Gutierrez-Arcelus M, Rich SS, Raychaudhuri S. Autoimmune diseases - connecting risk alleles with molecular traits of the immune system. Nat Rev Genet. 2016;17(3):160–74.
Article
Google Scholar
Ramos PS, Shedlock AM, Langefeld CD. Genetics of autoimmune diseases: insights from population genetics. J Hum Genet. 2015;60(11):657–64.
Article
CAS
Google Scholar
Visscher PM, Wray NR, Zhang Q, Sklar P, McCarthy MI, Brown MA, Yang J. 10 years of GWAS discovery: biology, function, and translation. Am J Hum Genet. 2017;101(1):5–22.
Article
CAS
Google Scholar
Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, et al. Finding the missing heritability of complex diseases. Nature. 2009;461(7265):747–53.
Article
CAS
Google Scholar
Farh KK-H, Marson A, Zhu J, Kleinewietfeld M, Housley WJ, Beik S, Shoresh N, Whitton H, Ryan RJ, Shishkin AA. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature. 2015;518(7539):337–43.
Article
CAS
Google Scholar
Consortium EP. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57–74.
Article
Google Scholar
Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, et al. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 2010;28(10):1045–8.
Article
CAS
Google Scholar
Bujold D, Morais DAL, Gauthier C, Cote C, Caron M, Kwan T, Chen KC, Laperle J, Markovits AN, Pastinen T, et al. The International Human Epigenome Consortium Data Portal. Cell Syst. 2016;3(5):496–9 e492.
Article
CAS
Google Scholar
Heinz S, Romanoski CE, Benner C, Glass CK. The selection and function of cell type-specific enhancers. Nat Rev Mol Cell Biol. 2015;16(3):144–54.
Article
CAS
Google Scholar
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007;39(3):311–8.
Article
CAS
Google Scholar
Bonev B, Cavalli G. Organization and function of the 3D genome. Nat Rev Genet. 2016;17(11):661–78.
Article
CAS
Google Scholar
Gómez-Díaz E, Corces VG. Architectural proteins: regulators of 3D genome organization in cell fate. Trends Cell Biol. 2014;24(11):703–11.
Article
Google Scholar
Nichols MH, Corces VG. A CTCF code for 3D genome architecture. Cell. 2015;162(4):703–5.
Article
CAS
Google Scholar
Krijger PHL, De Laat W. Regulation of disease-associated gene expression in the 3D genome. Nat Rev Mol Cell Biol. 2016;17(12):771–82
Article
CAS
Google Scholar
Yu M, Ren B. The three-dimensional organization of mammalian genomes. Annu Rev Cell Dev Biol. 2017;33:265–89.
Article
CAS
Google Scholar
Schaffner W. Enhancers, enhancers–from their discovery to today’s universe of transcription enhancers. Biol Chem. 2015;396(4):311–27.
Article
CAS
Google Scholar
Martin P, McGovern A, Orozco G, Duffus K, Yarwood A, Schoenfelder S, Cooper NJ, Barton A, Wallace C, Fraser P, Worthington J, Eyre S. Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci. Nat Commun. 2015;6:10069.
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485(7398):376–80.
Article
CAS
Google Scholar
Cremer T, Kurz A, Zirbel R, Dietzel S, Rinke B, Schröck E, Speicher MR, Mathieu U, Jauch A, Emmerich P. Role of chromosome territories in the functional compartmentalization of the cell nucleus. Cold Spring Harb Symp Quant Biol. 1993;58:777–92.
Article
CAS
Google Scholar
Bouwman BA, de Laat W. Getting the genome in shape: the formation of loops, domains and compartments. Genome Biol. 2015;16:154.
Lieberman-Aiden E, Van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326(5950):289–93.
Article
CAS
Google Scholar
Fortin JP, Hansen KD. Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data. Genome Biol. 2015;16:180.
Article
Google Scholar
Wang SY, Su JH, Beliveau BJ, Bintu B, Moffitt JR, Wu CT, Zhuang XW. Spatial organization of chromatin domains and compartments in single chromosomes. Science. 2016;353(6299):598–602.
Article
CAS
Google Scholar
Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berkum NL, Meisig J, Sedat J. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature. 2012;485(7398):381–5.
Article
CAS
Google Scholar
Sanborn AL, Rao SS, Huang S-C, Durand NC, Huntley MH, Jewett AI, Bochkov ID, Chinnappan D, Cutkosky A, Li J. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Proc Natl Acad Sci U S A. 2015;112(47):E6456–65.
Article
CAS
Google Scholar
Hansen AS, Pustova I, Cattoglio C, Tjian R, Darzacq X. CTCF and cohesin regulate chromatin loop stability with distinct dynamics. eLife. 2017;6:e25776.
Fudenberg G, Pollard K. Chromatin features constrain structural variation across evolutionary timescales. bioRxiv. 2018:285205.
Schmitt AD, Hu M, Jung I, Xu Z, Qiu YJ, Tan CL, Li Y, Lin S, Lin YI, Barr CL, et al. A compendium of chromatin contact maps reveals spatially active regions in the human genome. Cell Rep. 2016;17(8):2042–59.
Article
CAS
Google Scholar
Hnisz D, Day DS, Young RA. Insulated neighborhoods: structural and functional units of mammalian gene control. Cell. 2016;167(5):1188–200.
Article
CAS
Google Scholar
Dowen JM, Fan ZP, Hnisz D, Ren G, Abraham BJ, Zhang LN, Weintraub AS, Schuijers J, Lee TI, Zhao K. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell. 2014;159(2):374–87.
Article
CAS
Google Scholar
Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV. A map of the cis-regulatory sequences in the mouse genome. Nature. 2012;488(7409):116–20.
Article
CAS
Google Scholar
Katainen R, Dave K, Pitkänen E, Palin K, Kivioja T, Välimäki N, Gylfe AE, Ristolainen H, Hänninen UA, Cajuso T. CTCF/cohesin-binding sites are frequently mutated in cancer. Nat Genet. 2015;47(7):818–21.
Article
CAS
Google Scholar
Schmitt AD, Hu M, Ren B. Genome-wide mapping and analysis of chromosome architecture. Nat Rev Mol Cell Biol. 2016;17(12):743–55.
Article
CAS
Google Scholar
Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002;295(5558):1306–11.
Article
CAS
Google Scholar
Hagege H, Klous P, Braem C, Splinter E, Dekker J, Cathala G, De Laat W, Forné T. Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat Protoc. 2007;2(7):1722.
Article
CAS
Google Scholar
Nakagawa H, Chadwick RB, Peltomäki P, Plass C, Nakamura Y, de la Chapelle A. Loss of imprinting of the insulin-like growth factor II gene occurs by biallelic methylation in a core region of H19-associated CTCF-binding sites in colorectal cancer. Proc Natl Acad Sci U S A. 2001;98(2):591–6.
Article
CAS
Google Scholar
Kurukuti S, Tiwari VK, Tavoosidana G, Pugacheva E, Murrell A, Zhao Z, Lobanenkov V, Reik W, Ohlsson R. CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2. Proc Natl Acad Sci U S A. 2006;103(28):10684–9.
Article
CAS
Google Scholar
Nativio R, Sparago A, Ito Y, Weksberg R, Riccio A, Murrell A. Disruption of genomic neighbourhood at the imprinted IGF2-H19 locus in Beckwith–Wiedemann syndrome and Silver–Russell syndrome. Hum Mol Genet. 2011;20(7):1363–74.
Article
CAS
Google Scholar
Flavahan WA, Drier Y, Liau BB, Gillespie SM, Venteicher AS, Stemmer-Rachamimov AO, Suvà ML, Bernstein BE. Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature. 2016;529(7584):110–4.
Article
CAS
Google Scholar
Zhao Z, Tavoosidana G, Sjölinder M, Göndör A, Mariano P, Wang S, Kanduri C, Lezcano M, Sandhu KS, Singh U. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra-and interchromosomal interactions. Nat Genet. 2006;38(11):1341–7.
Article
CAS
Google Scholar
Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006;16(10):1299–309.
Article
CAS
Google Scholar
Hughes JR, Roberts N, McGowan S, Hay D, Giannoulatou E, Lynch M, De Gobbi M, Taylor S, Gibbons R, Higgs DR. Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet. 2014;46(2):205.
Article
CAS
Google Scholar
Durand NC, Robinson JT, Shamim MS, Machol I, Mesirov JP, Lander ES, Aiden EL. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Syst. 2016;3(1):99–101.
Article
CAS
Google Scholar
Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen C-A, Schmitt AD, Espinoza CA, Ren B. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature. 2013;503(7475):290.
Article
CAS
Google Scholar
Belaghzal H, Dekker J, Gibcus JH. Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. Methods. 2017;123:56–65.
Article
CAS
Google Scholar
Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, Cairns J, Wingett SW, Varnai C, Thiecke MJ, et al. Lineage-specific genome architecture links enhancers and non-coding disease variants to target gene promoters. Cell. 2016;167(5):1369–1384.e19.
Article
CAS
Google Scholar
Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, Laue ED, Tanay A, Fraser P. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature. 2013;502(7469):59–64.
Article
CAS
Google Scholar
Ramani V, Deng X, Qiu R, Gunderson KL, Steemers FJ, Disteche CM, Noble WS, Duan Z, Shendure J. Massively multiplex single-cell Hi-C. Nat Methods. 2017;14(3):263–6.
Article
CAS
Google Scholar
Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH. An oestrogen-receptor-α-bound human chromatin interactome. Nature. 2009;462(7269):58–64.
Article
CAS
Google Scholar
Mumbach MR, Rubin AJ, Flynn RA, Dai C, Khavari PA, Greenleaf WJ, Chang HY. HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nat Methods. 2016;13(11):919–22.
Article
CAS
Google Scholar
Fang R, Yu M, Li G, Chee S, Liu T, Schmitt AD, Ren B. Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq. Cell Res. 2016;26(12):1345–48.
Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR. Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements. Nat Genet. 2017;49(11):1602–12.
Article
CAS
Google Scholar
Kerpedjiev P, Abdennur N, Lekschas F, McCallum C, Dinkla K, Strobelt H, Luber JM, Ouellette SB, Ahzir A, Kumar N, Hwang J, Lee S, Alver BH, Pfister H, Mirny LA, Park PJ, Gehlenberg N. HiGlass: Web-based visual exploration and analysis of genome interaction maps. Genome Biology. 2018;19:125.
Lareau CA, Aryee MJ. Hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data. Nat Methods. 2018;15(3):155.
Article
CAS
Google Scholar
Wang S, Wen F, Wiley GB, Kinter MT, Gaffney PM. An enhancer element harboring variants associated with systemic lupus erythematosus engages the TNFAIP3 promoter to influence A20 expression. PLoS Genet. 2013;9(9):e1003750.
Article
CAS
Google Scholar
Graham RR, Cotsapas C, Davies L, Hackett R, Lessard CJ, Leon JM, Burtt NP, Guiducci C, Parkin M, Gates C. Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus. Nat Genet. 2008;40(9):1059–61.
Article
CAS
Google Scholar
Wang S, Wen F, Tessneer KL, Gaffney PM. TALEN-mediated enhancer knockout influences TNFAIP3 gene expression and mimics a molecular phenotype associated with systemic lupus erythematosus. Genes Immun. 2016;17(3):165–70.
Article
CAS
Google Scholar
Hernandez-Miranda LR, Ruffault P-L, Bouvier JC, Murray AJ, Morin-Surun M-P, Zampieri N, Cholewa-Waclaw JB, Ey E, Brunet J-F, Champagnat J. Genetic identification of a hindbrain nucleus essential for innate vocalization. Proc Natl Acad Sci U S A. 2017;114(30):8095–100.
Article
CAS
Google Scholar
McGovern A, Schoenfelder S, Martin P, Massey J, Duffus K, Plant D, Yarwood A, Pratt AG, Anderson AE, Isaacs JD. Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23. Genome Biol. 2016;17(1):212.
Article
Google Scholar
Hnisz D, Weintraub AS, Day DS, Valton A-L, Bak RO, Li CH, Goldmann J, Lajoie BR, Fan ZP, Sigova AA. Activation of proto-oncogenes by disruption of chromosome neighborhoods. Science. 2016;351(6280):1454–58.
Article
CAS
Google Scholar
Witcher M, Emerson BM. Epigenetic silencing of the p16INK4a tumor suppressor is associated with loss of CTCF binding and a chromatin boundary. Mol Cell. 2009;34(3):271–84.
Article
CAS
Google Scholar
Xiang J-F, Yin Q-F, Chen T, Zhang Y, Zhang X-O, Wu Z, Zhang S, Wang H-B, Ge J, Lu X. Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus. Cell Res. 2014;24(5):513–31.
Article
CAS
Google Scholar
Schmiedel BJ, Seumois G, Samaniego-Castruita D, Cayford J, Schulten V, Chavez L, Ay F, Sette A, Peters B, Vijayanand P. 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells. Nat Commun. 2016;7:13426.
Article
CAS
Google Scholar
Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O’shea CC, Park PJ, Ren B. The 4D nucleome project. Nature. 2017;549(7671):219.
Article
CAS
Google Scholar