Genomic variations in non-coding RNAs: Structure, function and regulation

Genomics

Volumn 107, Issue 2-3, 2016, Pages 59-68

  Bhartiya, Deeksha ^a,b   Scaria, Vinod ^a,b  

^a CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

^b ACADEMY OF SCIENTIFIC AND INNOVATIVE RESEARCH ACSIR   (India)

Author keywords

Humans; Long non coding RNAs; MicroRNAs; Non coding RNAs; SnoRNAs; Variations

Indexed keywords

CIRCULAR RNA; LONG UNTRANSLATED RNA; MICRORNA; SMALL NUCLEOLAR RNA; SMALL UNTRANSLATED RNA; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

CANCER RISK; COPY NUMBER VARIATION; DISEASE ASSOCIATION; GENE EXPRESSION; GENE MUTATION; GENETIC ASSOCIATION; GENETIC REGULATION; GENETIC VARIABILITY; HUMAN; INTERACTIONS WITH RNA; NEXT GENERATION SEQUENCING; PRIORITY JOURNAL; REVIEW; RNA SEQUENCE; RNA STRUCTURE; SINGLE NUCLEOTIDE POLYMORPHISM; CHEMISTRY; CONFORMATION; GENE EXPRESSION REGULATION; GENETIC PREDISPOSITION; GENETIC VARIATION; GENETICS; HUMAN GENOME;

GENE EXPRESSION REGULATION; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOME, HUMAN; HUMANS; NUCLEIC ACID CONFORMATION; RNA, SMALL NUCLEOLAR;

EID: 84958042041     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2016.01.005     Document Type: Review

References (166)

1. Finishing the euchromatic sequence of the human genome Nature 2004, 431:931-945.
2. Lander E.S. Initial impact of the sequencing of the human genome. Nature 2011, 470:187-197.
3. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., et al. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
4. Naidoo N., Pawitan Y., Soong R., Cooper D.N., Ku C.S. Human genetics and genomics a decade after the release of the draft sequence of the human genome. Hum. Genet. 2011, 5:577-622.
5. Churchill G.A. Fundamentals of experimental design for cDNA microarrays. Nat. Genet. 2002, 32(Suppl):490-495.
6. Mardis E.R. Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 2008, 9:387-402.
7. Morozova O., Marra M.A. Applications of next-generation sequencing technologies in functional genomics. Genomics 2008, 92:255-264.
8. Manolio T.A., Collins F.S., Cox N.J., Goldstein D.B., Hindorff L.A., Hunter D.J., et al. Finding the missing heritability of complex diseases. Nature 2009, 461:747-753.
9. Clarke A.J., Cooper D.N. GWAS: heritability missing in action?. Eur. J. Hum. Genet. 2010, 18:859-861.
10. Ku C.S., Naidoo N., Pawitan Y. Revisiting Mendelian disorders through exome sequencing. Hum. Genet. 2011, 129:351-370.
11. Jacquier A. The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat. Rev. Genet. 2009, 10:833-844.
12. Jensen T.H., Jacquier A., Libri D. Dealing with pervasive transcription. Mol. Cell 2013, 52:473-484.
13. Djebali S., Davis C.A., Merkel A., Dobin A., Lassmann T., Mortazavi A., et al. Landscape of transcription in human cells. Nature 2012, 489:101-108.
14. Harrow J., Frankish A., Gonzalez J.M., Tapanari E., Diekhans M., Kokocinski F., et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012, 22:1760-1774.
15. Derrien T., Johnson R., Bussotti G., Tanzer A., Djebali S., Tilgner H., et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012, 22:1775-1789.
16. Mercer T.R., Dinger M.E., Mattick J.S. Long non-coding RNAs: insights into functions. Nat. Rev. Genet. 2009, 10:155-159.
17. Visscher P.M., Brown M.A., McCarthy M.I., Yang J. Five years of GWAS discovery. Am. J. Hum. Genet. 2012, 90:7-24.
18. Welter D., Macarthur J., Morales J., Burdett T., Hall P., Junkins H., et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 2014, 42:D1001-D1006.
19. Abecasis G.R., Altshuler D., Auton A., Brooks L.D., Durbin R.M., Gibbs R.A., et al. A map of human genome variation from population-scale sequencing. Nature 2010, 467:1061-1073.
20. Manolio T.A., Collins F.S. The HapMap and genome-wide association studies in diagnosis and therapy. Annu. Rev. Med. 2009, 60:443-456.
21. Altshuler D.M., Gibbs R.A., Peltonen L., Dermitzakis E., Schaffner S.F., Yu F., et al. Integrating common and rare genetic variation in diverse human populations. Nature 2010, 467:52-58.
22. Mattick J.S., Makunin I.V. Non-coding RNA. Hum. Mol. Genet. 2006, 15(1):R17-R29. (Spec No).
23. Taft R.J., Pang K.C., Mercer T.R., Dinger M., Mattick J.S. Non-coding RNAs: regulators of disease. J. Pathol. 2010, 220:126-139.
24. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
25. Zhou X., Duan X., Qian J., Li F. Abundant conserved microRNA target sites in the 5'-untranslated region and coding sequence. Genetica 2009, 137:159-164.
26. Cuperus J.T., Fahlgren N., Carrington J.C. Evolution and functional diversification of MIRNA genes. Plant Cell 2011, 23:431-442.
27. Morozova N., Zinovyev A., Nonne N., Pritchard L.L., Gorban A.N., Harel-Bellan A. Kinetic signatures of microRNA modes of action. RNA 2012, 18:1635-1655. New York, N.Y.
28. Shi H., Xu J., Zhang G., Xu L., Li C., Wang L., et al. Walking the interactome to identify human miRNA-disease associations through the functional link between miRNA targets and disease genes. BMC Syst. Biol. 2013, 7:101.
29. Sayed D., Abdellatif M. MicroRNAs in development and disease. Physiol. Rev. 2011, 91:827-887.
30. Bejerano G., Pheasant M., Makunin I., Stephen S., Kent W.J., Mattick J.S., et al. Ultraconserved elements in the human genome. Science 2004, 304:1321-1325. New York, N.Y.
31. Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233.
32. Hariharan M., Scaria V., Brahmachari S.K. dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation. BMC Bioinf. 2009, 10:108.
33. Sethupathy P. Needles in the genetic haystack of lipid disorders: single nucleotide polymorphisms in the microRNA regulome. J. Lipid Res. 2013, 54:1168-1173.
34. Szeto C.Y., Lin C.H., Choi S.C., Yip T.T., Ngan R.K., Tsao G.S., et al. Integrated mRNA and microRNA transcriptome sequencing characterizes sequence variants and mRNA-microRNA regulatory network in nasopharyngeal carcinoma model systems. FEBS Open Bio. 2014, 4:128-140.
35. Jazdzewski K., Murray E.L., Franssila K., Jarzab B., Schoenberg D.R., de la Chapelle A. Common SNP in pre-miR-146a decreases mature miR expression and predisposes to papillary thyroid carcinoma. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:7269-7274.
36. Sun G., Yan J., Noltner K., Feng J., Li H., Sarkis D.A., et al. SNPs in human miRNA genes affect biogenesis and function. RNA 2009, 15:1640-1651. New York, N.Y.
37. Kim H.K., Prokunina-Olsson L., Chanock S.J. Common genetic variants in miR-1206 (8q24.2) and miR-612 (11q13.3) affect biogenesis of mature miRNA forms. PLoS One 2012, 7.
38. Mencia A., Modamio-Hoybjor S., Redshaw N., Morin M., Mayo-Merino F., Olavarrieta L., et al. Mutations in the seed region of human miR-96 are responsible for nonsyndromic progressive hearing loss. Nat. Genet. 2009, 41:609-613.
39. Rawlings-Goss R.A., Campbell M.C., Tishkoff S.A. Global population-specific variation in miRNA associated with cancer risk and clinical biomarkers. BMC Med. Genet. 2014, 7:53.
40. Qi L., Hu Y., Zhan Y., Wang J., Wang B.B., Xia H.F., et al. A SNP site in pri-miR-124 changes mature miR-124 expression but no contribution to Alzheimer's disease in a Mongolian population. Neurosci. Lett. 2012, 515:1-6.
41. Zhu J., Yang L., You W., Cui X., Chen Y., Hu J., et al. Genetic variation in miR-100 rs1834306 is associated with decreased risk for esophageal squamous cell carcinoma in Kazakh patients in northwest China. Int. J. Clin. Exp. Pathol. 2015, 8:7332-7340.
42. Boni V., Zarate R., Villa J.C., Bandres E., Gomez M.A., Maiello E., et al. Role of primary miRNA polymorphic variants in metastatic colon cancer patients treated with 5-fluorouracil and irinotecan. Pharm. J. 2011, 11:429-436.
43. Chen J., Qin Z., Jiang Y., Wang Y., He Y., Dai J., et al. Genetic variations in the flanking regions of miR-101-are associated with increased risk of breast cancer. PLoS One 2014, 9.
44. Tian T., Shu Y., Chen J., Hu Z., Xu L., Jin G., et al. A functional genetic variant in microRNA-196a2 is associated with increased susceptibility of lung cancer in Chinese. Cancer Epidemiol. Biomarkers Prev. 2009, 18:1183-1187.
45. Catucci I., Yang R., Verderio P., Pizzamiglio S., Heesen L., Hemminki K., et al. Evaluation of SNPs in miR-146a, miR196a2 and miR-499 as low-penetrance alleles in German and Italian familial breast cancer cases. Hum. Mutat. 2010, 31:E1052-E1057.
46. Jazdzewski K., de la Chapelle A. Genomic sequence matters: a SNP in microRNA-146a can turn anti-apoptotic. Cell Cycle 2009, 8:1642-1643. Georgetown, Tex.
47. Qi P., Dou T.H., Geng L., Zhou F.G., Gu X., Wang H., et al. Association of a variant in MIR 196A2 with susceptibility to hepatocellular carcinoma in male Chinese patients with chronic hepatitis B virus infection. Hum. Immunol. 2010, 71:621-626.
48. Yang R., Schlehe B., Hemminki K., Sutter C., Bugert P., Wappenschmidt B., et al. A genetic variant in the pre-miR-27a oncogene is associated with a reduced familial breast cancer risk. Breast Cancer Res. Treat. 2010, 121:693-702.
49. Wang B., Ma N., Wang Y. Association between the hsa-mir-27a variant and breast cancer risk: a meta-analysis. Asian Pac. J. Cancer Prev. 2012, 13:6207-6210.
50. Wang Z., Lai J., Wang Y., Nie W., Guan X. The Hsa-miR-27a rs895819 (A>G) polymorphism and cancer susceptibility. Gene 2013, 521:87-90.
51. Roy R., De Sarkar N., Ghose S., Paul R.R., Pal M., Bhattacharya C., et al. Genetic variations at microRNA and processing genes and risk of oral cancer. Tumour Biol. 2014, 35:3409-3414. The journal of the International Society for Oncodevelopmental Biology and Medicine.
52. Bhartiya D., Laddha S.V., Mukhopadhyay A., Scaria V. miRvar: a comprehensive database for genomic variations in microRNAs. Hum. Mutat. 2011, 32:E2226-E2245.
53. Han M., Zheng Y. Comprehensive analysis of single nucleotide polymorphisms in human microRNAs. PLoS One 2013, 8.
54. Gong J., Tong Y., Zhang H.M., Wang K., Hu T., Shan G., et al. Genome-wide identification of SNPs in microRNA genes and the SNP effects on microRNA target binding and biogenesis. Hum. Mutat. 2012, 33:254-263.
55. Zorc M., Skok D.J., Godnic I., Calin G.A., Horvat S., Jiang Z., et al. Catalog of microRNA seed polymorphisms in vertebrates. PLoS One 2012, 7.
56. Persengiev S., Kondova I., Bontrop R. Insights on the functional interactions between miRNAs and copy number variations in the aging brain. Front. Mol. Neurosci. 2013, 6:32.
57. Vaishnavi V., Manikandan M., Tiwary B.K., Munirajan A.K. Insights on the functional impact of microRNAs present in autism-associated copy number variants. PLoS One 2013, 8.
58. Wu X., Zhang D., Li G. Insights into the regulation of human CNV-miRNAs from the view of their target genes. BMC Genomics 2012, 13:707.
59. Calin G.A., Dumitru C.D., Shimizu M., Bichi R., Zupo S., Noch E., et al. Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc. Natl. Acad. Sci. U. S. A. 2002, 99:15524-15529.
60. Ota A., Tagawa H., Karnan S., Tsuzuki S., Karpas A., Kira S., et al. Identification and characterization of a novel gene, C13orf25, as a target for 13q31-q32 amplification in malignant lymphoma. Cancer Res. 2004, 64:3087-3095.
61. Marcinkowska M., Szymanski M., Krzyzosiak W.J., Kozlowski P. Copy number variation of microRNA genes in the human genome. BMC Genomics 2011, 12:183.
62. Wang Y., Hu X., Greshock J., Shen L., Yang X., Shao Z., et al. Genomic DNA copy-number alterations of the let-family in human cancers. PLoS One 2012, 7.
63. Huan T., Rong J., Liu C., Zhang X., Tanriverdi K., Joehanes R., et al. Genome-wide identification of microRNA expression quantitative trait loci. Nat. Commun. 2015, 6:6601.
64. Williamson V.S., Mamdani M., McMichael G.O., Kim A.H., Lee D., Bacanu S., et al. Expression quantitative trait loci (eQTLs) in microRNA genes are enriched for schizophrenia and bipolar disorder association signals. Psychol. Med. 2015, 45:2557-2569.
65. Quitadamo A., Tian L., Hall B., Shi X. An integrated network of microRNA and gene expression in ovarian cancer. BMC Bioinf. 2015, 16(Suppl. 5):S5.
66. Bachellerie J.P., Cavaille J., Huttenhofer A. The expanding snoRNA world. Biochimie 2002, 84:775-790.
67. Kiss-Laszlo Z., Henry Y., Kiss T. Sequence and structural elements of methylation guide snoRNAs essential for site-specific ribose methylation of pre-rRNA. EMBO J. 1998, 17:797-807.
68. Samarsky D.A., Fournier M.J., Singer R.H., Bertrand E. The snoRNA box C/D motif directs nucleolar targeting and also couples snoRNA synthesis and localization. EMBO J. 1998, 17:3747-3757.
69. Sahoo T., del Gaudio D., German J.R., Shinawi M., Peters S.U., Person R.E., et al. Prader-Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster. Nat. Genet. 2008, 40:719-721.
70. Bhartiya D., Talwar J., Hasija Y., Scaria V. Systematic curation and analysis of genomic variations and their potential functional consequences in snoRNA loci. Hum. Mutat. 2012, 33:E2367-E2374.
71. Matera A.G., Terns R.M., Terns M.P. Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat. Rev. Mol. Cell Biol. 2007, 8:209-220.
72. Jia Y., Mu J.C., Ackerman S.L. Mutation of a U2 snRNA gene causes global disruption of alternative splicing and neurodegeneration. Cell 2012, 148:296-308.
73. Siomi M.C., Sato K., Pezic D., Aravin A.A. PIWI-interacting small RNAs: the vanguard of genome defence. Nat. Rev. Mol. Cell Biol. 2011, 12:246-258.
74. Lukic S., Chen K. Human piRNAs are under selection in Africans and repress transposable elements. Mol. Biol. Evol. 2011, 28:3061-3067.
75. Parisien M., Wang X., Pan T. Diversity of human tRNA genes from the 1000-genomes project. RNA Biol. 2013, 10:1853-1867.
76. Esteller M. Non-coding RNAs in human disease. Nat. Rev. Genet. 2011, 12:861-874.
77. Zovoilis A., Mungall A.J., Moore R., Varhol R., Chu A., Wong T., et al. The expression level of small non-coding RNAs derived from the first exon of protein-coding genes is predictive of cancer status. EMBO Rep. 2014, 15:402-410.
78. Ernst C., Morton C.C. Identification and function of long non-coding RNA. Front. Cell. Neurosci. 2013, 7:168.
79. Kaushik K., Leonard V.E., Kv S., Lalwani M.K., Jalali S., Patowary A., et al. Dynamic expression of long non-coding RNAs (lncRNAs) in adult zebrafish. PLoS One 2013, 8.
80. Ulitsky I., Bartel D.P. lincRNAs: genomics, evolution, and mechanisms. Cell 2013, 154:26-46.
81. Froberg J.E., Yang L., Lee J.T. Guided by RNAs: X-inactivation as a model for lncRNA function. J. Mol. Biol. 2013, 425:3698-3706.
82. Jin G., Sun J., Isaacs S.D., Wiley K.E., Kim S.T., Chu L.W., et al. Human polymorphisms at long non-coding RNAs (lncRNAs) and association with prostate cancer risk. Carcinogenesis 2011, 32:1655-1659.
83. Liu Y., Pan S., Liu L., Zhai X., Liu J., Wen J., et al. A genetic variant in long non-coding RNA HULC contributes to risk of HBV-related hepatocellular carcinoma in a Chinese population. PLoS One 2012, 7.
84. Bhartiya D., Jalali S., Ghosh S., Scaria V. Distinct patterns of genetic variations in potential functional elements in long noncoding RNAs. Hum. Mutat. 2014, 35:192-201.
85. Cunnington M.S., Santibanez Koref M., Mayosi B.M., Burn J., Keavney B. Chromosome 9p21 SNPs associated with multiple disease phenotypes correlate with ANRIL expression. PLoS Genet. 2010, 6.
86. Pasmant E., Sabbagh A., Vidaud M., Bieche I. ANRIL, a long, noncoding RNA, is an unexpected major hotspot in GWAS. FASEB J. 2011, 25:444-448.
87. Jendrzejewski J., He H., Radomska H.S., Li W., Tomsic J., Liyanarachchi S., et al. The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:8646-8651.
88. van Dijk M., Thulluru H.K., Mulders J., Michel O.J., Poutsma A., Windhorst S., et al. HELLP babies link a novel lincRNA to the trophoblast cell cycle. J. Clin. Invest. 2012, 122:4003-4011.
89. Wan Y., Qu K., Ouyang Z., Chang H.Y. Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing. Nat. Protoc. 2013, 8:849-869.
90. Wen J., Liu Y., Liu J., Liu L., Song C., Han J., et al. Expression quantitative trait loci in long non-coding RNA ZNRD1-AS1 influence both HBV infection and hepatocellular carcinoma development. Mol. Carcinog. 2014.
91. Yin J., Wen J., Hang D., Han J., Jiang J., Song C., et al. Expression quantitative trait loci for CARD8 contributes to risk of two infection-related cancers-hepatocellular carcinoma and cervical cancer. PLoS One 2015, 10.
92. Ghosal S., Das S., Sen R., Basak P., Chakrabarti J. Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits. Front. Genet. 2013, 4:283.
93. Thomas L.F., Saetrom P. Circular RNAs are depleted of polymorphisms at microRNA binding sites. Bioinforma. 2014, 30:2243-2246. (Oxford, England).
94. Chen G., Qiu C., Zhang Q., Liu B., Cui Q. Genome-wide analysis of human SNPs at long intergenic noncoding RNAs. Hum. Mutat. 2013, 34:338-344.
95. Halvorsen M., Martin J.S., Broadaway S., Laederach A. Disease-associated mutations that alter the RNA structural ensemble. PLoS Genet. 2010, 6.
96. Martin J.S., Halvorsen M., Davis-Neulander L., Ritz J., Gopinath C., Beauregard A., et al. Structural effects of linkage disequilibrium on the transcriptome. RNA 2012, 18:77-87. (New York, N.Y.).
97. Johnson A.D., Trumbower H., Sadee W. RNA structures affected by single nucleotide polymorphisms in transcribed regions of the human genome. WebmedCentral BIOINFORMATICS 2011.
98. Sabarinathan R., Tafer H., Seemann S.E., Hofacker I.L., Stadler P.F., Gorodkin J. RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs. Hum. Mutat. 2013, 34:546-556.
99. Sabarinathan R., Tafer H., Seemann S.E., Hofacker I.L., Stadler P.F., Gorodkin J. The RNAsnp web server: predicting SNP effects on local RNA secondary structure. Nucleic Acids Res. 2013, 41:W475-W479.
100. Corley M., Solem A., Qu K., Chang H.Y., Laederach A. Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark. Nucleic Acids Res. 2015, 43:1859-1868.
101. Kertesz M., Wan Y., Mazor E., Rinn J.L., Nutter R.C., Chang H.Y., et al. Genome-wide measurement of RNA secondary structure in yeast. Nature 2010, 467:103-107.
102. Underwood J.G., Uzilov A.V., Katzman S., Onodera C.S., Mainzer J.E., Mathews D.H., et al. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat. Methods 2010, 7:995-1001.
103. Merino E.J., Wilkinson K.A., Coughlan J.L., Weeks K.M. RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE). J. Am. Chem. Soc. 2005, 127:4223-4231.
104. Wilkinson K.A., Merino E.J., Weeks K.M. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat. Protoc. 2006, 1:1610-1616.
105. Spitale R.C., Flynn R.A., Zhang Q.C., Crisalli P., Lee B., Jung J.W., et al. Structural imprints in vivo decode RNA regulatory mechanisms. Nature 2015, 519:486-490.
106. Mortimer S.A., Trapnell C., Aviran S., Pachter L., Lucks J.B. SHAPE-Seq: high-throughput RNA structure analysis. Curr. Protoc. Chem. Biol. 2012, 4:275-297.
107. Novikova I.V., Hennelly S.P., Sanbonmatsu K.Y. Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. Nucleic Acids Res. 2012, 40:5034-5051.
108. Wan Y., Qu K., Zhang Q.C., Flynn R.A., Manor O., Ouyang Z., et al. Landscape and variation of RNA secondary structure across the human transcriptome. Nature 2014, 505:706-709.
109. Dogan H., Can H., Otu H.H. Whole genome sequence of a Turkish individual. PLoS One 2014, 9.
110. Fujimoto A., Nakagawa H., Hosono N., Nakano K., Abe T., Boroevich K.A., et al. Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nat. Genet. 2010, 42:931-936.
111. Sudmant P.H., Rausch T., Gardner E.J., Handsaker R.E., Abyzov A., Huddleston J., et al. An integrated map of structural variation in 2504 human genomes. Nature 2015, 526:75-81.
112. Abdulla M.A., Ahmed I., Assawamakin A., Bhak J., Brahmachari S.K., Calacal G.C., et al. Mapping human genetic diversity in Asia. Science 2009, 326:1541-1545. (New York, N.Y.).
113. Patowary A., Purkanti R., Singh M., Chauhan R.K., Bhartiya D., Dwivedi O.P., et al. Systematic analysis and functional annotation of variations in the genome of an Indian individual. Hum. Mutat. 2012, 33:1133-1140.
114. Ku C.S., Naidoo N., Wu M., Soong R. Studying the epigenome using next generation sequencing. J. Med. Genet. 2011, 48:721-730.
115. Zhao Q., Zhang Y. Epigenome sequencing comes of age in development, differentiation and disease mechanism research. Epigenomics 2011, 3:207-220.
116. Elsner M., Mak H.C. A modENCODE snapshot. Nat. Biotechnol. 2011, 29:238-240.
117. Muers M. Functional genomics: the modENCODE guide to the genome. Nat. Rev. Genet. 2011, 12:80.
118. Sivasubbu S., Sachidanandan C., Scaria V. Time for the zebrafish ENCODE. J. Genet. 2013, 92:695-701.
119. Bedell V.M., Wang Y., Campbell J.M., Poshusta T.L., Starker C.G., Krug R.G., et al. In vivo genome editing using a high-efficiency TALEN system. Nature 2012, 491:114-118.
120. Ding Q., Lee Y.K., Schaefer E.A., Peters D.T., Veres A., Kim K., et al. A TALEN genome-editing system for generating human stem cell-based disease models. Cell Stem Cell 2013, 12:238-251.
121. Gaj T., Gersbach C.A., Barbas C.F. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 2013, 31:397-405.
122. Sebat J., Lakshmi B., Troge J., Alexander J., Young J., Lundin P., et al. Large-scale copy number polymorphism in the human genome. Science 2004, 305:525-528. (New York, N.Y.).
123. Locke J.M., Lango Allen H., Harries L.W. A rare SNP in pre-miR-34a is associated with increased levels of miR-34a in pancreatic beta cells. Acta Diabetol. 2013.
124. Chatzikyriakidou A., Voulgari P.V., Georgiou I., Drosos A.A. The role of microRNA-146a (miR-146a) and its target IL-1R-associated kinase (IRAK1) in psoriatic arthritis susceptibility. Scand. J. Immunol. 2010, 71:382-385.
125. Christensen B.C., Avissar-Whiting M., Ouellet L.G., Butler R.A., Nelson H.H., McClean M.D., et al. Mature microRNA sequence polymorphism in MIR196A2 is associated with risk and prognosis of head and neck cancer. Clin. Cancer Res. 2010, 16:3713-3720.
126. Dou T., Wu Q., Chen X., Ribas J., Ni X., Tang C., et al. A polymorphism of microRNA196a genome region was associated with decreased risk of glioma in Chinese population. J. Cancer Res. Clin. Oncol. 2010, 136:1853-1859.
127. Hoffman A.E., Zheng T., Yi C., Leaderer D., Weidhaas J., Slack F., et al. MicroRNA miR-196a-and breast cancer: a genetic and epigenetic association study and functional analysis. Cancer Res. 2009, 69:5970-5977.
128. Hu Y., Yu C.Y., Wang J.L., Guan J., Chen H.Y., Fang J.Y. MicroRNA sequence polymorphisms and the risk of different types of cancer. Sci. Rep. 2014, 4:3648.
129. Kontorovich T., Levy A., Korostishevsky M., Nir U., Friedman E. Single nucleotide polymorphisms in miRNA binding sites and miRNA genes as breast/ovarian cancer risk modifiers in Jewish high-risk women. Int. J. Cancer 2010, 127:589-597.
130. Yang H., Dinney C.P., Ye Y., Zhu Y., Grossman H.B., Wu X. Evaluation of genetic variants in microRNA-related genes and risk of bladder cancer. Cancer Res. 2008, 68:2530-2537.
131. Peng S., Kuang Z., Sheng C., Zhang Y., Xu H., Cheng Q. Association of microRNA-196a-gene polymorphism with gastric cancer risk in a Chinese population. Dig. Dis. Sci. 2010, 55:2288-2293.
132. Ryan B.M., McClary A.C., Valeri N., Robinson D., Paone A., Bowman E.D., et al. rs4919510 in hsa-mir-608 is associated with outcome but not risk of colorectal cancer. PLoS One 2012, 7.
133. Shen J., Ambrosone C.B., DiCioccio R.A., Odunsi K., Lele S.B., Zhao H. A functional polymorphism in the miR-146a gene and age of familial breast/ovarian cancer diagnosis. Carcinogenesis 2008, 29:1963-1966.
134. Wang M., Ye Y., Qian H., Song Z., Jia X., Zhang Z., et al. Common genetic variants in pre-microRNAs are associated with risk of coal workers' pneumoconiosis. J. Hum. Genet. 2010, 55:13-17.
135. Xu B., Feng N.H., Li P.C., Tao J., Wu D., Zhang Z.D., et al. A functional polymorphism in Pre-miR-146a gene is associated with prostate cancer risk and mature miR-146a expression in vivo. Prostate 2010, 70:467-472.
136. Ye Y., Wang K.K., Gu J., Yang H., Lin J., Ajani J.A., et al. Genetic variations in microRNA-related genes are novel susceptibility loci for esophageal cancer risk. Cancer Prev. Res. (Phila.) 2008, 1:460-469.
137. Zhou B., Rao L., Peng Y., Wang Y., Chen Y., Song Y., et al. Common genetic polymorphisms in pre-microRNAs were associated with increased risk of dilated cardiomyopathy. Clin. Chim. Acta 2010, 411:1287-1290.
138. Bhattacharya A., Ziebarth J.D., Cui Y. PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways. Nucleic Acids Res. 2014, 42:D86-D91.
139. Gong J., Liu W., Zhang J., Miao X., Guo A.Y. lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse. Nucleic Acids Res. 2015, 43:D181-D186.
140. Guo L., Du Y., Chang S., Zhang K., Wang J. rSNPBase: a database for curated regulatory SNPs. Nucleic Acids Res. 2014, 42:D1033-D1039.
141. Ning S., Zhao Z., Ye J., Wang P., Zhi H., Li R., et al. LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs. BMC Bioinf. 2014, 15:152.
142. Ning S., Zhao Z., Ye J., Wang P., Zhi H., Li R., et al. SNP@lincTFBS: an integrated database of polymorphisms in human LincRNA transcription factor binding sites. PLoS One 2014, 9.
143. Chen G., Wang Z., Wang D., Qiu C., Liu M., Chen X., et al. LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res. 2013, 41:D983-D986.
144. Bhartiya D., Pal K., Ghosh S., Kapoor S., Jalali S., Panwar B., et al. lncRNome: a comprehensive knowledgebase of human long noncoding RNAs. Database 2013, (2013). (bat034).
145. Meyer L.R., Zweig A.S., Hinrichs A.S., Karolchik D., Kuhn R.M., Wong M., et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 2013, 41:D64-D69.
146. Sherry S.T., Ward M.H., Kholodov M., Baker J., Phan L., Smigielski E.M., et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001, 29:308-311.
147. Gray K.A., Daugherty L.C., Gordon S.M., Seal R.L., Wright M.W., Bruford E.A. Genenames.org: the HGNC resources in 2013. Nucleic Acids Res. 2013, 41:D545-D552.
148. Griffiths-Jones S., Grocock R.J., van Dongen S., Bateman A., Enright A.J. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 2006, 34:D140-D144.
149. Lestrade L., Weber M.J. snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res. 2006, 34:D158-D162.
150. Khorshid M., Rodak C., Zavolan M. CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic Acids Res. 2011, 39:D245-D252.
151. Yang J.H., Qu L.H. DeepBase: annotation and discovery of microRNAs and other noncoding RNAs from deep-sequencing data. Methods Mol. Biol. 2012, 822:233-248. Clifton, N.J.
152. Yang J.H., Shao P., Zhou H., Chen Y.Q., Qu L.H. DeepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res. 2010, 38:D123-D130.
153. Voight B.F., Kudaravalli S., Wen X., Pritchard J.K. A map of recent positive selection in the human genome. PLoS Biol. 2006, 4.
154. The International HapMap Project Nature 2003, 426:789-796.
155. Ahmed F., Kaundal R., Raghava G.P. PHDcleav: a SVM based method for predicting human Dicer cleavage sites using sequence and secondary structure of miRNA precursors. BMC Bioinf. 2013, 14(Suppl. 14):S9.
156. Ahmed F., Ansari H.R., Raghava G.P. Prediction of guide strand of microRNAs from its sequence and secondary structure. BMC Bioinf. 2009, 10:105.
157. Ding Y., Chan C.Y., Lawrence C.E. Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res. 2004, 32:W135-W141.
158. Gruber A.R., Lorenz R., Bernhart S.H., Neubock R., Hofacker I.L. The Vienna RNA websuite. Nucleic Acids Res. 2008, 36:W70-W74.
159. Scaria V., Hariharan M., Arora A., Maiti S. Quadfinder: server for identification and analysis of quadruplex-forming motifs in nucleotide sequences. Nucleic Acids Res. 2006, 34:W683-W685.
160. Salari R., Kimchi-Sarfaty C., Gottesman M.M., Przytycka T.M. Sensitive measurement of single-nucleotide polymorphism-induced changes of RNA conformation: application to disease studies. Nucleic Acids Res. 2013, 41:44-53.
161. Bailey T.L., Boden M., Buske F.A., Frith M., Grant C.E., Clementi L., et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009, 37:W202-W208.
162. Chang T.H., Huang H.Y., Hsu J.B., Weng S.L., Horng J.T., Huang H.D. An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. BMC Bioinf. 2013, 14(Suppl. 2):S4.
163. Garcia D.M., Baek D., Shin C., Bell G.W., Grimson A., Bartel D.P. Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-and other microRNAs. Nat. Struct. Mol. Biol. 2011, 18:1139-1146.
164. Witkos T.M., Koscianska E., Krzyzosiak W.J. Practical aspects of microRNA target prediction. Curr. Mol. Med. 2011, 11:93-109.
165. John B., Enright A.J., Aravin A., Tuschl T., Sander C., Marks D.S. Human MicroRNA targets. PLoS Biol. 2004, 2.
166. Agostini F., Zanzoni A., Klus P., Marchese D., Cirillo D., Tartaglia G.G. catRAPID omics: a web server for large-scale prediction of protein-RNA interactions. Bioinformatics 2013, 29:2928-2930. Oxford, England.