Higher-order chromatin domains link eQTLs with the expression of far-away genes

Nucleic Acids Research

Volumn 42, Issue 1, 2014, Pages 87-96

  Duggal, Geet ^a   Wang, Hao ^a   Kingsford, Carl ^a  

^a Carnegie Mellon University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMATIN STRUCTURE; CHROMOSOME 1; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; GENE EXPRESSION REGULATION; GENE FREQUENCY; GENE INTERACTION; GENE MUTATION; GENE TARGETING; GENETIC ASSOCIATION; GENETIC DISTANCE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROMOTER REGION; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; CHROMATIN; CONFORMATION; GENE CONTROL; GENE EXPRESSION; HUMAN; HUMAN CELL; POINT MUTATION; REGULATORY SEQUENCE;

EID: 84891780257     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt857     Document Type: Article

References (35)

1. Gilad, Y., Rifkin, S.A. and Pritchard, J.K. (2008) Revealing the architecture of gene regulation: The promise of eQTL studies. Trends Genet., 24, 408-415
2. Cheung, V.G. and Spielman, R.S. (2009) Genetics of human gene expression: Mapping DNA variants that influence gene expression. Nat. Rev. Genet., 10, 595-604
3. Cookson, W., Liang, L., Abecasis, G., Moffatt, M. and Lathrop, M. (2009) Mapping complex disease traits with global gene expression. Nat. Rev. Genet., 10, 184-194
4. Davison, L.J., Wallace, C., Cooper, J.D., Cope, N.F., Wilson, N.K., Smyth, D.J., Howson, J.M., Saleh, N., Al-Jeffery, A., Angus, K.L. et al. (2012) Long-range DNA looping and gene expression analyses identify DEXI as an autoimmune disease candidate gene. Hum. Mol. Genet., 21, 322-333
5. Harismendy, O., Notani, D., Song, X., Rahim, N.G., Tanasa, B., Heintzman, N., Ren, B., Fu, X-D., Topol, E.J., Rosenfeld, M.G. et al. (2011) 9p21 DNA variants associated with coronary artery disease impair interferon- signalling response. Nature, 470, 264-268
6. Meyer, K.B., Maia, A.T., O'Reilly, M., Ghoussaini, M., Prathalingam, R., Porter-Gill, P., Ambs, S., Prokunina-Olsson, L., Carroll, J. and Ponder, B.A. (2011) A functional variant at a prostate cancer predisposition locus at 8q24 is associated with PVT1 expression. PLoS Genet., 7, e1002165
7. Sotelo, J., Esposito, D., Duhagon, M.A., Banfield, K., Mehalko, J., Liao, H., Stephens, R.M., Harris, T.J., Munroe, D.J. and Wu, X. (2010) Long-range enhancers on 8q24 regulate c-Myc. Proc. Natl Acad. Sci. USA, 107, 3001-3005
8. Sandhu, K.S., Li, G., Poh, H.M., Quek, Y.L.K., Sia, Y.Y., Peh, S.Q., Mulawadi, F.H., Lim, J., Sikic, M., Menghi, F. et al. (2012) Largescale functional organization of long-range chromatin interaction networks. Cell Rep., 2, 1207-1219
9. Wang, D., Rendon, A. and Wernisch, L. (2013) Transcription factor and chromatin features predict genes associated with eQTLs. Nucleic Acids Res., 41, 1450-1463
10. Gaffney, D.J., Veyrieras, J.B., Degner, J.F., Pique-Regi, R., Pai, A.A., Crawford, G.E., Stephens, M., Gilad, Y., Pritchard, J.K. et al. (2012) Dissecting the regulatory architecture of gene expression QTLs. Genome Biol., 13, R7
11. Dixon, J.R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J.S. and Ren, B. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485, 376-380
12. deWit, E. and deLaat, W. (2012) A decade of 3C technologies: Insights into nuclear organization. Genes Dev., 26, 11-24
13. Gibcus, J.H. and Dekker, J. (2013) The hierarchy of the 3D genome. Mol. Cell, 49, 773-782
14. Dimas, A.S., Deutsch, S., Stranger, B.E., Montgomery, S.B., Borel, C., Attar-Cohen, H., Ingle, C., Beazley, C., Arcelus, M.G., Sekowska, M. et al. (2009) Common regulatory variation impacts gene expression in a cell type-dependent manner. Science, 325, 1246-1250
15. Veyrieras, J.B., Kudaravalli, S., Kim, S.Y., Dermitzakis, E.T., Gilad, Y., Stephens, M. and Pritchard, J.K. (2008) High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet., 4, e1000214
16. Zeller, T., Wild, P., Szymczak, S., Rotival, M., Schillert, A., Castagne, R., Maouche, S., Germain, M., Lackner, K., Rossmann, H. et al. (2010) Genetics and beyond-The transcriptome of human monocytes and disease susceptibility. PLoS One, 5, e10693
17. Myers, A.J., Gibbs, J.R., Webster, J.A., Rohrer, K., Zhao, A., Marlowe, L., Kaleem, M., Leung, D., Bryden, L., Nath, P. et al. (2007) A survey of genetic human cortical gene expression. Nat. Genet., 39, 1494-1499
18. Schadt, E., Molony, C., Chudin, E., Hao, K., Yang, X., Lum, P.Y., Kasarskis, A., Zhang, B., Wang, S., Suver, C. et al. (2008) Mapping the genetic architecture of gene expression in human liver. PLoS Biol., 6, e107
19. Pickrell, J.K., Marioni, J.C., Pai, A.A., Degner, J.F., Engelhardt, B.E., Nkadori, E., Veyrieras, J.B., Stephens, M., Gilad, Y. and Pritchard, J.K. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature, 464, 768-772
20. Stranger, B.E., Nica, A.C., Forrest, M.S., Dimas, A., Bird, C.P., Beazley, C., Ingle, C.E., Dunning, M., Flicek, P., Koller, D. et al. (2007) Population genomics of human gene expression. Nat. Genet., 39, 1217-1224
21. Innocenti, F., Cooper, G.M., Stanaway, I.B., Gamazon, E.R., Smith, J.D., Mirkov, S., Ramirez, J., Liu, W., Lin, Y.S., Moloney, C. et al. (2011) Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue. PLoS Genet., 7, e1002078
22. Lieberman-Aiden, E., van Berkum, N.L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B.R., Sabo, P.J., Dorschner, M.O. et al. (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 326, 289-293
23. Yaffe, E. and Tanay, A. (2011) Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat. Genet., 43, 1059-1065
24. Filippova, D., Patro, R., Duggal, G. and Kingsford, C. (2013) Multiscale identification of topological domains in chromatin. To appear in Proceedings of the 13th Workshop on Algorithms in Bioinformatics (WABI), Vol. 8126, pp. 300-312
25. Flicek, P., Amode, M.R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S. et al. (2012) Ensembl 2012. Nucleic Acids Res., 40, D84-D90
26. Huang, B. and Jebara, T. (2011) Fast b-matching via sufficient selection belief propagation. In: Proceedings of the Fourteenth International Conference on Artificial Intelligence and Statistics
27. Niven, D.J., Berthiaume, L.R., Fick, G.H. and Laupland, K.B. (2012) Matched case-control studies: A review of reported statistical methodology. Clin. Epidemiol., 4, 99
28. Witten, D.M. and Noble, W.S. (2012) On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements. Nucleic Acids Res., 40, 3849-3855
29. Hwang, Y.C., Zheng, Q., Gregory, B.D. and Wang, L.S. (2013) High-Throughput identification of long-range regulatory elements and their target promoters in the human genome. Nucleic Acids Res., 41, 4835-4846
30. Degner, J.F., Pai, A.A., Pique-Regi, R., Veyrieras, J.B., Gaffney, D.J., Pickrell, J.K., DeLeon, S., Michelini, K., Lewellen, N., Crawford, G.E. et al. (2012) DNaseI sensitivity QTLs are a major determinant of human expression variation. Nature, 482, 390-394
31. Nora, E., Dekker, J and Heard, E. (2013) Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods? Bioessays, 35, 818-828
32. Bickmore, W.A. and van Steensel, B. (2013) Genome architecture: Domain organization of interphase chromosomes. Cell, 152, 1270-1284
33. Fudenberg, G., Getz, G., Meyerson, M. and Mirny, L.A. (2011) High order chromatin architecture shapes the landscape of chromosomal alterations in cancer. Nat. Biotechnol., 29, 1109-1113
34. Kalhor, R., Tjong, H., Jayathilaka, N., Alber, F. and Chen, L. (2011) Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat. Biotechnol., 30, 90-98
35. Zhang, Y., McCord, R.P., Ho, Y-J., Lajoie, B.R., Hildebrand, D.G., Simon, A.C., Becker, M.S., Alt, F.W. and Dekker, J. (2012) Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell, 148, 908-921