Genetic and epigenetic regulation of human lincrna gene expression

American Journal of Human Genetics

Volumn 93, Issue 6, 2013, Pages 1015-1026

  Popadin, Konstantin ^a,b,c   Gutierrez Arcelus, Maria ^a,b,d   Dermitzakis, Emmanouil T ^a,b,d,e   Antonarakis, Stylianos E ^a,b  

^a UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

^b Institute of Genetics and Genomics in Geneva (iGE3)   (Switzerland)

^c INSTITUTE FOR INFORMATION TRANSMISSION PROBLEMS   (Russian Federation)

^d SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^e KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA;

ARTICLE; CONTROLLED STUDY; DNA METHYLATION; ENHANCER REGION; EXON; FIBROBLAST; GENE CONTROL; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC REGULATION; GENETIC VARIABILITY; HUMAN; HUMAN CELL; HUMAN GENOME; LYMPHOBLASTOID CELL LINE; PRIORITY JOURNAL; PROMOTER REGION; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; T LYMPHOCYTE; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION;

CELL LINE; CHROMOSOME MAPPING; ENHANCER ELEMENTS, GENETIC; EPIGENESIS, GENETIC; EPIGENOMICS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; OPEN READING FRAMES; ORGAN SPECIFICITY; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; RNA, LONG NONCODING; TRANSCRIPTION INITIATION SITE;

EID: 84890256130     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2013.10.022     Document Type: Article

References (47)

1. J.T. Lee Epigenetic regulation by long noncoding RNAs Science 338 2012 1435 1439
2. P.A. Latos, F.M. Pauler, M.V. Koerner, H.B. Şenergin, Q.J. Hudson, R.R. Stocsits, W. Allhoff, S.H. Stricker, R.M. Klement, and K.E. Warczok Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing Science 338 2012 1469 1472
3. J. Ponjavic, P.L. Oliver, G. Lunter, and C.P. Ponting Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain PLoS Genet. 5 2009 e1000617
4. A. Pauli, J.L. Rinn, and A.F. Schier Non-coding RNAs as regulators of embryogenesis Nat. Rev. Genet. 12 2011 136 149
5. J.L. Rinn, and H.Y. Chang Genome regulation by long noncoding RNAs Annu. Rev. Biochem. 81 2012 145 166
6. I. Ulitsky, and D.P. Bartel lincRNAs: genomics, evolution, and mechanisms Cell 154 2013 26 46
7. A.M. Khalil, M. Guttman, M. Huarte, M. Garber, A. Raj, D. Rivea Morales, K. Thomas, A. Presser, B.E. Bernstein, and A. van Oudenaarden Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression Proc. Natl. Acad. Sci. USA 106 2009 11667 11672
8. M. Guttman, I. Amit, M. Garber, C. French, M.F. Lin, D. Feldser, M. Huarte, O. Zuk, B.W. Carey, and J.P. Cassady Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals Nature 458 2009 223 227
9. M. Guttman, J. Donaghey, B.W. Carey, M. Garber, J.K. Grenier, G. Munson, G. Young, A.B. Lucas, R. Ach, and L. Bruhn lincRNAs act in the circuitry controlling pluripotency and differentiation Nature 477 2011 295 300
10. T. Derrien, R. Johnson, G. Bussotti, A. Tanzer, S. Djebali, H. Tilgner, G. Guernec, D. Martin, A. Merkel, and D.G. Knowles The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression Genome Res. 22 2012 1775 1789
11. M. Guttman, and J.L. Rinn Modular regulatory principles of large non-coding RNAs Nature 482 2012 339 346
12. J. Ponjavic, C.P. Ponting, and G. Lunter Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs Genome Res. 17 2007 556 565
13. D. Managadze, I.B. Rogozin, D. Chernikova, S.A. Shabalina, and E.V. Koonin Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs Genome Biol. Evol. 3 2011 1390 1404
14. T.R. Mercer, M.E. Dinger, S.M. Sunkin, M.F. Mehler, and J.S. Mattick Specific expression of long noncoding RNAs in the mouse brain Proc. Natl. Acad. Sci. USA 105 2008 716 721
15. M.E. Dinger, P.P. Amaral, T.R. Mercer, K.C. Pang, S.J. Bruce, B.B. Gardiner, M.E. Askarian-Amiri, K. Ru, G. Soldà, and C. Simons Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation Genome Res. 18 2008 1433 1445
16. M.N. Cabili, C. Trapnell, L. Goff, M. Koziol, B. Tazon-Vega, A. Regev, and J.L. Rinn Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses Genes Dev. 25 2011 1915 1927
17. M.B. Clark, R.L. Johnston, M. Inostroza-Ponta, A.H. Fox, E. Fortini, P. Moscato, M.E. Dinger, and J.S. Mattick Genome-wide analysis of long noncoding RNA stability Genome Res. 22 2012 885 898
18. V.G. Cheung, R.S. Spielman, K.G. Ewens, T.M. Weber, M. Morley, and J.T. Burdick Mapping determinants of human gene expression by regional and genome-wide association Nature 437 2005 1365 1369
19. S.B. Montgomery, M. Sammeth, M. Gutierrez-Arcelus, R.P. Lach, C. Ingle, J. Nisbett, R. Guigo, and E.T. Dermitzakis Transcriptome genetics using second generation sequencing in a Caucasian population Nature 464 2010 773 777
20. J.K. Pickrell, J.C. Marioni, A.A. Pai, J.F. Degner, B.E. Engelhardt, E. Nkadori, J.-B. Veyrieras, M. Stephens, Y. Gilad, and J.K. Pritchard Understanding mechanisms underlying human gene expression variation with RNA sequencing Nature 464 2010 768 772
21. B.E. Stranger, M.S. Forrest, A.G. Clark, M.J. Minichiello, S. Deutsch, R. Lyle, S. Hunt, B. Kahl, S.E. Antonarakis, and S. Tavaré Genome-wide associations of gene expression variation in humans PLoS Genet. 1 2005 e78
22. A.S. Dimas, B.E. Stranger, C. Beazley, R.D. Finn, C.E. Ingle, M.S. Forrest, M.E. Ritchie, P. Deloukas, S. Tavaré, and E.T. Dermitzakis Modifier effects between regulatory and protein-coding variation PLoS Genet. 4 2008 e1000244
23. B.E. Stranger, A.C. Nica, M.S. Forrest, A. Dimas, C.P. Bird, C. Beazley, C.E. Ingle, M. Dunning, P. Flicek, and D. Koller Population genomics of human gene expression Nat. Genet. 39 2007 1217 1224
24. J.F. Degner, A.A. Pai, R. Pique-Regi, J.-B. Veyrieras, D.J. Gaffney, J.K. Pickrell, S. De Leon, K. Michelini, N. Lewellen, and G.E. Crawford DNasecI sensitivity QTLs are a major determinant of human expression variation Nature 482 2012 390 394
25. M. Gutierrez-Arcelus, T. Lappalainen, S.B. Montgomery, A. Buil, H. Ongen, A. Yurovsky, J. Bryois, T. Giger, L. Romano, and A. Planchon Passive and active DNA methylation and the interplay with genetic variation in gene regulation Elife 2 2013 e00523
26. J.C. Fay, and P.J. Wittkopp Evaluating the role of natural selection in the evolution of gene regulation Heredity (Edinb) 100 2008 191 199
27. S. Kudaravalli, J.-B. Veyrieras, B.E. Stranger, E.T. Dermitzakis, and J.K. Pritchard Gene expression levels are a target of recent natural selection in the human genome Mol. Biol. Evol. 26 2009 649 658
28. B.L. Browning, and S.R. Browning A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals Am. J. Hum. Genet. 84 2009 210 223
29. M. Bibikova, Z. Lin, L. Zhou, E. Chudin, E.W. Garcia, B. Wu, D. Doucet, N.J. Thomas, Y. Wang, and E. Vollmer High-throughput DNA methylation profiling using universal bead arrays Genome Res. 16 2006 383 393
30. M. Scutari Learning Bayesian Networks with the bnlearn R Package J. Stat. Softw. 35 2010 1 22
31. J. Harrow, A. Frankish, J.M. Gonzalez, E. Tapanari, M. Diekhans, F. Kokocinski, B.L. Aken, D. Barrell, A. Zadissa, and S. Searle GENCODE: The reference human genome annotation for The ENCODE Project Genome Res. 22 2012 1760 1774
32. J. Ernst, P. Kheradpour, T.S. Mikkelsen, N. Shoresh, L.D. Ward, C.B. Epstein, X. Zhang, L. Wang, R. Issner, and M. Coyne Mapping and analysis of chromatin state dynamics in nine human cell types Nature 473 2011 43 49
33. J. Ernst, and M. Kellis Discovery and characterization of chromatin states for systematic annotation of the human genome Nat. Biotechnol. 28 2010 817 825
34. A.P. Boyle, S. Davis, H.P. Shulha, P. Meltzer, E.H. Margulies, Z. Weng, T.S. Furey, and G.E. Crawford High-resolution mapping and characterization of open chromatin across the genome Cell 132 2008 311 322
35. I. Ulitsky, A. Shkumatava, C.H. Jan, H. Sive, and D.P. Bartel Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution Cell 147 2011 1537 1550
36. C. Andreini, L. Banci, I. Bertini, and A. Rosato Counting the zinc-proteins encoded in the human genome J. Proteome Res. 5 2006 196 201
37. V. Kumar, H.-J. Westra, J. Karjalainen, D.V. Zhernakova, T. Esko, B. Hrdlickova, R. Almeida, A. Zhernakova, E. Reinmaa, and U. Võsa Human disease-associated genetic variation impacts large intergenic non-coding RNA expression PLoS Genet. 9 2013 e1003201
38. U.A. ∅rom, and R. Shiekhattar Long non-coding RNAs and enhancers Curr. Opin. Genet. Dev. 21 2011 194 198
39. J.T. Bell, A.A. Pai, J.K. Pickrell, D.J. Gaffney, R. Pique-Regi, J.F. Degner, Y. Gilad, and J.K. Pritchard DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines Genome Biol. 12 2011 R10
40. J.R. Gibbs, M.P. van der Brug, D.G. Hernandez, B.J. Traynor, M.A. Nalls, S.-L. Lai, S. Arepalli, A. Dillman, I.P. Rafferty, and J. Troncoso Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain PLoS Genet. 6 2010 e1000952
41. M. Kulis, S. Heath, M. Bibikova, A.C. Queirós, A. Navarro, G. Clot, A. Martínez-Trillos, G. Castellano, I. Brun-Heath, and M. Pinyol Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia Nat. Genet. 44 2012 1236 1242
42. K.R. van Eijk, S. de Jong, M.P.M. Boks, T. Langeveld, F. Colas, J.H. Veldink, C.G.F. de Kovel, E. Janson, E. Strengman, and P. Langfelder Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects BMC Genomics 13 2012 636
43. D. Zhang, L. Cheng, J.A. Badner, C. Chen, Q. Chen, W. Luo, D.W. Craig, M. Redman, E.S. Gershon, and C. Liu Genetic control of individual differences in gene-specific methylation in human brain Am. J. Hum. Genet. 86 2010 411 419
44. Y. Gilad, A. Oshlack, and S.A. Rifkin Natural selection on gene expression Trends Genet. 22 2006 456 461
45. M.M. Albà, and J. Castresana Inverse relationship between evolutionary rate and age of mammalian genes Mol. Biol. Evol. 22 2005 598 606
46. Y.I. Wolf, P.S. Novichkov, G.P. Karev, E.V. Koonin, and D.J. Lipman The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages Proc. Natl. Acad. Sci. USA 106 2009 7273 7280
47. A. Vishnoi, S. Kryazhimskiy, G.A. Bazykin, S. Hannenhalli, and J.B. Plotkin Young proteins experience more variable selection pressures than old proteins Genome Res. 20 2010 1574 1581