Genome-wide identification of SNPs in MicroRNA genes and the SNP effects on MicroRNA target binding and biogenesis

Human Mutation

Volumn 33, Issue 1, 2012, Pages 254-263

  Gong, Jing ^a,b   Tong, Yin ^a   Zhang, Hong Mei ^a   Wang, Kai ^c   Hu, Tao ^a   Shan, Ge ^d   Sun, Jun ^b   Guo, An Yuan ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^c Shanghai Bioladder Co Ltd   (China)

^d UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

Database; Frequency; miRNASNP; Target loss and gain

Indexed keywords

LUCIFERASE; MICRORNA;

3' UNTRANSLATED REGION; ARTICLE; BIOGENESIS; CHICKEN; CHIMPANZEE; CONTROLLED STUDY; COW; DATA BASE; DOG; GENE IDENTIFICATION; GENE INTERACTION; GENE TARGETING; GENETIC ASSOCIATION; HORSE; HUMAN; MOUSE; NONHUMAN; PREDICTION; PRIORITY JOURNAL; RAT; SINGLE NUCLEOTIDE POLYMORPHISM; ZEBRA FISH;

3' UNTRANSLATED REGIONS; ANIMALS; BASE SEQUENCE; BINDING SITES; DATABASES, GENETIC; GENE EXPRESSION REGULATION; GENES, REPORTER; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LUCIFERASES; MICRORNAS; MOLECULAR SEQUENCE DATA; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84857691987     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.21641     Document Type: Article

References (54)

1. Bao L, Zhou M, Wu L, Lu L, Goldowitz D, Williams RW, Cui Y. 2007. PolymiRTS database: linking polymorphisms in microRNA target sites with complex traits. Nucleic Acids Res 35:D51-D54.
2. Barenboim M, Zoltick BJ, Guo Y, Weinberger DR. 2010. MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets. Hum Mutat 31:1223-1232.
3. Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R. 2009. The GOA database in 2009-an integrated Gene Ontology Annotation resource. Nucleic Acids Res 37:D396-D403.
4. Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281-297.
5. Bartel DP. 2009.MicroRNAs: target recognition and regulatory functions. Cell 136:215- 233.
6. Betel D,WilsonM, Gabow A,Marks DS, Sander C. 2008. The microRNA.org resource: targets and expression. Nucleic Acids Res 36:D149-D153.
7. Bhartiya D, Laddha SV, Mukhopadhyay A, Scaria V. 2011. miRvar: A comprehensive database for genomic variations in microRNAs. Hum Mutat 32:E2226-E2245.
8. Chin LJ, Ratner E, Leng S, Zhai R, Nallur S, Babar I, Muller RU, Straka E, Su L, Burki EA, Crowell RE, Patel R, Kulkarni T, Homer R, Zelterman D, Kidd KK, Zhu Y, Christiani DC, Belinsky SA, Slack FJ, Weidhaas JB. 2008. A SNP in a let-7 microRNA complementary site in the KRAS 3' untranslated region increases non-small cell lung cancer risk. Cancer Res 68:8535-8540.
9. Denman RB. 1993. Using RNAFOLD to predict the activity of small catalytic RNAs. Biotechniques 15:1090-1095.
10. Duan R, Pak C, Jin P. 2007. Single nucleotide polymorphism associated with mature miR-125a alters the processing of pri-miRNA. Hum Mol Genet 16:1124-1131.
11. Duan S, Mi S, Zhang W, Dolan ME. 2009. Comprehensive analysis of the impact of SNPs and CNVs on human microRNAs and their regulatory genes. RNA Biol 6:412-425.
12. Friedman RC, Farh KK, Burge CB, Bartel DP. 2009. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19:92-105.
13. Gottwein E,Cai X,Cullen BR. 2006.Anovel assay for viralmicroRNAfunction identifies a single nucleotide polymorphism that affects Drosha processing. J Virol 80:5321-5326.
14. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. 2007. MicroRNA targeting specificity inmammals: determinants beyond seed pairing.Mol Cell 27:91-105.
15. Hariharan M, Scaria V, Brahmachari SK. 2009. dbSMR: a novel resource of genomewide SNPs affecting microRNA mediated regulation. BMC Bioinformatics 10:108.
16. Harnprasopwat R, Ha D, Toyoshima T, Lodish H, Tojo A, Kotani A. 2010. Alteration of processing induced by a single nucleotide polymorphism in pri-miR-126. Biochem Biophys Res Commun 399:117-122.
17. Hiard S, Charlier C, Coppieters W, Georges M, Baurain D. 2010. Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates. Nucleic Acids Res 38:D640-D651.
18. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM,Mehta JP, Collins FS,Manolio TA. 2009. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 106:9362-9367.
19. Huang da W, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44-57.
20. Iwai N, Naraba H. 2005. Polymorphisms in human pre-miRNAs. Biochem Biophys Res Commun 331:1439-1444.
21. Jazdzewski K, Liyanarachchi S, Swierniak M, Pachucki J, Ringel MD, Jarzab B, de la Chapelle A. 2009. Polymorphic mature microRNAs from passenger strand of pre-miR-146a contribute to thyroid cancer. Proc Natl Acad Sci USA 106:1502-1505.
22. Jazdzewski K,Murray EL, Franssila K, Jarzab B, Schoenberg DR, de la Chapelle A. 2008. Common SNP in pre-miR-146a decreasesmaturemiR expression and predisposes to papillary thyroid carcinoma. Proc Natl Acad Sci USA 105:7269-7274.
23. Jiang Q, Wang Y, Hao Y, Juan L, Teng M, Zhang X, Li M, Wang G, Liu Y. 2009. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 37:D98-D104.
24. Kanehisa M, Goto S, Kawashima S, Okuno Y, HattoriM. 2004. The KEGG resource for deciphering the genome. Nucleic Acids Res 32:D277-D280.
25. Kapeller J, Houghton LA, Monnikes H, Walstab J, Moller D, Bonisch H, Burwinkel B, Autschbach F, Funke B, Lasitschka F and others. 2008. First evidence for an association of a functional variant in themicroRNA-510 target site of the serotonin receptor-type 3E gene with diarrhea predominant irritable bowel syndrome.Hum Mol Genet 17:2967-2977.
26. Kathiresan S, Melander O, Guiducci C, Surti A, Burtt NP, Rieder MJ, Cooper GM, Roos C, Voight BF, Havulinna AS and others. 2008. Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. Nat Genet 40:189-197.
27. Khvorova A, Reynolds A, Jayasena SD. 2003. Functional siRNAs and miRNAs exhibit strand bias. Cell 115:209-216.
28. Kozomara A, Griffiths-Jones S. 2011. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 39:D152-157.
29. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M and others. 2005. Combinatorial microRNA target predictions. Nat Genet 37:495-500.
30. Kruger J, Rehmsmeier M. 2006. RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res 34:W451-W454.
31. Lai EC. 2002.Micro RNAs are complementary to 3' UTR sequencemotifs thatmediate negative post-transcriptional regulation. Nat Genet 30:363-364.
32. Landi D, Gemignani F, Barale R, Landi S. 2008. A catalog of polymorphisms falling in microRNA-binding regions of cancer genes. DNA Cell Biol 27:35-43.
33. Lee HC, Yang CW, Chen CY, Au LC. 2011. Single point mutation of microRNA may cause butterfly effect on alteration of global gene expression. Biochem Biophys Res Commun 404:1065-1069.
34. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S and others. 2003. The nuclearRNase III Drosha initiatesmicroRNA processing.Nature 425:415-419.
35. Lewis BP, Burge CB, Bartel DP. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15-20.
36. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. 2003. Prediction of mammalian microRNA targets. Cell 115:787-798.
37. Li L, Meng T, Jia Z, Zhu G, Shi B. 2010. Single nucleotide polymorphism associated with nonsyndromic cleft palate influences the processing of miR-140. Am J Med Genet A 152A:856-862.
38. Liu Z, Li G, Wei S, Niu J, El-Naggar AK, Sturgis EM, Wei Q. 2010. Genetic variants in selected pre-microRNA genes and the risk of squamous cell carcinoma of the head and neck. Cancer 116:4753-4760.
39. Mencia A, Modamio-Hoybjor S, Redshaw N, Morin M, Mayo-Merino F, Olavarrieta L, Aguirre LA, del Castillo I, Steel KP, Dalmay T and others. 2009. Mutations in the seed region of human miR-96 are responsible for nonsyndromic progressive hearing loss. Nat Genet 41:609-613.
40. Okubo M, Tahara T, Shibata T, Yamashita H, Nakamura M, Yoshioka D, Yonemura J, Kamiya Y, Ishizuka T, Nakagawa Y and others. 2011. Association study of common genetic variants in pre-microRNAs in patients with ulcerative colitis. J Clin Immunol 31:69-73.
41. Peng S, Kuang Z, Sheng C, Zhang Y, Xu H, Cheng Q. 2009. Association of microRNA-196a-2 gene polymorphism with gastric cancer risk in a Chinese population. Dig Dis Sci 55:2288-2293.
42. Ryan BM, Robles AI, Harris CC. 2010. Genetic variation in microRNA networks: the implications for cancer research. Nat Rev Cancer 10:389-402.
43. Saunders MA, Liang H, Li WH. 2007. Human polymorphism at microRNAs and microRNA target sites. Proc Natl Acad Sci USA 104:3300-3305.
44. Sethupathy P, Borel C, Gagnebin M, Grant GR, Deutsch S, Elton TS, Hatzigeorgiou AG, Antonarakis SE. 2007. Human microRNA-155 on chromosome 21 differentially interactswith its polymorphic target in theAGTR1 3' untranslated region: a mechanism for functional single-nucleotide polymorphisms related to phenotypes. Am J Hum Genet 81:405-413.
45. Sethupathy P, Collins FS. 2008. MicroRNA target site polymorphisms and human disease. Trends Genet 24:489-497.
46. Sethupathy P, Corda B, Hatzigeorgiou AG. 2006. TarBase: a comprehensive database of experimentally supported animal microRNA targets. RNA 12:192-197.
47. Shastry BS. 2009. SNPs: impact on gene function and phenotype. Methods Mol Biol 578:3-22.
48. Sun G, Yan J, Noltner K, Feng J, Li H, Sarkis DA, Sommer SS, Rossi JJ. 2009. SNPs in human miRNA genes affect biogenesis and function. RNA 15:1640-1651.
49. SunQ,GuH, Zeng Y, Xia Y,Wang Y, Jing Y, Yang L,Wang B. 2010. Hsa-mir-27a genetic variant contributes to gastric cancer susceptibility through affecting miR-27a and target gene expression. Cancer Sci 101:2241-2247.
50. Voight BF, Kudaravalli S,Wen X, Pritchard JK. 2006. Amap of recent positive selection in the human genome. PLoS Biol 4:e72.
51. Wang G, van derWalt JM, Mayhew G, Li YJ, Zuchner S, ScottWK, Martin ER, Vance JM. 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.
52. Wang X, Liu P, Zhu H, Xu Y,Ma C, Dai X, Huang L, Liu Y, Zhang L, Qin C. 2009. miR-34a, a microRNA up-regulated in a double transgenic mousemodel of Alzheimer's disease, inhibits bcl2 translation. Brain Res Bull 80:268-273.
53. Wang X,Wang X. 2006. Systematic identification ofmicroRNA functions by combining target prediction and expression profiling. Nucleic Acids Res 34:1646-1652.
54. Zhang B, Wang Q, Pan X. 2007. MicroRNAs and their regulatory roles in animals and plants. J Cell Physiol 210:279-289.