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

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

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

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

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The long-range interaction landscape of gene promoters

Sanyal, A., Lajoie, B. R., Jain, G., & Dekker, J. (2012) · Nature · doi:10.1038/nature11279 · Cited by 1,489

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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Beyond the Sequence: Cellular Organization of Genome Function

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

Lamin A-dependent nuclear defects in human aging

Scaffidi, P., & Misteli, T. (2006) · Science · doi:10.1126/science.1127168 · Cited by 1,125

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

Peric-Hupkes, D., Meuleman, W., Pagie, L., Bruggeman, S. W. M., Solovei, I., Brugman, W., Gräf, S., Flicek, P., Kerkhoven, R. M., van Lohuizen, M., et al. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.03.016 · Cited by 1,050

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

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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

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

Zhao, Z., Tavoosidana, G., Sjölinder, M., Göndör, A., Mariano, P., Wang, S., Kanduri, C., Lezcano, M., Sandhu, K. S., Singh, U., et al. (2006) · Nature Genetics · doi:10.1038/ng1891 · Cited by 957

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 893

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

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

Goodarzi, A. A., Noon, A. T., Deckbar, D., Ziv, Y., Shiloh, Y., Löbrich, M., & Jeggo, P. A. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.05.017 · Cited by 836

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 823

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

Lanctôt, C., Cheutin, T., Cremer, M., Cavalli, G., & Cremer, T. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2041 · Cited by 781

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 742

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

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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 735

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

Deng, W., Lee, J., Wang, H., Miller, J., Reik, A., Gregory, P. D., Dean, A., & Blobel, G. A. (2012) · Cell · doi:10.1016/j.cell.2012.03.051 · Cited by 734

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

Caron, H. N., van Schaik, B. D. C., van der Mee, M., Baas, F., Riggins, G. J., Sluis, P. V., Hermus, M.-C., van Asperen, R., Boon, K., Voûte, P. A., et al. (2001) · Science · doi:10.1126/science.1056794 · Cited by 730

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 719

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

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 641

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

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

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

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

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

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 576

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 572

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 554

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 547

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 525

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 521

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

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

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 498

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

Eukaryotic DNA replication origins: many choices for appropriate answers

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

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 437

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

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

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 417

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

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

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 404

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

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

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

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 370

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

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 357

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

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

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 337

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

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

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 308

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 293

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

Ageing-related chromatin defects through loss of the NURD complex

Pegoraro, G., Kubben, N., Wickert, U., Göhler, H., Hoffmann, K., & Misteli, T. (2009) · Nature Cell Biology · doi:10.1038/ncb1971 · Cited by 276

Biogenesis of Nuclear BodiesPreprint

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

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 270

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

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 249

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

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 242

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 234

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

Genomics tools for unraveling chromosome architecture

van Steensel, B., & Dekker, J. (2010) · Nature Biotechnology · doi:10.1038/nbt.1680 · Cited by 227

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

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 217

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 214

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 214

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 205

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 205

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 204

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

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

Schwartz, Y. B., Linder-Basso, D., Kharchenko, P. V., Tolstorukov, M. Y., Kim, M., Li, H., Gorchakov, A. A., Minoda, A., Shanower, G., Alekseyenko, A. A., et al. (2012) · Genome Research · doi:10.1101/gr.138156.112 · Cited by 195

Sensing X Chromosome Pairs Before X Inactivation via a Novel X-Pairing Region of the Xic

Augui, S., Filion, G. J. P., Huart, S., Nora, E. P., Guggiari, M., Maresca, M., Stewart, A. F., & Heard, É. (2007) · Science · doi:10.1126/science.1149420 · Cited by 178

G9a selectively represses a class of late-replicating genes at the nuclear periphery

Yokochi, T., Poduch, K., Ryba, T., Lu, J., Hiratani, I., Tachibana, M., Shinkai, Y., & Gilbert, D. M. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0906142106 · Cited by 162

Constitutive heterochromatin reorganization during somatic cell reprogramming

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A Predictive Computational Model of the Dynamic 3D Interphase Yeast Nucleus

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