Functional implications of genome topology

An integrated encyclopedia of DNA elements in the human genome

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Topological domains in mammalian genomes identified by analysis of chromatin interactions

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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

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The Role of Chromatin during Transcription

Li, B., Carey, M., & Workman, J. L. (2007) · Cell · doi:10.1016/j.cell.2007.01.015 · Cited by 3,503 · see citing works

Mapping and analysis of chromatin state dynamics in nine human cell types

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Spatial partitioning of the regulatory landscape of the X-inactivation centre

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The accessible chromatin landscape of the human genome

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Three-dimensional folding and functional organization principles of the Drosophila genome

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A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

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Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

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The long-range interaction landscape of gene promoters

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Looping and Interaction between Hypersensitive Sites in the Active β-globin Locus

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Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

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Lamin A-Dependent Nuclear Defects in Human Aging

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Beyond the Sequence: Cellular Organization of Genome Function

Misteli, T. (2007) · Cell · doi:10.1016/j.cell.2007.01.028 · Cited by 1,140 · see citing works

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

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Hyperdynamic Plasticity of Chromatin Proteins in Pluripotent Embryonic Stem Cells

Meshorer, E., Yellajoshyula, D., George, E. M., Scambler, P. J., Brown, D. T., & Misteli, T. (2006) · Developmental Cell · doi:10.1016/j.devcel.2005.10.017 · Cited by 1,008 · see citing works

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

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Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions

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Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

Kharchenko, P. V., Alekseyenko, A. A., Schwartz, Y. B., Minoda, A., Riddle, N. C., Ernst, J., Sabo, P. J., Larschan, E., Gorchakov, A. A., Gu, T., et al. (2010) · Nature · doi:10.1038/nature09725 · Cited by 853 · see citing works

SIRT1 redistribution on chromatin promotes genomic stability but alters gene expression during aging

Oberdoerffer, P., Michan, S., McVay, M., Mostoslavsky, R., Vann, J., Park, S.-K., Hartlerode, A., Stegmuller, J., Hafner, A., Loerch, P., et al. (2008) · Cell · doi:10.1016/j.cell.2008.10.025 · Cited by 852 · see citing works

ATM Signaling Facilitates Repair of DNA Double-Strand Breaks Associated with Heterochromatin

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Transcriptional repression mediated by repositioning of genes to the nuclear lamina

Reddy, K. L., Zullo, J., Bertolino, E., & Singh, H. (2008) · Nature · doi:10.1038/nature06727 · Cited by 785 · see citing works

Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions

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Chromatin relaxation in response to DNA double-strand breaks is modulated by a novel ATM- and KAP-1 dependent pathway

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Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor

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The Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains

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Interchromosomal associations between alternatively expressed loci

Spilianakis, C. G., Lalioti, M. D., Town, T., Lee, G. R., & Flavell, R. A. (2005) · Nature · doi:10.1038/nature03574 · Cited by 726 · see citing works

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

Schoenfelder, S., Sexton, T., Chakalova, L., Cope, N. F., Horton, A., Andrews, S., Kurukuti, S., Mitchell, J. A., Umlauf, D., Dimitrova, D. S., et al. (2009) · Nature Genetics · doi:10.1038/ng.496 · Cited by 710 · see citing works

Global Transcription in Pluripotent Embryonic Stem Cells

Efroni, S., Duttagupta, R., Cheng, J., Dehghani, H., Hoeppner, D. J., Dash, C., Bazett‐Jones, D. P., Grice, S. F. J. L., McKay, R. D. G., Buetow, K. H., et al. (2008) · Cell stem cell · doi:10.1016/j.stem.2008.03.021 · Cited by 688 · see citing works

Intermingling of Chromosome Territories in Interphase Suggests Role in Translocations and Transcription-Dependent Associations

Branco, M. R., & Pombo, A. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040138 · Cited by 685 · see citing works

Interchromosomal Interactions and Olfactory Receptor Choice

Lomvardas, S., Barnea, G., Pisapia, D. J., Mendelsohn, M. M., Kirkland, J., & Axel, R. (2006) · Cell · doi:10.1016/j.cell.2006.06.035 · Cited by 633 · see citing works

Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell typesPreprint

Ryba, T., Hiratani, I., Lu, J., Itoh, M., Kulik, M. J., Zhang, J., Schulz, T. C., Robins, A. J., Dalton, S., & Gilbert, D. M. (2010) · Genome Research · doi:10.1101/gr.099655.109 · Cited by 608 · see citing works

Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery

Towbin, B. D., González-Aguilera, C., Sack, R., Gaidatzis, D., Kalck, V., Meister, P., Askjaer, P., & Gasser, S. M. (2012) · Cell · doi:10.1016/j.cell.2012.06.051 · Cited by 597 · see citing works

Recruitment to the Nuclear Periphery Can Alter Expression of Genes in Human Cells

Finlan, L. E., Sproul, D., Thomson, I., Boyle, S., Kerr, E. A., Perry, P., Ylstra, B., Chubb, J. R., & Bickmore, W. A. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000039 · Cited by 584 · see citing works

Chromatin Motion Is Constrained by Association with Nuclear Compartments in Human Cells

Chubb, J. R., Boyle, S., Perry, P., & Bickmore, W. A. (2002) · Current Biology · doi:10.1016/s0960-9822(02)00695-4 · Cited by 580 · see citing works

Nuclear Receptor-Induced Chromosomal Proximity and DNA Breaks Underlie Specific Translocations in Cancer

Lin, C., Yang, L., Tanasa, B., Hutt, K., Ju, B.-G., Ohgi, K. A., Zhang, J., Rose, D. W., Fu, X.-D., Glass, C. K., et al. (2009) · Cell · doi:10.1016/j.cell.2009.11.030 · Cited by 576 · see citing works

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation

Hiratani, I., Ryba, T., Itoh, M., Yokochi, T., Schwaiger, M., Chang, C., Lyou, Y., Townes, T. M., Schübeler, D., & Gilbert, D. M. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060245 · Cited by 548 · see citing works

Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations

Zhang, Y., McCord, R. P., Ho, Y.-J., Lajoie, B. R., Hildebrand, D. G., Simon, A. C., Becker, M. S., Alt, F. W., & Dekker, J. (2012) · Cell · doi:10.1016/j.cell.2012.02.002 · Cited by 545 · see citing works

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

Kalhor, R., Tjong, H., Jayathilaka, N., Alber, F., & Chen, L. (2011) · Nature Biotechnology · doi:10.1038/nbt.2057 · Cited by 532 · see citing works

Changes in chromatin structure and mobility in living cells at sites of DNA double-strand breaks

Kruhlak, M. J., Celeste, A., Dellaire, G., Fernandez-Capetillo, O., Müller, W. G., McNally, J. G., Bazett-Jones, D. P., & Nussenzweig, A. (2006) · The Journal of Cell Biology · doi:10.1083/jcb.200510015 · Cited by 518 · see citing works

Double-Strand Breaks in Heterochromatin Move Outside of a Dynamic HP1a Domain to Complete Recombinational Repair

Chiolo, I., Minoda, A., Colmenares, S. U., Polyzos, A. A., Costes, S. V., & Karpen, G. H. (2011) · Cell · doi:10.1016/j.cell.2011.02.012 · Cited by 516 · see citing works

Chd1 regulates open chromatin and pluripotency of embryonic stem cells

Gaspar‐Maia, A., Alajem, A., Polesso, F., Sridharan, R., Mason, M. J., Heidersbach, A. J., Ramalho‐Santos, J., McManus, M. T., Plath, K., Meshorer, E., et al. (2009) · Nature · doi:10.1038/nature08212 · Cited by 509 · see citing works

Positional stability of single double-strand breaks in mammalian cells

Soutoglou, E., Dorn, J. F., Sengupta, K., Jasin, M., Nussenzweig, A., Ried, T., Danuser, G., & Misteli, T. (2007) · Nature Cell Biology · doi:10.1038/ncb1591 · Cited by 509 · see citing works

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

Hou, C., Li, L., Qin, Z. S., & Corces, V. G. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.08.031 · Cited by 503 · see citing works

Genome-wide Translocation Sequencing Reveals Mechanisms of Chromosome Breaks and Rearrangements in B Cells

Chiarle, R., Zhang, Y., Frock, R. L., Lewis, S. M., Molinié, B., Ho, Y.-J., Myers, D. R., Choi, V. W., Compagno, M., Malkin, D. J., et al. (2011) · Cell · doi:10.1016/j.cell.2011.07.049 · Cited by 475 · see citing works

DNA Sequence-Dependent Compartmentalization and Silencing of Chromatin at the Nuclear Lamina

Zullo, J., Demarco, I. A., Piqué-Regi, R., Gaffney, D. J., Epstein, C. B., Spooner, C. J., Luperchio, T. R., Bernstein, B., Pritchard, J. K., Reddy, K. L., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.035 · Cited by 448 · see citing works

Eukaryotic DNA replication origins: many choices for appropriate answers

Méchali, M. (2010) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2976 · Cited by 441 · see citing works

Elevated histone expression promotes life span extension

Feser, J., Truong, D., Das, C., Carson, J. J., Kieft, J., Harkness, T., & Tyler, J. K. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.08.015 · Cited by 435 · see citing works

CTCF Mediates Interchromosomal Colocalization Between Igf2/H19 and Wsb1/Nf1

Ling, J. Q., Li, T., Hu, J., Vu, T. H., Chen, H. L., Qiu, X. W., Cherry, A. M., & Hoffman, A. R. (2006) · Science · doi:10.1126/science.1123191 · Cited by 434 · see citing works

Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila

Bantignies, F., Roure, V., Comet, I., Leblanc, B., Schuettengruber, B., Bonnet, J., Tixier, V., Mas, A., & Cavalli, G. (2011) · Cell · doi:10.1016/j.cell.2010.12.026 · Cited by 429 · see citing works

Reduced histone biosynthesis and chromatin changes arising from a damage signal at telomeres

O'Sullivan, R. J., Kubicek, S., Schreiber, S. L., & Karlseder, J. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1897 · Cited by 416 · see citing works

Spatial proximity of translocation-prone gene loci in human lymphomas

Roix, J. J., McQueen, P. G., Munson, P. J., Parada, L. A., & Misteli, T. (2003) · Nature Genetics · doi:10.1038/ng1177 · Cited by 414 · see citing works

HP1-β mobilization promotes chromatin changes that initiate the DNA damage response

Ayoub, N., Jeyasekharan, A. D. D., Bernal, J. A., & Venkitaraman, A. R. (2008) · Nature · doi:10.1038/nature06875 · Cited by 404 · see citing works

A Drosophila Polycomb group complex includes Zeste and dTAFII proteins

Saurin, A. J., Shao, Z., Erdjument‐Bromage, H., Tempst, P., & Kingston, R. E. (2001) · Nature · doi:10.1038/35088096 · Cited by 403 · see citing works

The Dynamic Architecture of Hox Gene Clusters

Noordermeer, D., Leleu, M., Splinter, E., Rougemont, J., de Laat, W. L., & Duboule, D. (2011) · Science · doi:10.1126/science.1207194 · Cited by 391 · see citing works

A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence

Kumaran, R. I., & Spector, D. L. (2008) · The Journal of Cell Biology · doi:10.1083/jcb.200706060 · Cited by 388 · see citing works

Tissue-specific spatial organization of genomes

Parada, L. A., McQueen, P. G., & Misteli, T. (2004) · Genome biology · doi:10.1186/gb-2004-5-7-r44 · Cited by 379 · see citing works

Increased chromosome mobility facilitates homology search during recombination

Miné-Hattab, J., & Rothstein, R. J. (2012) · Nature Cell Biology · doi:10.1038/ncb2472 · Cited by 364 · see citing works

Nuclear Aggregation of Olfactory Receptor Genes Governs Their Monogenic Expression

Clowney, E. J., LeGros, M., Mosley, C., Clowney, F., Markenscoff-Papadimitriou, E., Myllys, M., Barnea, G., Larabell, C. A., & Lomvardas, S. (2012) · Cell · doi:10.1016/j.cell.2012.09.043 · Cited by 362 · see citing works

Translocation-Capture Sequencing Reveals the Extent and Nature of Chromosomal Rearrangements in B Lymphocytes

Klein, I. A., Resch, W., Janković, M., Oliveira, T. Y., Yamane, A., Nakahashi, H., Virgilio, M. D., Bothmer, A., Nussenzweig, A., Robbiani, D. F., et al. (2011) · Cell · doi:10.1016/j.cell.2011.07.048 · Cited by 353 · see citing works

Gene loops juxtapose promoters and terminators in yeast

O'Sullivan, J. M., Tan‐Wong, S. M., Morillon, A., Lee, B., Coles, J., Mellor, J., & Proudfoot, N. J. (2004) · Nature Genetics · doi:10.1038/ng1411 · Cited by 346 · see citing works

Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing

Schübeler, D., Scalzo, D., Kooperberg, C. L., van Steensel, B., Delrow, J. J., & Groudine, M. T. (2002) · Nature Genetics · doi:10.1038/ng1005 · Cited by 343 · see citing works

PRC1 and Suv39h specify parental asymmetry at constitutive heterochromatin in early mouse embryos

Puschendorf, M., Terranova, R., Boutsma, E., Mao, X., Isono, K., Brykczynska, U., Kolb, C., Otte, A. P., Koseki, H., Orkin, S. H., et al. (2008) · Nature Genetics · doi:10.1038/ng.99 · Cited by 333 · see citing works

Increased mobility of double-strand breaks requires Mec1, Rad9 and the homologous recombination machinery

Dion, V., Kalck, V., Horigome, C., Towbin, B. D., & Gasser, S. M. (2012) · Nature Cell Biology · doi:10.1038/ncb2465 · Cited by 315 · see citing works

Genome-wide studies highlight indirect links between human replication origins and gene regulation

Cadoret, J., Meisch, F., Hassan‐Zadeh, V., Luyten, I., Guillet, C., Duret, L., Quesneville, H., & Prioleau, M. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0805208105 · Cited by 314 · see citing works

Ageing-related chromatin defects through loss of the NURD complex

Pegoraro, G., Kubben, N., Wickert, U., Goehler, H., Hoffmann, K., & Misteli, T. (2009) · Nature Cell Biology · doi:10.1038/ncb1971 · Cited by 293 · see citing works

Broad chromosomal domains of histone modification patterns in C. elegansPreprint

Liu, T., Rechtsteiner, A., Egelhofer, T. A., Vielle, A., Latorre, I., Cheung, M.-S., Ercan, S., Ikegami, K., Jensen, M., Kolasinska-Zwierz, P., et al. (2010) · Genome Research · doi:10.1101/gr.115519.110 · Cited by 291 · see citing works

Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex

Lanzuolo, C., Roure, V., Dekker, J., Bantignies, F., & Orlando, V. (2007) · Nature Cell Biology · doi:10.1038/ncb1637 · Cited by 289 · see citing works

Replication timing and transcriptional control: beyond cause and effect

Gilbert, D. M. (2002) · Current Opinion in Cell Biology · doi:10.1016/s0955-0674(02)00326-5 · Cited by 288 · see citing works

esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function

Ho, L., Miller, E. L., Ronan, J. L., Ho, W. Q., Jothi, R., & Crabtree, G. R. (2011) · Nature Cell Biology · doi:10.1038/ncb2285 · Cited by 274 · see citing works

Biogenesis of Nuclear BodiesPreprint

Dundr, M., & Misteli, T. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a000711 · Cited by 274 · see citing works

Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complexPreprint

Tan‐Wong, S. M., Wijayatilake, H. D., & Proudfoot, N. J. (2009) · Genes & Development · doi:10.1101/gad.1823209 · Cited by 260 · see citing works

General transcription factors bind promoters repressed by Polycomb group proteins

Breiling, A., Turner, B. M., Bianchi, M. E., & Orlando, V. (2001) · Nature · doi:10.1038/35088090 · Cited by 242 · see citing works

Gene Loops Enhance Transcriptional Directionality

Tan‐Wong, S. M., Zaugg, J. B., Camblong, J., Xu, Z., Zhang, D. W., Mischo, H. E., Ansari, A. Z., Luscombe, N. M., Steinmetz, L. M., & Proudfoot, N. J. (2012) · Science · doi:10.1126/science.1224350 · Cited by 241 · see citing works

Virus Infection Induces NF-κB-Dependent Interchromosomal Associations Mediating Monoallelic IFN-β Gene Expression

Apostolou, E., & Thanos, D. (2008) · Cell · doi:10.1016/j.cell.2008.05.052 · Cited by 240 · see citing works

Role for perinuclear chromosome tethering in maintenance of genome stability

Mekhail, K., Seebacher, J., Gygi, S. P., & Moazed, D. (2008) · Nature · doi:10.1038/nature07460 · Cited by 233 · see citing works

γH2AX Foci Form Preferentially in Euchromatin after Ionising-Radiation

Cowell, I. G., Sunter, N. J., Singh, P. B., Austin, C. A., Durkacz, B. W., & Tilby, M. J. (2007) · PLoS ONE · doi:10.1371/journal.pone.0001057 · Cited by 225 · see citing works

Promyelocytic leukemia nuclear bodies associate with transcriptionally active genomic regions

Wang, J., Shiels, C., Sasieni, P. D., Wu, P. J., Islam, S. A., Freemont, P. S., & Sheer, D. (2004) · The Journal of Cell Biology · doi:10.1083/jcb.200305142 · Cited by 224 · see citing works

Genomics tools for unraveling chromosome architecture

van Steensel, B., & Dekker, J. (2010) · Nature Biotechnology · doi:10.1038/nbt.1680 · Cited by 216 · see citing works

The spatial dynamics of tissue-specific promoters during C. elegans developmentPreprint

Meister, P., Towbin, B. D., Pike, B. L., Ponti, A., & Gasser, S. M. (2010) · Genes & Development · doi:10.1101/gad.559610 · Cited by 212 · see citing works

Replication timing and transcriptional control: beyond cause and effect — part III

Rivera‐Mulia, J. C., & Gilbert, D. M. (2016) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2016.03.022 · Cited by 208 · see citing works

PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping

Tiwari, V. K., McGarvey, K. M., Licchesi, J. D. F., Ohm, J. E., Herman, J. G., Schübeler, D., & Baylin, S. B. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060306 · Cited by 205 · see citing works

Alternative Epigenetic Chromatin States of Polycomb Target Genes

Schwartz, Y. B., Kahn, T. G., Stenberg, P., Ohno, K., Bourgon, R., & Pirrotta, V. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000805 · Cited by 202 · see citing works

Physical tethering and volume exclusion determine higher-order genome organization in budding yeastPreprint

Tjong, H., Gong, K. Q., Chen, L., & Alber, F. (2012) · Genome Research · doi:10.1101/gr.129437.111 · Cited by 200 · see citing works

Genome–nuclear lamina interactions and gene regulation

Kind, J., & van Steensel, B. (2010) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2010.04.002 · Cited by 195 · see citing works

DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes

Hakim, O., Resch, W., Yamane, A., Klein, I. A., Kieffer-Kwon, K.-R., Janković, M., Oliveira, T. Y., Bothmer, A., Voss, T. C., Ansarah-Sobrinho, C., et al. (2012) · Nature · doi:10.1038/nature10909 · Cited by 195 · see citing works

Nature and function of insulator protein binding sites in the Drosophila genomePreprint

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