3C-based technologies to study the shape of the genome

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898 · see citing works

Topological domains in mammalian genomes identified by analysis of chromatin interactions

Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829 · see citing works

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716 · see citing works

Capturing Chromosome Conformation

Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652 · see citing works

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

Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., et al. (2012) · Nature · doi:10.1038/nature11049 · Cited by 2,895 · see citing works

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

Sexton, T., Yaffe, E., Kenigsberg, E., Bantignies, F., Leblanc, B., Hoichman, M., Parrinello, H., Tanay, A., & Cavalli, G. (2012) · Cell · doi:10.1016/j.cell.2012.01.010 · Cited by 1,983 · see citing works

An oestrogen-receptor-α-bound human chromatin interactome

Fullwood, M. J., Liu, M. H., Pan, Y. F., Liu, J., Han, X., Mohamed, Y. B., Orlov, Y. L., Velkov, S., Ho, A., Poh, H. M., et al. (2009) · Nature · doi:10.1038/nature08497 · Cited by 1,728 · see citing works

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 · see citing works

Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C)

Simonis, M., Klous, P., Splinter, E., Moshkin, Y., Willemsen, R., de Wit, E., van Steensel, B., & de Laat, W. (2006) · Nature Genetics · doi:10.1038/ng1896 · Cited by 1,386 · see citing works

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

Tolhuis, B., Palstra, R.-J., Splinter, E., Grosveld, F., & de Laat, W. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00781-5 · Cited by 1,344 · see citing works

Hi–C: A comprehensive technique to capture the conformation of genomes

Belton, J.-M., McCord, R. P., Gibcus, J. H., Naumova, N., Zhan, Y., & Dekker, J. (2012) · Methods · doi:10.1016/j.ymeth.2012.05.001 · Cited by 1,260 · see citing works

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

Li, G., Ruan, X., Auerbach, R. K., Sandhu, K. S., Zheng, M., Wang, P., Poh, H. M., Goh, Y., Lim, J., Zhang, J., et al. (2012) · Cell · doi:10.1016/j.cell.2011.12.014 · Cited by 1,232 · see citing works

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elementsPreprint

Dostie, J., Richmond, T., Arnaout, R., Selzer, R. R., Lee, W. L., Honan, T., Rubio, E. D., Krumm, A., Lamb, J., Nusbaum, C., et al. (2006) · Genome Research · doi:10.1101/gr.5571506 · Cited by 1,182 · see citing works

A three-dimensional model of the yeast genome

Duan, Z., Andronescu, M., Schutz, K., McIlwain, S. J., Kim, Y. J., Lee, C., Shendure, J., Fields, S., Blau, C. A., & Noble, W. S. (2010) · Nature · doi:10.1038/nature08973 · Cited by 1,012 · see citing works

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 · see citing works

Three-Dimensional Maps of All Chromosomes in Human Male Fibroblast Nuclei and Prometaphase Rosettes

Bolzer, A., Kreth, G., Solovei, I. V., Koehler, D., Saracoglu, K., Fauth, C., Müller, S., Eils, R., Cremer, C. G., Speicher, M. R., et al. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030157 · Cited by 839 · see citing works

Nuclear organization of the genome and the potential for gene regulation

Fraser, P., & Bickmore, W. (2007) · Nature · doi:10.1038/nature05916 · Cited by 734 · 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

A decade of 3C technologies: insights into nuclear organizationPreprint

de Wit, E., & de Laat, W. L. (2012) · Genes & Development · doi:10.1101/gad.179804.111 · Cited by 701 · see citing works

Long-range chromatin regulatory interactions in vivo

Carter, D., Chakalova, L., Osborne, C. S., Dai, Y.-F., & Fraser, P. (2002) · Nature Genetics · doi:10.1038/ng1051 · Cited by 663 · see citing works

CTCF-mediated functional chromatin interactome in pluripotent cells

Handoko, L., Han, X., Li, G., Ngan, C. Y., Chew, E. G. Y., Schnapp, M., Lee, C. W. H., Ye, C., Ping, J. L. H., Mulawadi, F. H., et al. (2011) · Nature Genetics · doi:10.1038/ng.857 · Cited by 614 · see citing works

Loss of silent-chromatin looping and impaired imprinting of DLX5 in Rett syndrome

Horike, S., Cai, S., Miyano, M., Cheng, J., & Kohwi-shigematsu, T. (2004) · Nature Genetics · doi:10.1038/ng1491 · Cited by 585 · see citing works

The β-globin nuclear compartment in development and erythroid differentiation

Palstra, R.-J., Tolhuis, B., Splinter, E., Nijmeijer, R., Grosveld, F., & de Laat, W. (2003) · Nature Genetics · doi:10.1038/ng1244 · Cited by 559 · 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

Proximity among Distant Regulatory Elements at the β-Globin Locus Requires GATA-1 and FOG-1

Vakoc, C. R., Letting, D. L., Gheldof, N., Sawado, T., Bender, M. A., Groudine, M., Weiss, M. J., Dekker, J., & Blobel, G. A. (2005) · Molecular Cell · doi:10.1016/j.molcel.2004.12.028 · Cited by 490 · see citing works

Integrative analysis of the cancer transcriptome

Rhodes, D. R., & Chinnaiyan, A. M. (2005) · Nature Genetics · doi:10.1038/ng1570 · Cited by 490 · 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

Robust 4C-seq data analysis to screen for regulatory DNA interactions

van de Werken, H. J. G., Landan, G., Holwerda, S. J. B., Hoichman, M., Klous, P., Chachik, R., Splinter, E., Valdes‐Quezada, C., Öz, Y., Bouwman, B. A. M., et al. (2012) · Nature Methods · doi:10.1038/nmeth.2173 · Cited by 376 · see citing works

The active spatial organization of the β-<i>globin</i> locus requires the transcription factor EKLF

Drissen, R., Palstra, R.-J., Gillemans, N., Splinter, E., Grosveld, F., Philipsen, S., & de Laat, W. (2004) · Genes &amp; Development · doi:10.1101/gad.317004 · Cited by 352 · see citing works

The three 'C' s of chromosome conformation capture: controls, controls, controls

Dekker, J. (2005) · Nature Methods · doi:10.1038/nmeth823 · Cited by 347 · see citing works

An evaluation of 3C-based methods to capture DNA interactions

Simonis, M., Kooren, J. A., & de Laat, W. L. (2007) · Nature Methods · doi:10.1038/nmeth1114 · Cited by 301 · see citing works

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

Baù, D., Sanyal, A., Lajoie, B. R., Capriotti, E., Byron, M., Lawrence, J. B., Dekker, J., & Martı́-Renom, M. A. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1936 · Cited by 267 · see citing works

Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation

Splinter, E., de Wit, E., van de Werken, H. J. G., Klous, P., & de Laat, W. L. (2012) · Methods · doi:10.1016/j.ymeth.2012.04.009 · Cited by 224 · see citing works

Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation

Tanizawa, H., Iwasaki, O., Tanaka, A., Capizzi, J. R., Wickramasinghe, P., Lee, M., Fu, Z., & Noma, K.-I. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq955 · Cited by 223 · 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 Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation

Martı́-Renom, M. A. (2012) · Lecture notes in computer science · doi:10.1007/978-3-642-29627-7_16 · Cited by 206 · see citing works

The Three-Dimensional Architecture of a Bacterial Genome

Umbarger, M., Toro, E., Wright, M. A., Porreca, G., Baù, D., Hong, S.-H., Fero, M., Zhu, L., Martí-Renom, M., McAdams, H., et al. (2011) · Molecules and Cells · doi:10.1016/j.molcel.2011.09.010 · Cited by 200 · 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

Analysis of long-range chromatin interactions using Chromosome Conformation Capture

Naumova, N., Smith, E. M., Zhan, Y., & Dekker, J. (2012) · Methods · doi:10.1016/j.ymeth.2012.07.022 · Cited by 178 · see citing works

Interactions among Polycomb Domains Are Guided by Chromosome Architecture

Tolhuis, B., Blom, M., Kerkhoven, R. M., Pagie, L., Teunissen, H., Nieuwland, M., Simonis, M., de Laat, W. L., van Lohuizen, M., & van Steensel, B. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001343 · Cited by 174 · see citing works

Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended Chromosome Conformation Capture methodology

Würtele, H., & Chartrand, P. (2006) · Chromosome Research · doi:10.1007/s10577-006-1075-0 · Cited by 147 · see citing works

Genome structure determination via 3C-based data integration by the Integrative Modeling Platform

Baù, D., & Martı́-Renom, M. A. (2012) · Methods · doi:10.1016/j.ymeth.2012.04.004 · Cited by 95 · see citing works

ChIA-PET analysis of transcriptional chromatin interactions

Zhang, J., Poh, H. M., Peh, S. Q., Sia, Y. Y., Li, G., Mulawadi, F. H., Goh, Y., Fullwood, M. J., Sung, W.-K. K., Ruan, X., et al. (2012) · Methods · doi:10.1016/j.ymeth.2012.08.009 · Cited by 93 · see citing works

Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition

Lower, K. M., Hughes, J. R., De Gobbi, M., Henderson, S., Viprakasit, V., Fisher, C., Goriely, A., Ayyub, H., Sloane-Stanley, J., Vernimmen, D., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909331106 · Cited by 92 · see citing works

The complex transcription regulatory landscape of our genome: control in three dimensions

Splinter, E., & de Laat, W. L. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.344 · Cited by 64 · see citing works

From cells to chromatin: Capturing snapshots of genome organization with 5C technology

Ferraiuolo, M. A., Sanyal, A., Naumova, N., Dekker, J., & Dostie, J. (2012) · Methods · doi:10.1016/j.ymeth.2012.10.011 · Cited by 50 · see citing works

SATB1-mediated functional packaging of chromatin into loops

Kohwi-shigematsu, T., Kohwi, Y., Takahashi, K., Richards, H. W., Ayers, S. D., Han, H., & Cai, S. (2012) · Methods · doi:10.1016/j.ymeth.2012.06.019 · Cited by 50 · see citing works

A genome-wide 3C-method for characterizing the three-dimensional architectures of genomes

Duan, Z., Andronescu, M., Schutz, K., Lee, C., Shendure, J., Fields, S., Noble, W. S., & Blau, C. A. (2012) · Methods · doi:10.1016/j.ymeth.2012.06.018 · Cited by 35 · see citing works

Throwing transcription for a loop: expression of the genome in the 3D nucleus

Hou, C., & Corces, V. G. (2011) · Chromosoma · doi:10.1007/s00412-011-0352-7 · Cited by 30 · see citing works

3C Technologies in plants

Hövel, I., Louwers, M., & Stam, M. E. (2012) · Methods · doi:10.1016/j.ymeth.2012.06.010 · Cited by 18 · see citing works

A model for the 3D chromatin architecture of pro and eukaryotes

Heermann, D. W., Jerabek, H., Liu, L., & Li, Y. (2012) · Methods · doi:10.1016/j.ymeth.2012.04.010 · Cited by 18 · see citing works

Chromosome conformation capture assays in bacteria

Umbarger, M. A. (2012) · Methods · doi:10.1016/j.ymeth.2012.06.017 · Cited by 8 · see citing works

Chromosome conformation capture on chip in single Drosophila melanogaster tissues

Tolhuis, B., Blom, M., & van Lohuizen, M. (2012) · Methods · doi:10.1016/j.ymeth.2012.04.003 · Cited by 7 · see citing works

Insulator dysfunction and oncogene activation in IDH mutant gliomas

Flavahan, W. A., Drier, Y., Liau, B. B., Gillespie, S. M., Venteicher, A. S., Stemmer-Rachamimov, A. O., Suvà, M. L., & Bernstein, B. E. (2016) · Nature · doi:10.1038/nature16490 · Cited by 1,288 · see citing works

Sequencing depth and coverage: key considerations in genomic analyses

Sims, D., Sudbery, I. M., Ilott, N. E., Heger, A., & Ponting, C. P. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3642 · Cited by 1,403 · see citing works

CTCF: an architectural protein bridging genome topology and function

Ong, C., & Corces, V. G. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3663 · Cited by 1,044 · see citing works

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

Quinodoz, S. A., Ollikainen, N., Tabak, B., Palla, A., Schmidt, J. M., Detmar, E., Lai, M. M., Shishkin, A. A., Bhat, P., Takei, Y., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.024 · Cited by 892 · see citing works

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

Hughes, J. R., Roberts, N., McGowan, S., Hay, D., Giannoulatou, E., Lynch, M., De Gobbi, M., Taylor, S., Gibbons, R., & Higgs, D. R. (2014) · Nature Genetics · doi:10.1038/ng.2871 · Cited by 461 · see citing works

Role of non-coding sequence variants in cancer

Khurana, E., Fu, Y., Chakravarty, D., Demichelis, F., Rubin, M. A., & Gerstein, M. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2015.17 · Cited by 449 · see citing works

The 3D genome in transcriptional regulation and pluripotency

Gorkin, D. U., Leung, D., & Ren, B. (2014) · Cell Stem Cell · doi:10.1016/j.stem.2014.05.017 · Cited by 391 · see citing works

Telomere position effect: regulation of gene expression with progressive telomere shortening over long distancesPreprint

Robin, J. D., Ludlow, A. T., Batten, K. G., Magdinier, F., Stadler, G., Wagner, K. R., Shay, J. W., & Wright, W. E. (2014) · Genes & Development · doi:10.1101/gad.251041.114 · Cited by 327 · see citing works

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment

Beagan, J. A., Duong, M. T., Titus, K. R., Zhou, L., Cao, Z., Ma, J., Lachanski, C. V., Gillis, D. R., & Phillips-Cremins, J. E. (2017) · Genome Research · doi:10.1101/gr.215160.116 · Cited by 299 · see citing works

CTCF as a multifunctional protein in genome regulation and gene expression

Kim, S., Yu, N., & Kaang, B. (2015) · Experimental & Molecular Medicine · doi:10.1038/emm.2015.33 · Cited by 293 · see citing works

Enhancer Function: Mechanistic and Genome-Wide Insights Come Together

Plank, J. L., & Dean, A. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.06.015 · Cited by 246 · see citing works

Synbiotic control of inflammation and infection in severe acute pancreatitis: a prospective, randomized, double blind study.

Oláh, A., Belágyi, T., Pótó, L., Romics, L., & Bengmark, S. (2007) · PubMed · Cited by 223 · see citing works

High-quality genome (re)assembly using chromosomal contact data

Marie-Nelly, H., Marbouty, M., Cournac, A., Flot, J., Liti, G., Poggi-Parodi, D., Syan, S., Guillén, N., Margeot, A., Zimmer, C., et al. (2014) · Nature Communications · doi:10.1038/ncomms6695 · Cited by 165 · see citing works

“Cat’s Cradling” the 3D Genome by the Act of LncRNA Transcription

Melé, M., & Rinn, J. L. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.05.011 · Cited by 143 · see citing works

The 3D folding of metazoan genomes correlates with the association of similar repetitive elements

Cournac, A., Koszul, R., & Mozziconacci, J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1292 · Cited by 110 · see citing works

Enhancer deregulation in cancer and other diseases

Herz, H. (2016) · BioEssays · doi:10.1002/bies.201600106 · Cited by 107 · see citing works

Gene regulation at a distance: From remote enhancers to 3D regulatory ensembles

Spitz, F. (2016) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2016.06.017 · Cited by 94 · see citing works

Hox gene regulation and timing in embryogenesis

Montavon, T., & Soshnikova, N. V. (2014) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2014.06.005 · Cited by 78 · see citing works

Deciphering Hi-C: from 3D genome to function

Kong, S.-Y., & Zhang, Y. (2019) · Cell Biology and Toxicology · doi:10.1007/s10565-018-09456-2 · Cited by 72 · see citing works

Unraveling the 3D genome: genomics tools for multiscale exploration

Risca, V. I., & Greenleaf, W. J. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.03.010 · Cited by 75 · see citing works

Nanoscale spatial organization of the HoxD gene cluster in distinct transcriptional states

Fabre, P. J., Benke, A., Joye, E., Huynh, T. H. N., Manley, S., & Duboule, D. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1517972112 · Cited by 75 · see citing works

Computational models of large-scale genome architecture.

Rosa, A., & Zimmer, C. (2014) · International Review of Cell and Molecular Biology · doi:10.1016/b978-0-12-800046-5.00009-6 · Cited by 74 · see citing works

Structure, function and evolution of topologically associating domains (TADs) atHOX loci

Lonfat, N., & Duboule, D. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.04.024 · Cited by 65 · see citing works

Allele-specific transcriptional regulation of IRF4 in melanocytes is mediated by chromatin looping of the intronic rs12203592 enhancer to the IRF4 promoter

Visser, M., Palstra, R.-J., & Kayser, M. (2015) · Human Molecular Genetics · doi:10.1093/hmg/ddv029 · Cited by 57 · see citing works

Chromosome domain architecture and dynamic organization of the fission yeast genome

Mizuguchi, T., Barrowman, J., & Grewal, S. I. S. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.06.008 · Cited by 63 · see citing works

Non-coding genetic variation in cancer

Cuykendall, T. N., Rubin, M. A., & Khurana, E. (2017) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2016.12.017 · Cited by 55 · see citing works

SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding

Quinodoz, S. A., Bhat, P., Chovanec, P., Jachowicz, J. W., Ollikainen, N., Detmar, E., Soehalim, E., & Guttman, M. (2022) · Nature Protocols · doi:10.1038/s41596-021-00633-y · Cited by 55 · see citing works

The statistical-mechanics of chromosome conformation capture

O'Sullivan, J. M., Hendy, M. D., Pichugina, T., Wake, G. C., & Langowski, J. (2013) · Nucleus · doi:10.4161/nucl.26513 · Cited by 55 · see citing works

Three-dimensional genome organization in immune cell fate and function

Cuartero, S., Stik, G., & Stadhouders, R. (2022) · Nature reviews. Immunology · doi:10.1038/s41577-022-00774-5 · Cited by 55 · see citing works

Identification of Functional Variants in the FAM13A Chronic Obstructive Pulmonary Disease Genome-Wide Association Study Locus by Massively Parallel Reporter Assays

Castaldi, P. J., Guo, F., Qiao, D., Du, F., Naing, Z. Z. C., Li, Y., Pham, B., Mikkelsen, T. S., Cho, M. H., Silverman, E. K., et al. (2018) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201802-0337oc · Cited by 51 · see citing works

Contact genomics: scaffolding and phasing (meta)genomes using chromosome 3D physical signatures

Flot, J., Marie-Nelly, H., & Koszul, R. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.04.034 · Cited by 44 · see citing works

RXR heterodimers orchestrate transcriptional control of neurogenesis and cell fate specification

Simándi, Z., Horváth, A., Cuaranta‐Monroy, I., Sauer, S., Deleuze, J., & Nagy, L. (2017) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2017.07.033 · Cited by 37 · see citing works

Topological Domains, Metagenes, and the Emergence of Pleiotropic Regulations at Hox Loci

Darbellay, F., & Duboule, D. (2016) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2015.11.022 · Cited by 34 · see citing works

Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation

Wang, J., Lan, X., Hsu, P.-Y., Hsu, H.-K., Huang, K., Parvin, J. D., Huang, T. H. ‐., & Jin, V. X. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-70 · Cited by 34 · see citing works

SuperTAD: robust detection of hierarchical topologically associated domains with optimized structural information

Zhang, Y., Wang, M., & Li, S. C. (2021) · Genome biology · doi:10.1186/s13059-020-02234-6 · Cited by 31 · see citing works

Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan

Guerreiro, I. M., Gitto, S., Nóvoa, A., Codourey, J., Huynh, T. H. N., Gonzãlez, F., Milinkovitch, M. C., Mallo, M., & Duboule, D. (2016) · eLife · doi:10.7554/elife.16087 · Cited by 30 · see citing works

Super-Enhancers and CTCF in Early Embryonic Cell Fate Decisions

Agrawal, P., & Rao, S. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.653669 · Cited by 30 · see citing works

Chromatin features, RNA polymerase II and the comparative expression of lens genes encoding crystallins, transcription factors, and autophagy mediators.

Sun, J., Rockowitz, S., Chauss, D., Wang, P., Kantorow, M., Zheng, D., & Cvekl, A. (2015) · PubMed Central · Cited by 30 · see citing works

Gene regulation during development in the light of topologically associating domains

Remeseiro, S., Hörnblad, A., & Spitz, F. (2015) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.218 · Cited by 30 · see citing works

Genomic Looping: A Key Principle of Chromatin Organization

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An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping

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