Impacts of variation in the human genome on gene regulation

Journal of Molecular Biology

Volumn 425, Issue 21, 2013, Pages 3970-3977

  Haraksingh, Rajini R ^a   Snyder, Michael P ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

gene expression; gene regulation; genetic variation; structural variation; transcription

Indexed keywords

DNA;

CODING; COPY NUMBER VARIATION; DNA SEQUENCE; GENE CONTROL; GENE DELETION; GENE EXPRESSION; GENETIC VARIABILITY; GENOME; HUMAN; HUMAN GENOME; PHENOTYPE; PRIORITY JOURNAL; REVIEW; RNA SEQUENCE;

CD; CNV; COPY NUMBER VARIATION; CROHN'S DISEASE; GENE EXPRESSION; GENE REGULATION; GENETIC VARIATION; MNV; MULTINUCLEOTIDE VARIANT; RNA SEQUENCING; RNA-SEQ; SINGLE-NUCLEOTIDE POLYMORPHISM; SINGLE-NUCLEOTIDE VARIANT; SNP; SNV; STRUCTURAL VARIATION; SV; TRANSCRIPTION;

GENE EXPRESSION REGULATION; GENETIC VARIATION; GENOME, HUMAN; HUMANS; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA;

EID: 84885188208     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2013.07.015     Document Type: Review

References (59)

1. G.R. Abecasis, A. Auton, L.D. Brooks, M.A. DePristo, R.M. Durbin, and R.E. Handsaker An integrated map of genetic variation from 1,092 human genomes Nature 491 2012 56 65
2. M.J. Clark, R. Chen, H.Y. Lam, K.J. Karczewski, G. Euskirchen, and A.J. Butte Performance comparison of exome DNA sequencing technologies Nat Biotechnol 29 2011 908 914
3. G.P. Consortium A map of human genome variation from population-scale sequencing Nature 467 2010 1061 1073
4. S.B. Montgomery, D.L. Goode, E. Kvikstad, C.A. Albers, Z.D. Zhang, and X.J. Mu The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes Genome Res 23 2013 749 761
5. G.H. Perry, N.J. Dominy, K.G. Claw, A.S. Lee, H. Fiegler, and R. Redon Diet and the evolution of human amylase gene copy number variation Nat Genet 39 2007 1256 1260
6. C. Stewart, D. Kural, M.P. Strömberg, J.A. Walker, M.K. Konkel, and A.M. Stütz A comprehensive map of mobile element insertion polymorphisms in humans PLoS Genet 7 2011 e1002236
7. R.E. Mills, K. Walter, C. Stewart, R.E. Handsaker, K. Chen, and C. Alkan Mapping copy number variation by population-scale genome sequencing Nature 470 2011 59 65
8. D.F. Conrad, D. Pinto, R. Redon, L. Feuk, O. Gokcumen, and Y. Zhang Origins and functional impact of copy number variation in the human genome Nature 464 2010 704 712
9. I.H. Consortium A haplotype map of the human genome Nature 437 2005 1299 1320
10. E. Tuzun, A.J. Sharp, J.A. Bailey, R. Kaul, V.A. Morrison, and L.M. Pertz Fine-scale structural variation of the human genome Nat Genet 37 2005 727 732
11. R. Redon, S. Ishikawa, K.R. Fitch, L. Feuk, G.H. Perry, and T.D. Andrews Global variation in copy number in the human genome Nature 444 2006 444 454
12. J.O. Korbel, A.E. Urban, J.P. Affourtit, B. Godwin, F. Grubert, and J.F. Simons Paired-end mapping reveals extensive structural variation in the human genome Science 318 2007 420 426
13. Ryan E. Mills, Klaudia Walter, Donald A. Stewart, Robert Handsaker, Chen Ken, and Can Alkan Mapping structural variation at fine-scale by population-scale genome sequencing 2010
14. E.S. Lander, L.M. Linton, B. Birren, C. Nusbaum, M.C. Zody, and J. Baldwin Initial sequencing and analysis of the human genome Nature 409 2001 860 921
15. B. Schuster-Böckler, D. Conrad, and A. Bateman Dosage sensitivity shapes the evolution of copy-number varied regions PLoS One 5 2010 e9474
16. Z. Wang, M. Gerstein, and M. Snyder RNA-Seq: a revolutionary tool for transcriptomics Nat Rev Genet 10 2009 57 63
17. J.Z. Levin, M. Yassour, X. Adiconis, C. Nusbaum, D.A. Thompson, and N. Friedman Comprehensive comparative analysis of strand-specific RNA sequencing methods Nat Methods 7 2010 709 715
18. B.S. Shastry SNPs: impact on gene function and phenotype Methods Mol Biol 578 2009 3 22
19. K. Usdin The biological effects of simple tandem repeats: lessons from the repeat expansion diseases Genome Res 18 2008 1011 1019
20. H.T. Orr, and H.Y. Zoghbi Trinucleotide repeat disorders Annu Rev Neurosci 30 2007 575 621
21. S.S. Deeb Genetics of variation in human color vision and the retinal cone mosaic Curr Opin Genet Dev 16 2006 301 307
22. Y. Cai, X. Yu, S. Hu, and J. Yu A brief review on the mechanisms of miRNA regulation Genomics Proteomics Bioinformatics 7 2009 147 154
23. I. Johansson, E. Lundqvist, L. Bertilsson, M.L. Dahl, F. Sjöqvist, and M. Ingelman-Sundberg Inherited amplification of an active gene in the cytochrome P450 CYP2D locus as a cause of ultrarapid metabolism of debrisoquine Proc Natl Acad Sci U S A 90 1993 11825 11829
24. S.A. McCarroll, A. Huett, P. Kuballa, S.D. Chilewski, A. Landry, and P. Goyette Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease 2008 Nat Genet
25. C.R. Marshall, and S.W. Scherer Detection and characterization of copy number variation in autism spectrum disorder Methods Mol Biol 838 2012 115 135
26. D.F. Levinson, J. Duan, S. Oh, K. Wang, A.R. Sanders, and J. Shi Copy number variants in schizophrenia: confirmation of five previous findings and new evidence for 3q29 microdeletions and VIPR2 duplications Am J Psychiatry 168 2011 302 316
27. D. Malhotra, S. McCarthy, J.J. Michaelson, V. Vacic, K.E. Burdick, and S. Yoon High frequencies of de novo CNVs in bipolar disorder and schizophrenia Neuron 72 2011 951 963
28. N. Pankratz, A. Dumitriu, K.N. Hetrick, M. Sun, J.C. Latourelle, and J.B. Wilk Copy number variation in familial Parkinson disease PLoS One 6 2011 e20988
29. Y. Kawamura, T. Otowa, A. Koike, N. Sugaya, E. Yoshida, and S. Yasuda A genome-wide CNV association study on panic disorder in a Japanese population J Hum Genet 56 2011 852 856
30. T.V. Fernandez, S.J. Sanders, I.R. Yurkiewicz, A.G. Ercan-Sencicek, Y.S. Kim, and D.O. Fishman Rare copy number variants in tourette syndrome disrupt genes in histaminergic pathways and overlap with autism Biol Psychiatry 71 2012 392 402
31. R. Pfundt, and J.A. Veltman Structural genomic variation in intellectual disability Methods Mol Biol 838 2012 77 95
32. R.A. Yeo, S.W. Gangestad, J. Liu, V.D. Calhoun, and K.E. Hutchison Rare copy number deletions predict individual variation in intelligence PLoS One 6 2011 e16339
33. E. Gonzalez, H. Kulkarni, H. Bolivar, A. Mangano, R. Sanchez, and G. Catano The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility Science 307 2005 1434 1440
34. E.J. Hollox, U. Huffmeier, P.L. Zeeuwen, R. Palla, J. Lascorz, and D. Rodijk-Olthuis Psoriasis is associated with increased beta-defensin genomic copy number Nat Genet 40 2008 23 25
35. Y. Zhang, R. Haraksingh, F. Grubert, A. Abyzov, M. Gerstein, and S. Weissman Child development and structural variation in the human genome Child Dev 84 2013 34 48
36. A. Dauber, Y. Yu, M.C. Turchin, C.W. Chiang, Y.A. Meng, and E.W. Demerath Genome-wide association of copy-number variation reveals an association between short stature and the presence of low-frequency genomic deletions Am J Hum Genet 89 2011 751 759
37. R. Hai, Y.F. Pei, H. Shen, L. Zhang, X.G. Liu, and Y. Lin Genome-wide association study of copy number variation identified gremlin1 as a candidate gene for lean body mass J Hum Genet 57 2012 33 37
38. B.E. Stranger, M.S. Forrest, M. Dunning, C.E. Ingle, C. Beazley, and N. Thorne Relative impact of nucleotide and copy number variation on gene expression phenotypes Science 315 2007 848 853
39. M. Kasowski, F. Grubert, C. Heffelfinger, M. Hariharan, A. Asabere, and S.M. Waszak Variation in transcription factor binding among humans Science 328 2010 232 235
40. A. Schlattl, S. Anders, S.M. Waszak, W. Huber, and J.O. Korbel Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions Genome Res 21 2011 2004 2013
41. R. Luo, S.J. Sanders, Y. Tian, I. Voineagu, N. Huang, and S.H. Chu Genome-wide transcriptome profiling reveals the functional impact of rare de novo and recurrent CNVs in autism spectrum disorders Am J Hum Genet 91 2012 38 55
42. L. Harewood, E. Chaignat, and A. Reymond Structural variation and its effect on expression Methods Mol Biol 838 2012 173 186
43. C.N. Henrichsen, E. Chaignat, and A. Reymond Copy number variants, diseases and gene expression Hum Mol Genet 18 2009 R1 R8
44. A. Itsara, G.M. Cooper, C. Baker, S. Girirajan, J. Li, and D. Absher Population analysis of large copy number variants and hotspots of human genetic disease Am J Hum Genet 84 2009 148 161
45. S. Girirajan, Z. Brkanac, B.P. Coe, C. Baker, L. Vives, and T.H. Vu Relative burden of large CNVs on a range of neurodevelopmental phenotypes PLoS Genet 7 2011 e1002334
46. C.N. Henrichsen, N. Vinckenbosch, S. Zöllner, E. Chaignat, S. Pradervand, and F. Schütz Segmental copy number variation shapes tissue transcriptomes Nat Genet 41 2009 424 429
47. A. Reymond, C.N. Henrichsen, L. Harewood, and G. Merla Side effects of genome structural changes Curr Opin Genet Dev 17 2007 381 386
48. L. Harewood, F. Schütz, S. Boyle, P. Perry, M. Delorenzi, and W.A. Bickmore The effect of translocation-induced nuclear reorganization on gene expression Genome Res 20 2010 554 564
49. T.E. Reddy, J. Gertz, F. Pauli, K.S. Kucera, K.E. Varley, and K.M. Newberry Effects of sequence variation on differential allelic transcription factor occupancy and gene expression Genome Res 22 2012 860 869
50. E.P. Consortium The ENCODE (ENCyclopedia Of DNA Elements) Project Science 306 2004 636 640
51. E. Birney, J.A. Stamatoyannopoulos, A. Dutta, R. Guigó, T.R. Gingeras, and E.H. Margulies Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature 447 2007 799 816
52. E.P. Consortium A user's guide to the encyclopedia of DNA elements (ENCODE) PLoS Biol 9 2011 e1001046
53. I. Dunham, A. Kundaje, S.F. Aldred, P.J. Collins, C.A. Davis, and F. Doyle An integrated encyclopedia of DNA elements in the human genome Nature 489 2012 57 74
54. R. Chen, G.I. Mias, J. Li-Pook-Than, L. Jiang, H.Y. Lam, and E. Miriami Personal omics profiling reveals dynamic molecular and medical phenotypes Cell 148 2012 1293 1307
55. C. Cheng, R. Alexander, R. Min, J. Leng, K.Y. Yip, and J. Rozowsky Understanding transcriptional regulation by integrative analysis of transcription factor binding data Genome Res 22 2012 1658 1667
56. J. Wang, J. Zhuang, S. Iyer, X. Lin, T.W. Whitfield, and M.C. Greven Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors Genome Res 22 2012 1798 1812
57. Y. Gilad Using genomic tools to study regulatory evolution Methods Mol Biol 856 2012 335 361
58. L.J. Core, J.J. Waterfall, and J.T. Lis Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters Science 322 2008 1845 1848
59. L.S. Churchman, and J.S. Weissman Nascent transcript sequencing visualizes transcription at nucleotide resolution Nature 469 2011 368 373