Distinct patterns of genetic variations in potential functional elements in long noncoding RNAs

Human Mutation

Volumn 35, Issue 2, 2014, Pages 192-201

  Bhartiya, Deeksha ^a,b   Jalali, Saakshi ^a,b   Ghosh, Sourav ^a,b   Scaria, Vinod ^a  

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

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

Author keywords

Disease; Genome; Long noncoding RNAs; Variation

Indexed keywords

LONG UNTRANSLATED RNA;

ARTICLE; BINDING SITE; GENE; GENE FREQUENCY; GENE LOCUS; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOTYPE PHENOTYPE CORRELATION; HUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CODING GENE; PROTEIN RNA BINDING; RNA PROCESSING; RNA SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM;

DISEASE; GENOME; LONG NONCODING RNAS; VARIATION;

ANIMALS; BINDING SITES; COMPUTATIONAL BIOLOGY; GENE FREQUENCY; GENETIC VARIATION; GENOME; GENOME-WIDE ASSOCIATION STUDY; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; RNA, LONG NONCODING;

EID: 84891907341     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.22472     Document Type: Article

References (75)

1. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. 2010. A map of human genome variation from population-scale sequencing. Nature 467:1061-1073.
2. Ahn SM, Kim TH, Lee S, Kim D, Ghang H, Kim DS, Kim BC, Kim SY, Kim WY, Kim C, Park D, Lee YS, et al. 2009. The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res 19:1622-1629.
3. Altmann A, Weber P, Bader D, Preuss M, Binder EB, Muller-Myhsok B. 2012. A beginners guide to SNP calling from high-throughput DNA-sequencing data. Hum Genet 131:1541-1554.
4. Amiel J, de PL, Henrion-Caude A. 2012. miRNA, development and disease. Adv Genet 80:1-36.
5. Askarian-Amiri ME, Crawford J, French JD, Smart CE, Smith MA, Clark MB, Ru K, Mercer TR, Thompson ER, Lakhani SR, Vargas AC, Campbell IG, et al. 2011. SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA 17:878-891.
6. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53-59.
7. Bhartiya D, Kapoor S, Jalali S, Sati S, Kaushik K, Sachidanandan C, Sivasubbu S, Scaria V. 2012a. Conceptual approaches for lncRNA drug discovery and future strategies. Expert Opin Drug Discov 7:503-513.
8. Bhartiya D, Laddha SV, Mukhopadhyay A, Scaria V. 2011. miRvar: a comprehensive database for genomic variations in microRNAs. Hum Mutat 32:E2226-E2245.
9. Bhartiya D, Pal K, Ghosh S, Kapoor S, Jalali S, Panwar B, Jain S, Sati S, Sengupta S, Sachidanandan C, Raghava GP, Sivasubbu S, et al. 2013. lncRNome: a comprehensive knowledgebase of human long noncoding RNAs. Database (Oxford) 2013:bat034.
10. Bhartiya D, Talwar J, Hasija Y, Scaria V. 2012b. Systematic curation and analysis of genomic variations and their potential functional consequences in snoRNA loci. Hum Mutat 33:E2367-E2374.
11. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, et al. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816.
12. Borel C, Antonarakis SE. 2008. Functional genetic variation of human miRNAs and phenotypic consequences. Mamm Genome 19:503-509.
13. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. 2011. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25:1915-1927.
14. Chen G, Qiu C, Zhang Q, Liu B, Cui Q. 2012. Genome-wide analysis of human SNPs at long intergenic noncoding RNAs. Hum Mutat:10.
15. Cirulli ET, Kasperaviciute D, Attix DK, Need AC, Ge D, Gibson G, Goldstein DB. 2010. Common genetic variation and performance on standardized cognitive tests. Eur J Hum Genet 18:815-820.
16. Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G, Dahl F, Fernandez A, et al. 2010. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327:78-81.
17. Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J, Kaul R, Khatun J, Lajoie BR, et al. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489:57-74.
18. ENCODE Project Consortium. 2004. The ENCODE (encyclopedia of DNA elements) Project. Science 306:636-640.
19. Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, et al. 2007. A second generation human haplotype map of over 3.1 million SNPs. Nature 449:851-861.
20. Goldman M, Craft B, Swatloski T, Ellrott K, Cline M, Diekhans M, Ma S, Wilks C, Stuart J, Haussler D, Zhu J. 2013. The UCSC Cancer Genomics Browser: update 2013. Nucleic Acids Res 41:D949-D954.
21. Gonzaga-Jauregui C, Lupski JR, Gibbs RA. 2012. Human genome sequencing in health and disease. Annu Rev Med 63:35-61.
22. Gutschner T, Hammerle M, Eissmann M, Hsu J, Kim Y, Hung G, Revenko A, Arun G, Stentrup M, Gross M, Zornig M, Macleod AR, Spector DL, Diederichs S. 2013. The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells. Cancer Res.
23. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, et al. 2009. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458:223-227.
24. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr., Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, et al. 2010. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141:129-141.
25. Hall LL, Lawrence JB. 2010. XIST RNA and architecture of the inactive X chromosome: implications for the repeat genome. Cold Spring Harb Symp Quant Biol 75:345-356.
26. Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, et al. 2006. GENCODE: producing a reference annotation for ENCODE. Genome Biol 7:S4-S9.
27. Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, et al. 2012. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 22:1760-1774.
28. 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.
29. Holley CL, Topkara VK. 2011. An introduction to small non-coding RNAs: miRNA and snoRNA. Cardiovasc Drugs Ther 25:151-159.
30. Internaltional HapMap Consortium. 2003. The International HapMap Project. Nature 426:789-796.
31. Jalali S, Bhartiya D, Lalwani MK, Sivasubbu S, Scaria V. 2013. Systematic transcriptome wide analysis of lncRNA-miRNA interactions. PLoS One 8:e53823.
32. Jalali S, Jayaraj GG, Scaria V. 2012. Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs. Biol Direct 7:25-27.
33. Jarinova O, Ekker M. 2012. Regulatory variations in the era of next-generation sequencing: implications for clinical molecular diagnostics. Hum Mutat 33: 1021-1030.
34. Jin G, Sun J, Isaacs SD, Wiley KE, Kim ST, Chu LW, Zhang Z, Zhao H, Zheng SL, Isaacs WB, Xu J. 2011. Human polymorphisms at long non-coding RNAs (lncRNAs) and association with prostate cancer risk. Carcinogenesis 32:1655-1659.
35. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermuller J, Hofacker IL, Bell I, Cheung E, et al. 2007a. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316:1484-1488.
36. Kapranov P, Willingham AT, Gingeras TR. 2007b. Genome-wide transcription and the implications for genomic organization. Nat Rev Genet 8:413-423.
37. Kim HK, Prokunina-Olsson L, Chanock SJ. 2012. Common genetic variants in miR-1206 (8q24.2) and miR-612 (11q13.3) affect biogenesis of mature miRNA forms. PLoS One 7:e47454.
38. Kim SY, Lohmueller KE, Albrechtsen A, Li Y, Korneliussen T, Tian G, Grarup N, Jiang T, Andersen G, Witte D, Jorgensen T, Hansen T, et al. 2011. Estimation of allele frequency and association mapping using next-generation sequencing data. BMC Bioinformatics 12:231.
39. Kumar V, Westra HJ, Karjalainen J, Zhernakova DV, Esko T, Hrdlickova B, Almeida R, Zhernakova A, Reinmaa E, Vosa U, Hofker MH, Fehrmann RS, et al. 2013. Human disease-associated genetic variation impacts large intergenic non-coding RNA expression. PLoS Genet 9:e1003201.
40. Kutter C, Watt S, Stefflova K, Wilson MD, Goncalves A, Ponting CP, Odom DT, Marques AC. 2012. Rapid turnover of long noncoding RNAs and the evolution of gene expression. PLoS Genet 8:e1002841.
41. Lee SK, Calin GA. 2011. Non-coding RNAs and cancer: new paradigms in oncology. Discov Med 11:245-254.
42. Leonardo TR, Schultheisz HL, Loring JF, Laurent LC. 2012. The functions of microRNAs in pluripotency and reprogramming. Nat Cell Biol 14:1114-1121.
43. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, Lin Y, MacDonald JR, et al. 2007. The diploid genome sequence of an individual human. PLoS Biol 5:e254.
44. Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J. 2009. SNP detection for massively parallel whole-genome resequencing. Genome Res 19:1124-1132.
45. Li H, Ruan J, Durbin R. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18:1851-1858.
46. Liao J, Yu L, Mei Y, Guarnera M, Shen J, Li R, Liu Z, Jiang F. 2010. Small nucleolar RNA signatures as biomarkers for non-small-cell lung cancer. Mol Cancer 9:198.
47. Linhares JJ, Azevedo M Jr., Siufi AA, de Carvalho CV, Wolgien MD, Noronha EC, Bonetti TC, da Silva ID. 2012. Evaluation of single nucleotide polymorphisms in microRNAs (hsa-miR-196a2 rs11614913 C/T) from Brazilian women with breast cancer. BMC Med Genet 13:119.
48. Mansiaux Y, Carrat F. 2012. Contribution of genome-wide association studies to scientific research: a bibliometric survey of the citation impacts of GWAS and candidate gene studies published during the same period and in the same journals. PLoS One 7:e51408.
49. McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, Zhang Z, Ranade SS, et al. 2009. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 19:1527-1541.
50. Mercer TR, Dinger ME, Mattick JS. 2009. Long non-coding RNAs: insights into functions. Nat Rev Genet 10:155-159.
51. Mishra PJ, Bertino JR. 2009. MicroRNA polymorphisms: the future of pharmacogenomics, molecular epidemiology and individualized medicine. Pharmacogenomics 10:399-416.
52. Mo YY. 2012. MicroRNA regulatory networks and human disease. Cell Mol Life Sci 69:3529-3531.
53. Moran VA, Perera RJ, Khalil AM. 2012. Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs. Nucleic Acids Res 40:6391-6400.
54. Mu XJ, Lu ZJ, Kong Y, Lam HY, 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.
55. Nagano T, Fraser P. 2011. No-nonsense functions for long noncoding RNAs. Cell 145:178-181.
56. Nie L, Wu HJ, Hsu JM, Chang SS, Labaff AM, Li CW, Wang Y, Hsu JL, Hung MC. 2012. Long non-coding RNAs: versatile master regulators of gene expression and crucial players in cancer. Am J Transl Res 4:127-150.
57. Paraskevopoulou MD, Georgakilas G, Kostoulas N, Reczko M, Maragkakis M, Dalamagas TM, Hatzigeorgiou AG. 2013. DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Nucleic Acids Res 41:D239-D245.
58. Pastinen T. 2010. Genome-wide allele-specific analysis: insights into regulatory variation. Nat Rev Genet 11:533-538.
59. Patowary A, Purkanti R, Singh M, Chauhan RK, Bhartiya D, Dwivedi OP, Chauhan G, Bharadwaj D, Sivasubbu S, Scaria V. 2012. Systematic analysis and functional annotation of variations in the genome of an Indian individual. Hum Mutat 33:1133-1140.
60. Pushkarev D, Neff NF, Quake SR. 2009. Single-molecule sequencing of an individual human genome. Nat Biotechnol 27:847-850.
61. Reis EM, Nakaya HI, Louro R, Canavez FC, Flatschart AV, Almeida GT, Egidio CM, Paquola AC, Machado AA, Festa F, Yamamoto D, Alvarenga R, et al. 2004. Antisense intronic non-coding RNA levels correlate to the degree of tumor differentiation in prostate cancer. Oncogene 23:6684-6692.
62. Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, et al. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409:928-933.
63. Salleh MZ, Lee LS, Ismet RI, Patowary A, Joshi K, Pasha A, Ahmed AZ, Janor RM, Hamzah AS, et al. 2013. Systematic pharmacogenomics analysis of a Malay whole genome: proof of concept for personalized medicine. PLoS One 23:e71554.
64. Scaria V, Pasha A. 2012. Long non-coding RNAs in infection biology. Front Genet 3:308.
65. Smigielski EM, Sirotkin K, Ward M, Sherry ST. 2000. dbSNP: a database of single nucleotide polymorphisms. Nucleic Acids Res 28:352-355.
66. Spitale RC, Tsai MC, Chang HY. 2011. RNA templating the epigenome: long noncoding RNAs as molecular scaffolds. Epigenetics 6:539-543.
67. Tano K, Akimitsu N. 2012. Long non-coding RNAs in cancer progression. Front Genet 3:219.
68. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, et al. 2001. The sequence of the human genome. Science 291:1304-1351.
69. Voight BF, Kudaravalli S, Wen X, Pritchard JK. 2006. A map of recent positive selection in the human genome. PLoS Biol 4:e72.
70. Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Zhang J, Guo Y, Feng B, et al. 2008. The diploid genome sequence of an Asian individual. Nature 456:60-65.
71. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, et al. 2008. The complete genome of an individual by massively parallel DNA sequencing. Nature 452: 872-876.
72. Wutz A, Gribnau J. 2007. X inactivation Xplained. Curr Opin Genet Dev 17:387-393.
73. Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH. 2011. starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. Nucleic Acids Res 39:D202-D209.
74. Yang JH, Shao P, Zhou H, Chen YQ, Qu LH. 2010. deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res 38:D123-D130.
75. Zhong S, Chen Z, Xu J, Li W, Zhao J. 2012. Pre-mir-27a rs895819 polymorphism and cancer risk: a meta-analysis. Mol Biol Rep 40:3181-3186.