Genet 69: 1-14.
60. Weir BS, (1996) Genetic data analysis II: methods for discrete population genetic data Sunderland, Mass. Sinauer Associates pp. xii,445.
61. Weir BS, Cockerham CC, (1979) Estimation of linkage disequilibrium in randomly mating population. Heredity 42: 105-111.