Baranello, 2014, CTCF and cohesin cooperate to organize the 3D structure of the mammalian genome, Proc. Natl. Acad. Sci. USA, 111, 889, 10.1073/pnas.1321957111
Bell, 1999, The protein CTCF is required for the enhancer blocking activity of vertebrate insulators, Cell, 98, 387, 10.1016/S0092-8674(00)81967-4
Boyer, 2006, Polycomb complexes repress developmental regulators in murine embryonic stem cells, Nature, 441, 349, 10.1038/nature04733
Bracken, 2006, Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions, Genes Dev., 20, 1123, 10.1101/gad.381706
Cavalli, 2013, Functional implications of genome topology, Nat. Struct. Mol. Biol., 20, 290, 10.1038/nsmb.2474
Chepelev, 2012, Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization, Cell Res., 22, 490, 10.1038/cr.2012.15
Cuddapah, 2009, Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains, Genome Res., 19, 24, 10.1101/gr.082800.108
de Wit, 2013, The pluripotent genome in three dimensions is shaped around pluripotency factors, Nature, 501, 227, 10.1038/nature12420
DeMare, 2013, The genomic landscape of cohesin-associated chromatin interactions, Genome Res., 23, 1224, 10.1101/gr.156570.113
Denholtz, 2013, Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization, Cell Stem Cell, 13, 602, 10.1016/j.stem.2013.08.013
Dixon, 2012, Topological domains in mammalian genomes identified by analysis of chromatin interactions, Nature, 485, 376, 10.1038/nature11082
Dowen, 2013, Multiple structural maintenance of chromosome complexes at transcriptional regulatory elements, Stem Cell Rev., 1, 371, 10.1016/j.stemcr.2013.09.002
Essafi, 2011, A wt1-controlled chromatin switching mechanism underpins tissue-specific wnt4 activation and repression, Dev. Cell, 21, 559, 10.1016/j.devcel.2011.07.014
Felsenfeld, 2004, Chromatin boundaries and chromatin domains, Cold Spring Harb. Symp. Quant. Biol., 69, 245, 10.1101/sqb.2004.69.245
Filippova, 2014, Identification of alternative topological domains in chromatin, Algorithms Mol. Biol., 9, 14, 10.1186/1748-7188-9-14
Fullwood, 2009, An oestrogen-receptor-alpha-bound human chromatin interactome, Nature, 462, 58, 10.1038/nature08497
Gibcus, 2013, The hierarchy of the 3D genome, Mol. Cell, 49, 773, 10.1016/j.molcel.2013.02.011
Goh, 2012, Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) for mapping chromatin interactions and understanding transcription regulation, J. Vis. Exp., 10.3791/3770
Gorkin, 2014, The 3D genome in transcriptional regulation and pluripotency, Cell Stem Cell, 14, 762, 10.1016/j.stem.2014.05.017
Gröschel, 2014, A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia, Cell, 157, 369, 10.1016/j.cell.2014.02.019
Guo, 2011, CTCF-binding elements mediate control of V(D)J recombination, Nature, 477, 424, 10.1038/nature10495
Handoko, 2011, CTCF-mediated functional chromatin interactome in pluripotent cells, Nat. Genet., 43, 630, 10.1038/ng.857
Hawkins, 2011, Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency, Cell Res., 21, 1393, 10.1038/cr.2011.146
Hnisz, 2013, Super-enhancers in the control of cell identity and disease, Cell, 155, 934, 10.1016/j.cell.2013.09.053
Kagey, 2010, Mediator and cohesin connect gene expression and chromatin architecture, Nature, 467, 430, 10.1038/nature09380
Kaspi, 2013, Brief report: miR-290-295 regulate embryonic stem cell differentiation propensities by repressing Pax6, Stem Cells, 31, 2266, 10.1002/stem.1465
Kieffer-Kwon, 2013, Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation, Cell, 155, 1507, 10.1016/j.cell.2013.11.039
Kim, 2007, Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome, Cell, 128, 1231, 10.1016/j.cell.2006.12.048
Lee, 2013, Transcriptional regulation and its misregulation in disease, Cell, 152, 1237, 10.1016/j.cell.2013.02.014
Lee, 2006, Control of developmental regulators by Polycomb in human embryonic stem cells, Cell, 125, 301, 10.1016/j.cell.2006.02.043
Lelli, 2012, Disentangling the many layers of eukaryotic transcriptional regulation, Annu. Rev. Genet., 46, 43, 10.1146/annurev-genet-110711-155437
Li, 2010, ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing, Genome Biol., 11, R22, 10.1186/gb-2010-11-2-r22
Li, 2012, Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation, Cell, 148, 84, 10.1016/j.cell.2011.12.014
Margueron, 2011, The Polycomb complex PRC2 and its mark in life, Nature, 469, 343, 10.1038/nature09784
Merkenschlager, 2013, CTCF and cohesin: linking gene regulatory elements with their targets, Cell, 152, 1285, 10.1016/j.cell.2013.02.029
Meuleman, 2013, Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence, Genome Res., 23, 270, 10.1101/gr.141028.112
Naumova, 2013, Organization of the mitotic chromosome, Science, 342, 948, 10.1126/science.1236083
Nègre, 2006, Chromosomal distribution of PcG proteins during Drosophila development, PLoS Biol., 4, e170, 10.1371/journal.pbio.0040170
Ng, 2011, The transcriptional and signalling networks of pluripotency, Nat. Cell Biol., 13, 490, 10.1038/ncb0511-490
Nora, 2012, Spatial partitioning of the regulatory landscape of the X-inactivation centre, Nature, 485, 381, 10.1038/nature11049
Ong, 2014, CTCF: an architectural protein bridging genome topology and function, Nat. Rev. Genet., 15, 234, 10.1038/nrg3663
Orkin, 2011, Chromatin connections to pluripotency and cellular reprogramming, Cell, 145, 835, 10.1016/j.cell.2011.05.019
Parelho, 2008, Cohesins functionally associate with CTCF on mammalian chromosome arms, Cell, 132, 422, 10.1016/j.cell.2008.01.011
Phillips, 2009, CTCF: master weaver of the genome, Cell, 137, 1194, 10.1016/j.cell.2009.06.001
Phillips-Cremins, 2013, Chromatin insulators: linking genome organization to cellular function, Mol. Cell, 50, 461, 10.1016/j.molcel.2013.04.018
Phillips-Cremins, 2013, Architectural protein subclasses shape 3D organization of genomes during lineage commitment, Cell, 153, 1281, 10.1016/j.cell.2013.04.053
Roeder, 2005, Transcriptional regulation and the role of diverse coactivators in animal cells, FEBS Lett., 579, 909, 10.1016/j.febslet.2004.12.007
Rubio, 2008, CTCF physically links cohesin to chromatin, Proc. Natl. Acad. Sci. USA, 105, 8309, 10.1073/pnas.0801273105
Sanyal, 2012, The long-range interaction landscape of gene promoters, Nature, 489, 109, 10.1038/nature11279
Schaaf, 2013, Cohesin and polycomb proteins functionally interact to control transcription at silenced and active genes, PLoS Genet., 9, e1003560, 10.1371/journal.pgen.1003560
Schwartz, 2006, Genome-wide analysis of Polycomb targets in Drosophila melanogaster, Nat. Genet., 38, 700, 10.1038/ng1817
Schwartz, 2012, Nature and function of insulator protein binding sites in the Drosophila genome, Genome Res., 22, 2188, 10.1101/gr.138156.112
Seitan, 2013, Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments, Genome Res., 23, 2066, 10.1101/gr.161620.113
Sexton, 2012, Three-dimensional folding and functional organization principles of the Drosophila genome, Cell, 148, 458, 10.1016/j.cell.2012.01.010
Shen, 2012, A map of the cis-regulatory sequences in the mouse genome, Nature, 488, 116, 10.1038/nature11243
Smallwood, 2013, Genome organization and long-range regulation of gene expression by enhancers, Curr. Opin. Cell Biol., 25, 387, 10.1016/j.ceb.2013.02.005
Sofueva, 2013, Cohesin-mediated interactions organize chromosomal domain architecture, EMBO J., 32, 3119, 10.1038/emboj.2013.237
Soshnikova, 2010, Functional analysis of CTCF during mammalian limb development, Dev. Cell, 19, 819, 10.1016/j.devcel.2010.11.009
Spitz, 2012, Transcription factors: from enhancer binding to developmental control, Nat. Rev. Genet., 13, 613, 10.1038/nrg3207
Squazzo, 2006, Suz12 binds to silenced regions of the genome in a cell-type-specific manner, Genome Res., 16, 890, 10.1101/gr.5306606
Tolhuis, 2006, Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster, Nat. Genet., 38, 694, 10.1038/ng1792
Valenzuela, 2006, Chromatin insulators, Annu. Rev. Genet., 40, 107, 10.1146/annurev.genet.39.073003.113546
Van Bortle, 2012, Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains, Genome Res., 22, 2176, 10.1101/gr.136788.111
Wang, 2014, NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers, Proc. Natl. Acad. Sci. USA, 111, 705, 10.1073/pnas.1315023111
Wen, 2009, Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells, Nat. Genet., 41, 246, 10.1038/ng.297
Wendt, 2008, Cohesin mediates transcriptional insulation by CCCTC-binding factor, Nature, 451, 796, 10.1038/nature06634
Whyte, 2012, Enhancer decommissioning by LSD1 during embryonic stem cell differentiation, Nature, 482, 221, 10.1038/nature10805
Whyte, 2013, Master transcription factors and mediator establish super-enhancers at key cell identity genes, Cell, 153, 307, 10.1016/j.cell.2013.03.035
Young, 2011, Control of the embryonic stem cell state, Cell, 144, 940, 10.1016/j.cell.2011.01.032
Zuin, 2014, Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells, Proc. Natl. Acad. Sci. USA, 111, 996, 10.1073/pnas.1317788111
Zhang, 2013, Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations, Nature, 504, 306, 10.1038/nature12716