Bickmore WA. The spatial organization of the human genome. Annu Rev Genomics Hum Genet. 2013;14:67–84.
Article
CAS
PubMed
Google Scholar
Bonora G, Plath K, Denholtz M. A mechanistic link between gene regulation and genome architecture in mammalian development. Curr Opin Genet Dev. 2014;27:92–101.
Article
CAS
PubMed
Google Scholar
de Laat W, Duboule D. Topology of mammalian developmental enhancers and their regulatory landscapes. Nature. 2013;502:499–506.
Article
PubMed
Google Scholar
Cancer Genome Atlas N. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490:61–70.
Article
Google Scholar
Stephens PJ, Tarpey PS, Davies H, Van Loo P, Greenman C, Wedge DC, et al. The landscape of cancer genes and mutational processes in breast cancer. Nature. 2012;486:400–4.
PubMed Central
CAS
PubMed
Google Scholar
Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, et al. Mutational landscape and significance across 12 major cancer types. Nature. 2013;502:333–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Suva ML, Riggi N, Bernstein BE. Epigenetic reprogramming in cancer. Science. 2013;339:1567–70.
Article
CAS
PubMed
Google Scholar
Zink D, Fischer AH, Nickerson JA. Nuclear structure in cancer cells. Nat Rev Cancer. 2004;4:677–87.
Article
CAS
PubMed
Google Scholar
Dey P. Cancer nucleus: morphology and beyond. Diagn Cytopathol. 2010;38:382–90.
PubMed
Google Scholar
Gibcus JH, Dekker J. The hierarchy of the 3D genome. Mol Cell. 2013;49:773–82.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cremer T, Cremer M, Dietzel S, Muller S, Solovei I, Fakan S. Chromosome territories--a functional nuclear landscape. Curr Opin Cell Biol. 2006;18:307–16.
Article
CAS
PubMed
Google Scholar
Cremer M, von Hase J, Volm T, Brero A, Kreth G, Walter J, et al. Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells. Chromosome Res. 2001;9:541–67.
Article
CAS
PubMed
Google Scholar
Bolzer A, Kreth G, Solovei I, Koehler D, Saracoglu K, Fauth C, et al. Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol. 2005;3:e157.
Article
PubMed Central
PubMed
Google Scholar
Cremer T, Cremer M. Chromosome territories. Cold Spring Harb Perspect Biol. 2010;2:a003889.
Article
PubMed Central
PubMed
Google Scholar
Nye AC, Rajendran RR, Stenoien DL, Mancini MA, Katzenellenbogen BS, Belmont AS. Alteration of large-scale chromatin structure by estrogen receptor. Mol Cell Biol. 2002;22:3437–49.
Article
PubMed Central
CAS
PubMed
Google Scholar
Meaburn KJ, Gudla PR, Khan S, Lockett SJ, Misteli T. Disease-specific gene repositioning in breast cancer. J Cell Biol. 2009;187:801–12.
Article
PubMed Central
CAS
PubMed
Google Scholar
Meaburn KJ, Misteli T. Locus-specific and activity-independent gene repositioning during early tumorigenesis. J Cell Biol. 2008;180:39–50.
Article
PubMed Central
CAS
PubMed
Google Scholar
Roix JJ, McQueen PG, Munson PJ, Parada LA, Misteli T. Spatial proximity of translocation-prone gene loci in human lymphomas. Nat Genet. 2003;34:287–91.
Article
CAS
PubMed
Google Scholar
Rocha PP, Micsinai M, Kim JR, Hewitt SL, Souza PP, Trimarchi T, et al. Close proximity to Igh is a contributing factor to AID-mediated translocations. Mol Cell. 2012;47:873–85.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhang Y, McCord RP, Ho YJ, Lajoie BR, Hildebrand DG, Simon AC, et al. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell. 2012;148:908–21.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326:289–93.
Article
PubMed Central
CAS
PubMed
Google Scholar
McCord RP, Nazario-Toole A, Zhang H, Chines PS, Zhan Y, Erdos MR, et al. Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome. Genome Res. 2013;23:260–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Seitan VC, Faure AJ, Zhan Y, McCord RP, Lajoie BR, Ing-Simmons E, et al. Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments. Genome Res. 2013;23:2066–77.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485:376–80.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature. 2012;485:381–5.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nora EP, Dekker J, Heard E. Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods? Bioessays. 2013;35:818–28.
Article
PubMed Central
CAS
PubMed
Google Scholar
Giorgetti L, Galupa R, Nora EP, Piolot T, Lam F, Dekker J, et al. Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription. Cell. 2014;157:950–63.
Article
PubMed Central
CAS
PubMed
Google Scholar
Le Dily F, Bau D, Pohl A, Vicent GP, Serra F, Soronellas D, et al. Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation. Genes Dev. 2014;28:2151–62.
Article
PubMed Central
PubMed
Google Scholar
Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature. 2009;462:58–64.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012;148:84–98.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hah N, Murakami S, Nagari A, Danko CG, Kraus WL. Enhancer transcripts mark active estrogen receptor binding sites. Genome Res. 2013;23:1210–23.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hsu PY, Hsu HK, Lan X, Juan L, Yan PS, Labanowska J, et al. Amplification of distant estrogen response elements deregulates target genes associated with tamoxifen resistance in breast cancer. Cancer Cell. 2013;24:197–212.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mourad R, Hsu PY, Juan L, Shen C, Koneru P, Lin H, et al. Estrogen induces global reorganization of chromatin structure in human breast cancer cells. PLoS One. 2014;9:e113354.
Article
PubMed Central
PubMed
Google Scholar
Wang J, Lan X, Hsu PY, Hsu HK, Huang K, Parvin J, et al. Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation. BMC Genomics. 2013;14:70.
Article
PubMed Central
CAS
PubMed
Google Scholar
Osmanbeyoglu HU, Lu KN, Oesterreich S, Day RS, Benos PV, Coronnello C, et al. Estrogen represses gene expression through reconfiguring chromatin structures. Nucleic Acids Res. 2013;41:8061–71.
Article
PubMed Central
CAS
PubMed
Google Scholar
Barnett DH, Sheng S, Charn TH, Waheed A, Sly WS, Lin CY, et al. Estrogen receptor regulation of carbonic anhydrase XII through a distal enhancer in breast cancer. Cancer Res. 2008;68:3505–15.
Article
CAS
PubMed
Google Scholar
Bretschneider N, Kangaspeska S, Seifert M, Reid G, Gannon F, Denger S. E2-mediated cathepsin D (CTSD) activation involves looping of distal enhancer elements. Mol Oncol. 2008;2:182–90.
Article
PubMed
Google Scholar
Saramaki A, Diermeier S, Kellner R, Laitinen H, Vaisanen S, Carlberg C. Cyclical chromatin looping and transcription factor association on the regulatory regions of the p21 (CDKN1A) gene in response to 1alpha,25-dihydroxyvitamin D3. J Biol Chem. 2009;284:8073–82.
Article
PubMed Central
CAS
PubMed
Google Scholar
Matilainen JM, Malinen M, Turunen MM, Carlberg C, Vaisanen S. The number of vitamin D receptor binding sites defines the different vitamin D responsiveness of the CYP24 gene in malignant and normal mammary cells. J Biol Chem. 2010;285:24174–83.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wright JB, Brown SJ, Cole MD. Upregulation of c-MYC in cis through a large chromatin loop linked to a cancer risk-associated single-nucleotide polymorphism in colorectal cancer cells. Mol Cell Biol. 2010;30:1411–20.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zeitz MJ, Ay F, Heidmann JD, Lerner PL, Noble WS, Steelman BN, et al. Genomic interaction profiles in breast cancer reveal altered chromatin architecture. PLoS One. 2013;8:e73974.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dryden NH, Broome LR, Dudbridge F, Johnson N, Orr N, Schoenfelder S, et al. Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C. Genome Res. 2014;24:1854–68.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hughes JR, Roberts N, McGowan S, Hay D, Giannoulatou E, Lynch M, et al. Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat Genet. 2014;46:205–12.
Article
CAS
PubMed
Google Scholar
Rousseau M, Ferraiuolo MA, Crutchley JL, Wang XQ, Miura H, Blanchette M, et al. Classifying leukemia types with chromatin conformation data. Genome Biol. 2014;15:R60.
Article
PubMed Central
PubMed
Google Scholar
Misteli T. Higher-order genome organization in human disease. Cold Spring Harb Perspect Biol. 2010;2:a000794.
Article
PubMed Central
PubMed
Google Scholar
Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J. Hi-C: a comprehensive technique to capture the conformation of genomes. Methods. 2012;58:268–76.
Article
CAS
PubMed
Google Scholar
Lajoie BR, Dekker J, Kaplan N. The Hitchhiker’s guide to Hi-C analysis: Practical guidelines. Methods. 2015;72:65–75.
Article
CAS
PubMed
Google Scholar
Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR, et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods. 2012;9:999–1003.
Article
CAS
PubMed
Google Scholar
Davidson JM, Gorringe KL, Chin SF, Orsetti B, Besret C, Courtay-Cahen C, et al. Molecular cytogenetic analysis of breast cancer cell lines. Br J Cancer. 2000;83:1309–17.
Article
PubMed Central
CAS
PubMed
Google Scholar
Marella NV, Malyavantham KS, Wang J, Matsui S, Liang P, Berezney R. Cytogenetic and cDNA microarray expression analysis of MCF10 human breast cancer progression cell lines. Cancer Res. 2009;69:5946–53.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kao J, Salari K, Bocanegra M, Choi YL, Girard L, Gandhi J, et al. Molecular profiling of breast cancer cell lines defines relevant tumor models and provides a resource for cancer gene discovery. PLoS One. 2009;4:e6146.
Article
PubMed Central
PubMed
Google Scholar
Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, et al. Chromatin architecture reorganization during stem cell differentiation. Nature. 2015;518:331–6.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159:1665–80.
Article
CAS
PubMed
Google Scholar
Van Bortle K, Nichols MH, Li L, Ong CT, Takenaka N, Qin ZS, et al. Insulator function and topological domain border strength scale with architectural protein occupancy. Genome Biol. 2014;15:R82.
Article
PubMed Central
PubMed
Google Scholar
Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, et al. Topologically associating domains are stable units of replication-timing regulation. Nature. 2014;515:402–5.
Article
PubMed Central
CAS
PubMed
Google Scholar
Duggal G, Wang H, Kingsford C. Higher-order chromatin domains link eQTLs with the expression of far-away genes. Nucleic Acids Res. 2014;42:87–96.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li Q, Seo JH, Stranger B, McKenna A, Pe’er I, Laframboise T, et al. Integrative eQTL-based analyses reveal the biology of breast cancer risk loci. Cell. 2013;152:633–41.
Article
PubMed Central
CAS
PubMed
Google Scholar
Barbieri M, Chotalia M, Fraser J, Lavitas LM, Dostie J, Pombo A, et al. A model of the large-scale organization of chromatin. Biochem Soc Trans. 2013;41:508–12.
Article
CAS
PubMed
Google Scholar
Parada LA, McQueen PG, Munson PJ, Misteli T. Conservation of relative chromosome positioning in normal and cancer cells. Curr Biol. 2002;12:1692–7.
Article
CAS
PubMed
Google Scholar
Chuang CH, Belmont AS. Moving chromatin within the interphase nucleus-controlled transitions? Semin Cell Dev Biol. 2007;18:698–706.
Article
PubMed Central
CAS
PubMed
Google Scholar
Therizols P, Illingworth RS, Courilleau C, Boyle S, Wood AJ, Bickmore WA. Chromatin decondensation is sufficient to alter nuclear organization in embryonic stem cells. Science. 2014;346:1238–42.
Article
CAS
PubMed
Google Scholar
Draskovic I, Arnoult N, Steiner V, Bacchetti S, Lomonte P, Londono-Vallejo A. Probing PML body function in ALT cells reveals spatiotemporal requirements for telomere recombination. Proc Natl Acad Sci U S A. 2009;106:15726–31.
Article
PubMed Central
CAS
PubMed
Google Scholar
Heaphy CM, Subhawong AP, Hong SM, Goggins MG, Montgomery EA, Gabrielson E, et al. Prevalence of the alternative lengthening of telomeres telomere maintenance mechanism in human cancer subtypes. Am J Pathol. 2011;179:1608–15.
Article
PubMed Central
CAS
PubMed
Google Scholar
Debnath J, Muthuswamy SK, Brugge JS. Morphogenesis and oncogenesis of MCF-10A mammary epithelial acini grown in three-dimensional basement membrane cultures. Methods. 2003;30:256–68.
Article
CAS
PubMed
Google Scholar
Song L, Florea L, Langmead B. Lighter: fast and memory-efficient sequencing error correction without counting. Genome Biol. 2014;15:509.
Article
PubMed Central
PubMed
Google Scholar
Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:323.
Article
PubMed Central
CAS
PubMed
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Article
PubMed Central
PubMed
Google Scholar
Berriz GF, Beaver JE, Cenik C, Tasan M, Roth FP. Next generation software for functional trend analysis. Bioinformatics. 2009;25:3043-3044.
Shen L, Shao N, Liu X, Nestler E. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics. 2014;15:284.
Article
PubMed Central
PubMed
Google Scholar
Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature. 2012;489:109–13.
Article
PubMed Central
CAS
PubMed
Google Scholar
Quinlan AR. BEDTools: The Swiss-army tool for genome feature analysis. Curr Protoc Bioinformatics. 2014;47:11 12 11–34.
Google Scholar