Effects of GWAS-associated genetic variants on lncRNAs within IBD and T1D candidate loci

PLoS ONE

Volumn 9, Issue 8, 2014, Pages

  Mirza, Aashiq H ^a,b,c   Kaur, Simranjeet ^a,b   Brorsson, Caroline A ^a   Pociot, Flemming ^a,c  

^a GENTOFTE UNIVERSITY HOSPITAL   (Denmark)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA;

ARTICLE; CONTROLLED STUDY; DNA FLANKING REGION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; INFLAMMATORY BOWEL DISEASE; INSULIN DEPENDENT DIABETES MELLITUS; PHENOTYPE; QUANTITATIVE TRAIT LOCUS; RNA CONFORMATION; RNA SEQUENCE; RNA STRUCTURE; SINGLE NUCLEOTIDE POLYMORPHISM; TISSUE SPECIFICITY; ANIMAL; BIOSYNTHESIS; FEMALE; GENETICS; GENOME-WIDE ASSOCIATION STUDY; HUMAN; MALE; METABOLISM; MOUSE; RAT;

ANIMALS; DIABETES MELLITUS, TYPE 1; FEMALE; GENETIC LOCI; GENOME-WIDE ASSOCIATION STUDY; HUMANS; INFLAMMATORY BOWEL DISEASES; LINKAGE DISEQUILIBRIUM; MALE; MICE; POLYMORPHISM, SINGLE NUCLEOTIDE; RATS; RNA, LONG NONCODING;

EID: 84937502692     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0105723     Document Type: Article

References (77)

1. Ponting CP, Oliver PL, Reik W (2009) Evolution and functions of long noncoding RNAs. Cell 136: 629-641.
2. Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, et al. (2010) Long noncoding RNAs with enhancer-like function in human cells. Cell 143: 46-58.
3. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, et al. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25: 1915-1927.
4. Chodroff RA, Goodstadt L, Sirey TM, Oliver PL, Davies KE, et al. (2010) Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes. Genome Biol 11: R72.
5. Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, et al. (2009) Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol 7: e1000112.
6. Kino T, Hurt DE, Ichijo T, Nader N, Chrousos GP (2010) Noncoding RNA gas5 is a growth arrest-and starvation-associated repressor of the glucocorticoid receptor. Sci Signal 3: ra8.
7. Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, et al. (2013) Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment. Cell 152: 570-583.
8. Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG, et al. (2005) A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Sci Signal 309: 1570.
9. Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, et al. (2010) The nuclearretained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 39: 925-938.
10. Cabianca DS, Casa V, Bodega B, Xynos A, Ginelli E, et al. (2012) A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell 149: 819-831.
11. Meola N, Pizzo M, Alfano G, Surace EM, Banfi S (2012) The long noncoding RNA Vax2os1 controls the cell cycle progression of photoreceptor progenitors in the mouse retina. RNA 18: 111-123.
12. Hung T, Wang Y, Lin MF, Koegel AK, Kotake Y, et al. (2011) Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet 43: 621-629.
13. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, et al. (2010) Long noncoding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464: 1071-1076.
14. Mercer TR, Dinger ME, Mattick JS (2009) Long non-coding RNAs: insights into functions. Nat Rev Genet 10: 155-159.
15. Wang KC, Chang HY (2011) Molecular mechanisms of long noncoding RNAs. Mol Cell 43: 904-914.
16. Guttman M, Rinn JL (2012) Modular regulatory principles of large non-coding RNAs. Nature 482: 339-346.
17. Selbach M, Schwanhäusser B, Thierfelder N, Fang Z, Khanin R, et al. (2008) Widespread changes in protein synthesis induced by microRNAs. Nature 455: 58-63.
18. Nagano T, Fraser P (2011) No-nonsense functions for long noncoding RNAs. Cell 145: 178-181.
19. Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, et al. (2011) A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147: 358-369.
20. Wilusz JE, Sunwoo H, Spector DL (2009) Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 23: 1494-1504.
21. Xu Z, Wei W, Gagneur J, Clauder-Münster S, Smolik M, et al (2011) Antisense expression increases gene expression variability and locus interdependency. Mol Syst Biol 7: 468
22. Wapinski O, Chang HY (2011) Long noncoding RNAs and human disease. Trends Cell Biol 21: 354-361.
23. Chen G, Wang Z, Wang D, Qiu C, Liu M, et al. (2013) LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res 41: D983-D986.
24. Pasmant E, Sabbagh A, Vidaud M, Bièche I (2011) ANRIL, a long, noncoding RNA, is an unexpected major hotspot in GWAS. FASEB J 25: 444-448.
25. Carpenter S, Aiello D, Atianand MK, Ricci EP, Gandhi P, et al. (2013) A long noncoding RNA mediates both activation and repression of immune response genes. Science 341: 789-792.
26. Martin L, Chang HY (2012) Uncovering the role of genomic "dark matter" in human disease. J Clin Invest 122: 1589-1595.
27. Jendrzejewski J, He H, Radomska HS, Li W, Tomsic J, et al. (2012) 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 109: 8646-8651.
28. Moran I, Akerman l, van de Bunt M, Xie R, Benazra M, et al. (2012) Human β cell transcriptome analysis uncovers lncRNAs that are tissue-specific, dynamically regulated, and abnormally expressed in type 2 diabetes. Cell Metab 16: 435-448.
29. McCarthy MI, Hirschhorn JN (2008) Genome-wide association studies: potential next steps on a genetic journey. Hum Mol Genet 17: R156-R165.
30. Altshuler D, Daly MJ, Lander ES (2008) Genetic mapping in human disease. Science 322: 881-888.
31. Lettre G, Rioux JD (2008) Autoimmune diseases: insights from genome-wide association studies. Hum Mol Genet 17: R116-R121.
32. Pennisi E (2010) 1000 Genomes Project gives new map of genetic diversity. Science 330: 574-575.
33. Kumar V, Wijmenga C, Withoff S (2012) From genome-wide association studies to disease mechanisms: celiac disease as a model for autoimmune diseases. Semin Immunopathol 34: 567-580
34. 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.
35. Chen G, Qiu C, Zhang Q, Liu B, Cui Q (2013) Genome-Wide Analysis of Human SNPs at Long Intergenic Noncoding RNAs. Human Mutat 34: 338- 344.
36. Kumar V, Westra HJ, Karjalainen J, Zhernakova DV, Esko T, et al. (2013) Human disease-associated genetic variation impacts large intergenic non-coding RNA expression. PLoS Genet 9: e1003201.
37. Michaelson JJ, Loguercio S, Beyer A (2009) Detection and interpretation of expression quantitative trait loci (eQTL). Methods 48: 265-276.
38. Halvorsen M, Martin JS, Broadaway S, Laederach A (2010) Disease-associated mutations that alter the RNA structural ensemble. PLoS Genet 6: e1001074.
39. Wang K, Baldassano R, Zhang H, Qu HQ, Imielinski M, et al. (2010) Comparative genetic analysis of inflammatory bowel disease and type 1 diabetes implicates multiple loci with opposite effects. Hum Mol Genet 19: 2059-2067.
40. Kapranov P, Willingham AT, Gingeras TR (2007) Genome-wide transcription and the implications for genomic organization. Nat Rev Genet 8: 413-423. (Pubitemid 46789245)
41. Costantini M, Bernardi G (2008) Replication timing, chromosomal bands, and isochores. Proc. Natl. Acad. Sci. USA 105: 3433-3437. (Pubitemid 351723570)
42. Cohen N, Dagan T, Stone L, Graur D (2005) GC composition of the human genome: in search of isochores. Mol Biol Evol. 22: 1260-1272. (Pubitemid 40577764)
43. Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, et al. (2012) Annotation of functional variation in personal genomes using RegulomeDB. Genome Res 22: 1790-1797.
44. Lonsdale J, Thomas J, Salvatore M, Phillips R, Lo E, et al. (2013) The Genotype-Tissue Expression (GTEx) project. Nat Genet 45: 580-585.
45. Voight BF, Kudaravalli S, Wen X, Pritchard JK (2006) A map of recent positive selection in the human genome. PLoS Biol 4: e72.
46. Di Rienzo A, Hudson RR (2005) An evolutionary framework for common diseases: the ancestral-susceptibility model. Trends Genet 21: 596-601. (Pubitemid 41429287)
47. Stefansson H, Helgason A, Thorleifsson G, Steinthorsdottir V, Masson G, et al. (2005) A common inversion under selection in Europeans. Nat Genet 37: 129-137.
48. Vander Molen J, Frisse LM, Fullerton SM, Qian Y, Del Bosque-Plata L, et al. (2005) Population Genetics of CAPN10 and GPR35: Implications for the Evolution of Type 2 Diabetes Variants. Am J Hum Genet 76: 548-560. (Pubitemid 40432163)
49. Gibbs RA, Belmont JW, Hardenbol P, Willis TD, Yu F, et al. (2003) The International HapMap project. Nature 426: 789-796.
50. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, et al. (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22: 1775-1789.
51. Cooper JD, Smyth DJ, Smiles AM, Plagnol V, Walker NM, et al. (2008) Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. Nat Genet 40: 1399-1401.
52. Barrett JC, Clayton DG, Concannon P, Akolkar B, Cooper JD, et al. (2009) Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nat Genet 41: 703-707.
53. Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, et al. (2008) Genomewide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet 40: 955-962.
54. Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, et al. (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477: 295-300.
55. Niazi F, Valadkhan S (2012) Computational analysis of functional long noncoding RNAs reveals lack of peptide-coding capacity and parallels with 3′ UTRs. RNA 18: 825-843.
56. Gong C, Maquat LE (2011) lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 39 UTRs via Alu elements. Nature 470: 284-288.
57. Burd CE, Jeck WR, Liu Y, Sanoff HK, Wang Z, et al. (2010) Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet 6: e1001233.
58. Harismendy O, Notani D, Song X, Rahim NG, Tanasa B, et al. (2011) 9p21 DNA variants associated with coronary artery disease impair interferon-y signalling response. Nature 470: 264-268.
59. Petretto E, Bottolo L, Langley SR, Heinig M, McDermott-Roe C, et al. (2010) New insights into the genetic control of gene expression using a Bayesian multi-tissue approach. PLoS Comput Biol 6:e1000737.
60. Grundberg E, Small KS, Hedman AK, Nica AC, Buil A, et al. (2012) Mapping cis- and trans-regulatory effects across multiple tissues in twins. Nat Genet 44: 1084-1089.
61. Fay JC, Wittkopp PJ (2008) Evaluating the role of natural selection in the evolution of gene regulation. Heredity (Edinb) 100: 191-199. (Pubitemid 351156873)
62. Kudaravalli S, Veyrieras JB, Stranger BE, Dermitzakis ET, Pritchard JK (2009) Gene expression levels are a target of recent natural selection in the human genome. Mol Biol Evol 26: 649-658.
63. Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS (2008) Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A 105: 716-721. (Pubitemid 351171774)
64. Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce JS, et al. (2008) Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 18: 1433-1445.
65. Roychoudhuri R, Hirahara K, Mousavi K, Clever D, Klebanoff CA, et al. (2013) BACH2 represses effector programs to stabilize T(reg)-mediated immune homeostasis. Nature 498: 506-10.
66. International Parkinson's Disease Genomics Consortium (IPDGC), Wellcome Trust Case Control Consortium 2 (WTCCC2) (2011) A two-stage meta-analysis identifies several new loci for Parkinson's disease. PLoS Genet 7:e1002142.
67. Martin JS, Halvorsen M, Davis-Neulander L, Ritz J, Gopinath C, et al. (2012) Structural effects of linkage disequilibrium on the transcriptome. RNA. 18: 77-87.
68. Merelli I, Viti F, Milanesi L (2012) IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis. BMC Bioinformatics 13: S5.
69. Burren OS, Adlem EC, Achuthan P, Christensen M, Coulson RM, et al. (2011) T1DBase: update 2011, organization and presentation of large-scale data sets for type 1 diabetes research. Nucleic Acids Res 39: D997-D1001.
70. Xie C, Yuan J, Li H, Li M, Zhao G, et al. (2013) NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res 42: D98-D103.
71. Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, et al. (2012) Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 491: 119-124.
72. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
73. Smit AFA, Hubley R, Green P. RepeatMasker website. Available: http://repeatmasker.org Version: open-4.0.3 (RMLib: 20130422 & Dfam: 1.2). Accessed 2013 June 19.
74. Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, et al. (2013) RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs. Human Mutat 34: 546-556.
75. Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-10. (Pubitemid 34679544)
76. ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
77. Johnson AD, Handsaker RE, Pulit S, Nizzari MM, O'Donnell CJ, et al. (2008) SNAP: A web-based tool for identification and annotation of proxy SNPs using HapMap. Bioinformatics 24: 2938-2939. Kidney Diseases