Chromosomal dynamics at the Shh locus: limb bud-specific differential regulation of competence and active transcription

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

Sonic hedgehog mediates the polarizing activity of the ZPA

Riddle, R. D., Johnson, R. L., Laufer, E., & Tabin, C. J. (1993) · Cell · doi:10.1016/0092-8674(93)90626-2 · Cited by 2,285 · 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

A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly

Lettice, L. A. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg180 · Cited by 1,164 · see citing works

Active genes dynamically colocalize to shared sites of ongoing transcription

Osborne, C. S., Chakalova, L., Brown, K. E., Carter, D., Horton, A., Debrand, E., Goyenechea, B., Mitchell, J. A., Lopes, S. M. C. D. S., Reik, W., et al. (2004) · Nature Genetics · doi:10.1038/ng1423 · Cited by 1,046 · see citing works

Evidence for an Expansion-Based Temporal Shh Gradient in Specifying Vertebrate Digit Identities

Harfe, B. D., Scherz, P., Nissim, S., Tian, H., McMahon, A. P., & Tabin, C. J. (2004) · Cell · doi:10.1016/j.cell.2004.07.024 · Cited by 970 · see citing works

1 Developmental roles and clinical significance of Hedgehog signaling

McMahon, A. P., Ingham, P. W., & Tabin, C. J. (2003) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/s0070-2153(03)53002-2 · Cited by 913 · see citing works

Long-Range Control of Gene Expression: Emerging Mechanisms and Disruption in Disease

Kleinjan, D. A., & van Heyningen, V. (2004) · The American Journal of Human Genetics · doi:10.1086/426833 · Cited by 868 · see citing works

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 · 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

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

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

Local application of retinoic acid to the limb bond mimics the action of the polarizing region

Tickle, C. A., Alberts, B., Wolpert, L., & Lee, J. (1982) · Nature · doi:10.1038/296564a0 · Cited by 663 · see citing works

Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcriptionPreprint

Chambeyron, S., & Bickmore, W. A. (2004) · Genes & Development · doi:10.1101/gad.292104 · Cited by 618 · see citing works

Coordinate expression of the murine Hox-5 complex homoeobox-containing genes during limb pattern formation

Dollé, P., Izpisúa‐Belmonte, J. C., Falkenstein, H., Renucci, A., & Duboule, D. (1989) · Nature · doi:10.1038/342767a0 · Cited by 608 · see citing works

Chromosome territories – a functional nuclear landscape

Cremer, T., Cremer, M., Dietzel, S., Müller, S., Solovei, I. V., & Fakan, S. (2006) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2006.04.007 · Cited by 601 · see citing works

Functions of FGF signalling from the apical ectodermal ridge in limb development

Sun, X., Mariani, F. V., & Martin, G. (2002) · Nature · doi:10.1038/nature00902 · Cited by 581 · see citing works

Cytogenetic analysis by chromosome painting using dop‐pcr amplified flow‐sorted chromosomes

Telenius, H., Ponder, B. A. J., Tunnacliffe, A., Pelmear, A., Carter, N. P., Ferguson-Smith, M. A., Behmel, A., Nordenskjöld, M., & Pfragner, R. (1992) · Genes Chromosomes and Cancer · doi:10.1002/gcc.2870040311 · Cited by 572 · see citing works

Dynamics of Single mRNPs in Nuclei of Living Cells

Shav‐Tal, Y., Darzacq, X., Shenoy, S. M., Fusco, D. N., Janicki, S. M., Spector, D. L., & Singer, R. H. (2004) · Science · doi:10.1126/science.1099754 · Cited by 494 · see citing works

Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei

Volpi, E. V., Chevret, E., Jones, T., Vatcheva, R., Williamson, J. A., Beck, S., Campbell, R. D., Goldsworthy, M. E., Powis, S. H., Ragoussis, J., et al. (2000) · Journal of Cell Science · doi:10.1242/jcs.113.9.1565 · Cited by 441 · 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

Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates

Tanabe, H., Müller, S., Neusser, M., Hase, J. V., Calcagno, E., Cremer, M., Solovei, I. V., Cremer, C. G., & Cremer, T. J. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.072618599 · Cited by 399 · see citing works

Elimination of a long-range cis-regulatory module causes complete loss of limb-specificShhexpression and truncation of the mouse limb

Sagai, T., Hosoya, M., Mizushina, Y., Tamura, M., & Shiroishi, T. (2005) · Development · doi:10.1242/dev.01613 · Cited by 379 · see citing works

Remote control of gene transcription

West, A. G., & Fraser, P. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi104 · Cited by 302 · see citing works

Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH

Mahy, N. L., Perry, P. E., & Bickmore, W. A. (2002) · The Journal of Cell Biology · doi:10.1083/jcb.200207115 · Cited by 295 · see citing works

A Dual Role for <i>Hox</i> Genes in Limb Anterior-Posterior Asymmetry

Zákány, J., Kmita, M., & Duboule, D. (2004) · Science · doi:10.1126/science.1096049 · Cited by 271 · see citing works

Spatial Preservation of Nuclear Chromatin Architecture during Three-Dimensional Fluorescence in Situ Hybridization (3D-FISH)

Solovei, I. V., Cavallo, A., Schermelleh, L., Jaunin, F., Scasselati, C., Cmarko, D., Cremer, C. G., Fakan, S., & Cremer, T. J. (2002) · Experimental Cell Research · doi:10.1006/excr.2002.5513 · Cited by 267 · see citing works

Early developmental arrest of mammalian limbs lacking HoxA/HoxD gene function

Kmita, M., Tarchini, B., Zákány, J., Logan, M. P. O., Tabin, C. J., & Duboule, D. (2005) · Nature · doi:10.1038/nature03648 · Cited by 263 · see citing works

Spatial Relationship between Transcription Sites and Chromosome Territories

Verschure, P. J., van der Kraan, I., Manders, E. M. M., & DRIEL, R. V. (1999) · The Journal of Cell Biology · doi:10.1083/jcb.147.1.13 · Cited by 250 · see citing works

A functional screen for sonic hedgehog regulatory elements across a 1 Mb interval identifies long-range ventral forebrain enhancers

Jeong, Y., El-Jaick, K. B., Roessler, E., Muenke, M., & Epstein, D. J. (2006) · Development · doi:10.1242/dev.02239 · Cited by 227 · see citing works

Spatial organization of active and inactive genes and noncoding DNA within chromosome territories

Mahy, N. L., Perry, P. E., Gilchrist, S., Baldock, R., & Bickmore, W. A. (2002) · The Journal of Cell Biology · doi:10.1083/jcb.200111071 · Cited by 225 · see citing works

Subchromosomal Positioning of the Epidermal Differentiation Complex (EDC) in Keratinocyte and Lymphoblast Interphase Nuclei

Williams, R. R. E., Broad, S., Sheer, D., & Ragoussis, J. (2002) · Experimental Cell Research · doi:10.1006/excr.2001.5400 · Cited by 210 · see citing works

The number of polarizing region cells required to specify additional digits in the developing chick wing

Tickle, C. A. (1981) · Nature · doi:10.1038/289295a0 · Cited by 208 · see citing works

Coregulated human globin genes are frequently in spatial proximity when active

Brown, J. M., Leach, J., Reittie, J. E., Atzberger, A., Lee-Prudhoe, J., Wood, W. G., Higgs, D. R., Iborra, F. J., & Buckle, V. J. (2006) · The Journal of Cell Biology · doi:10.1083/jcb.200507073 · Cited by 204 · see citing works

Nuclear re-organisation of the Hoxb complex during mouse embryonic development

Chambeyron, S., Silva, N. D., Lawson, K. A., & Bickmore, W. A. (2005) · Development · doi:10.1242/dev.01813 · Cited by 202 · see citing works

Nuclear reorganisation and chromatin decondensation are conserved, but distinct, mechanisms linked to Hox gene activation

Morey, C., Silva, N. D., Perry, P., & Bickmore, W. A. (2007) · Development · doi:10.1242/dev.02779 · Cited by 194 · see citing works

The genome and the nucleus: a marriage made by evolution

Foster, H. A., & Bridger, J. M. (2005) · Chromosoma · doi:10.1007/s00412-005-0016-6 · Cited by 183 · see citing works

Pbx1/Pbx2requirement for distal limb patterning is mediated by the hierarchical control of Hox gene spatial distribution andShhexpression

Capellini, T. D., Giacomo, G. D., Salsi, V., Brendolan, A., Ferretti, E., Srivastava, D., Zappavigna, V., & Selleri, L. (2006) · Development · doi:10.1242/dev.02395 · Cited by 178 · see citing works

Regionalization of Sonic hedgehog transcription along the anteroposterior axis of the mouse central nervous system is regulated by Hnf3-dependent and -independent mechanisms

Epstein, D. J., McMahon, A. P., & Joyner, A. L. (1999) · Development · doi:10.1242/dev.126.2.281 · Cited by 170 · see citing works

Phylogenetic conservation of a limb-specific, cis-acting regulator of Sonic hedgehog (Shh)

Sagai, T., Masuya, H., Tamura, M., Shimizu, K., Yada, Y., Wakana, S., Gondo, Y., Noda, T., & Shiroishi, T. (2004) · Mammalian Genome · doi:10.1007/s00335-033-2317-5 · Cited by 163 · see citing works

Transcription Sites Are Not Correlated with Chromosome Territories in Wheat Nuclei

Abranches, R., Beven, A. F., Aragón-Alcaide, L., & Shaw, P. (1998) · The Journal of Cell Biology · doi:10.1083/jcb.143.1.5 · Cited by 154 · see citing works

Hoxd-12 differentially affects preaxial and postaxial chondrogenic branches in the limb and regulates Sonic hedgehog in a positive feedback loop

Knežević, V., Santo, R. J. D., Schughart, K., Huffstadt, U., Chiang, C. C., Mahon, K. A., & Mackem, S. (1997) · Development · doi:10.1242/dev.124.22.4523 · Cited by 131 · see citing works

A genetic analysis of chromosome territory looping: diverse roles for distal regulatory elements

Ragoczy, T., Telling, A., Sawado, T., Groudine, M. T., & Kosak, S. T. (2003) · Chromosome Research · doi:10.1023/a:1024939130361 · Cited by 123 · see citing works

Multigenic Control of the Localization of the Zone of Polarizing Activity in Limb Morphogenesis in the Mouse

Masuya, H., Sagai, T., Moriwaki, K., & Shiroishi, T. (1997) · Developmental Biology · doi:10.1006/dbio.1996.8457 · Cited by 112 · see citing works

Chromatin looping and the probability of transcription

Li, Q., Barkess, G., & QIAN, H. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.02.004 · Cited by 95 · see citing works

Topology of genes and nontranscribed sequences in human interphase nuclei

Scheuermann, M. O., Tajbakhsh, J., Kurz, A., Saracoglu, K., Eils, R., & Lichter, P. (2004) · Experimental Cell Research · doi:10.1016/j.yexcr.2004.08.031 · Cited by 86 · see citing works

FISH : a practical approach

Beatty, B., Mai, S., & Squire, J. (2002) · Oxford University Press eBooks · Cited by 85 · see citing works

Transcribed genes are localized according to chromosomal position within polarized Drosophila embryonic nuclei

Wilkie, G. S., Shermoen, A. W., O’Farrell, P. H., & Davis, I. (1999) · Current Biology · doi:10.1016/s0960-9822(99)80509-0 · Cited by 79 · see citing works

FISH on three-dimensionally preserved nuclei

Solovei, I. V., Walter, J., Cremer, M., Habermann, F. A., Schermelleh, L., & Cremer, T. J. (2002) · doi:10.1093/oso/9780199638833.003.0007 · Cited by 70 · see citing works

A series of ENU-induced single-base substitutions in a long-range cis-element altering Sonic hedgehog expression in the developing mouse limb bud

Masuya, H., Sezutsu, H., Sakuraba, Y., Sagai, T., Hosoya, M., Kaneda, H., Miura, I., Kobayashi, K., Sumiyama, K., Shimizu, A., et al. (2007) · Genomics · doi:10.1016/j.ygeno.2006.09.005 · Cited by 64 · see citing works

Nascent RNA synthesis in the context of chromatin architecture

Sadoni, N., & Zink, D. (2004) · Chromosome Research · doi:10.1023/b:chro.0000034739.96307.8d · Cited by 21 · see citing works

Seven-fluorochrome mouse M-FISH for high-resolution analysis of interchromosomal rearrangements

Jentsch, I., Geigl, J. B., Klein, C. A., & Speicher, M. R. (2003) · Cytogenetic and Genome Research · doi:10.1159/000076294 · Cited by 20 · see citing works

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212 · see citing works

Transcription factors: from enhancer binding to developmental control

Spitz, F., & Furlong, E. E. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3207 · Cited by 2,227 · see citing works

Transcriptional enhancers: from properties to genome-wide predictions

Shlyueva, D., Stampfel, G., & Stark, A. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3682 · Cited by 1,356 · see citing works

Organization and function of the 3D genome

Bonev, B., & Cavalli, G. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.112 · Cited by 1,174 · 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

Long-range enhancer–promoter contacts in gene expression control

Schoenfelder, S., & Fraser, P. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0128-0 · Cited by 1,102 · see citing works

Functional and Mechanistic Diversity of Distal Transcription Enhancers

Bulger, M., & Groudine, M. (2011) · Cell · doi:10.1016/j.cell.2011.01.024 · Cited by 803 · see citing works

Genomic views of distant-acting enhancers

Visel, A., Rubin, E. M., & Pennacchio, L. A. (2009) · Nature · doi:10.1038/nature08451 · Cited by 610 · see citing works

Topology of mammalian developmental enhancers and their regulatory landscapes

de Laat, W., & Duboule, D. (2013) · Nature · doi:10.1038/nature12753 · Cited by 521 · see citing works

Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription

Giorgetti, L., Galupa, R., Nora, E. P., Piolot, T., Lam, F., Dekker, J., Tiana, G., & Heard, E. (2014) · Cell · doi:10.1016/j.cell.2014.03.025 · Cited by 460 · see citing works

Looping Back to Leap Forward: Transcription Enters a New Era

Levine, M., Cattoglio, C., & Tjian, R. (2014) · Cell · doi:10.1016/j.cell.2014.02.009 · Cited by 481 · see citing works

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

Montavon, T., Soshnikova, N., Mascrez, B., Joye, E., Thevenet, L., Splinter, E., de Laat, W., Spitz, F., & Duboule, D. (2011) · Cell · doi:10.1016/j.cell.2011.10.023 · Cited by 477 · see citing works

Transcriptional Enhancers in Animal Development and Evolution

Levine, M. (2010) · Current Biology · doi:10.1016/j.cub.2010.06.070 · Cited by 449 · see citing works

Functional and topological characteristics of mammalian regulatory domains

Symmons, O., Uslu, V. V., Tsujimura, T., Ruf, S., Nassari, S., Schwarzer, W., Ettwiller, L., & Spitz, F. (2014) · Genome Research · doi:10.1101/gr.163519.113 · Cited by 455 · see citing works

Vertebrate limb bud development: moving towards integrative analysis of organogenesis

Zeller, R., López-Ríos, J., & Zuniga, A. (2009) · Nature reviews genetics · doi:10.1038/nrg2681 · Cited by 469 · see citing works

Breaking TADs: How Alterations of Chromatin Domains Result in Disease

Lupiáñez, D. G., Spielmann, M., & Mundlos, S. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.01.003 · Cited by 439 · see citing works

Nonlinear control of transcription through enhancer–promoter interactions

Zuin, J., Roth, G., Zhan, Y., Cramard, J., Redolfi, J., Piskadlo, E., Mach, P., Kryzhanovska, M., Tihanyi, G., Kohler, H., et al. (2022) · Nature · doi:10.1038/s41586-022-04570-y · Cited by 415 · see citing works

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

de la Torre-Ubieta, L., Stein, J. L., Won, H., Opland, C. K., Liang, D., Lu, D., & Geschwind, D. H. (2018) · Cell · doi:10.1016/j.cell.2017.12.014 · Cited by 353 · see citing works

The Spatial Organization of the Human Genome

Bickmore, W. A. (2013) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-091212-153515 · Cited by 391 · see citing works

MYRF is a membrane-associated transcription factor that autoproteolytically cleaves to directly activate myelin genes

Bujalka, H., Koenning, M., Jackson, S., Perreau, V. M., Pope, B., Hay, C. M., Mitew, S., Hill, A. F., Lu, Q. R., Wegner, M., et al. (2013) · PLoS Biology · doi:10.1371/journal.pbio.1001625 · Cited by 271 · see citing works

Distinct Roles of Hand2 in Initiating Polarity and Posterior Shh Expression during the Onset of Mouse Limb Bud Development

Galli, A., Robay, D., Osterwalder, M., Bao, X., Bénazet, J.-D., Tariq, M., Paro, R., Mackem, S., & Zeller, R. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000901 · Cited by 270 · see citing works

Cohesin and CTCF control the dynamics of chromosome folding

Mach, P., Kos, P. I., Zhan, Y., Cramard, J., Gaudin, S., Tünnermann, J., Marchi, E., Eglinger, J., Zuin, J., Kryzhanovska, M., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01232-7 · Cited by 269 · see citing works

Nuclear compartmentalization as a mechanism of quantitative control of gene expression

Bhat, P., Honson, D. D., & Guttman, M. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00387-1 · Cited by 230 · see citing works

Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridizationPreprint

Williamson, I., Berlivet, S., Eskeland, R., Boyle, S., Illingworth, R. S., Paquette, D., Dostie, J., & Bickmore, W. A. (2014) · Genes & Development · doi:10.1101/gad.251694.114 · Cited by 229 · see citing works

Enhancer and promoter interactions—long distance calls

Krivega, I., & Dean, A. (2012) · Current Opinion in Genetics &amp; Development · doi:10.1016/j.gde.2011.11.001 · Cited by 225 · see citing works

An Overview of Genome Organization and How We Got There: from FISH to Hi-C

Fraser, J., Williamson, I., Bickmore, W. A., & Dostie, J. (2015) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00006-15 · Cited by 218 · see citing works

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances

Symmons, O., Pan, L., Remeseiro, S., Aktas, T., Klein, F., Huber, W., & Spitz, F. (2016) · Developmental Cell · doi:10.1016/j.devcel.2016.10.015 · Cited by 222 · see citing works

Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function

McCord, R. P., Kaplan, N., & Giorgetti, L. (2020) · Molecular Cell · doi:10.1016/j.molcel.2019.12.021 · Cited by 204 · see citing works

Limb development: a paradigm of gene regulation

Petit, F., Sears, K. E., & Ahituv, N. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2016.167 · Cited by 188 · see citing works

What’s Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism

Symmons, O., & Raj, A. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.05.023 · Cited by 180 · 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

In search of the determinants of enhancer–promoter interaction specificity

van Arensbergen, J., van Steensel, B., & Bussemaker, H. J. (2014) · Trends in Cell Biology · doi:10.1016/j.tcb.2014.07.004 · Cited by 172 · see citing works

Preformed chromatin topology assists transcriptional robustness of <i>Shh</i> during limb development

Paliou, C., Guckelberger, P., Schöpflin, R., Heinrich, V., Esposito, A., Chiariello, A. M., Bianco, S., Annunziatella, C., Helmuth, J., Haas, S., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1900672116 · Cited by 163 · see citing works

A Muscle-Specific Enhancer RNA Mediates Cohesin Recruitment and Regulates Transcription In trans

Tsai, P.-F., Dell’Orso, S., Rodriguez, J., Vivanco, K. O., Ko, K.-D., Jiang, K., Juan, A. H., Sarshad, A. A., Vian, L., Tran, M. D., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.06.008 · Cited by 178 · see citing works

Clustering of Tissue-Specific Sub-TADs Accompanies the Regulation of HoxA Genes in Developing Limbs

Berlivet, S., Paquette, D., Dumouchel, A., Langlais, D., Dostie, J., & Kmita, M. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1004018 · Cited by 170 · see citing works

Non-exomic and synonymous variants in ABCA4 are an important cause of Stargardt disease

Braun, T. A., Mullins, R. F., Wagner, A. H., Andorf, J. L., Johnston, R. M., Bakall, B., DeLuca, A. P., Fishman, G. A., Lam, B. L., Weleber, R. G., et al. (2013) · Human Molecular Genetics · doi:10.1093/hmg/ddt367 · Cited by 178 · see citing works

Sonic Hedgehog Signaling in Limb Development

Tickle, C. A., & Towers, M. (2017) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2017.00014 · Cited by 178 · see citing works

Genomics of Long-Range Regulatory Elements

Noonan, J. P., & McCallion, A. S. (2010) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082509-141651 · Cited by 159 · see citing works

Unraveling Hematopoiesis through the Lens of Genomics

Liggett, L. A., & Sankaran, V. G. (2020) · Cell · doi:10.1016/j.cell.2020.08.030 · Cited by 163 · see citing works

The transcriptional interactome: gene expression in 3D

Schoenfelder, S., Clay, I., & Fraser, P. (2010) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2010.02.002 · Cited by 158 · see citing works

The spatial organization of transcriptional control

Hafner, A., & Boettiger, A. N. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00526-0 · Cited by 150 · see citing works

Opposing Functions of the ETS Factor Family Define Shh Spatial Expression in Limb Buds and Underlie Polydactyly

Lettice, L. A., Williamson, I., Wiltshire, J. H., Peluso, S., Devenney, P. S., Hill, A. E., Essafi, A., Hagman, J., Mort, R., Grimes, G., et al. (2012) · Developmental Cell · doi:10.1016/j.devcel.2011.12.010 · Cited by 153 · see citing works

The Hierarchy of Transcriptional Activation: From Enhancer to Promoter

Vernimmen, D., & Bickmore, W. A. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.10.004 · Cited by 155 · see citing works

Looking beyond the genes: the role of non-coding variants in human disease

Spielmann, M., & Mundlos, S. (2016) · Human Molecular Genetics · doi:10.1093/hmg/ddw205 · Cited by 143 · see citing works

Variegated gene expression caused by cell-specific long-range DNA interactions

Noordermeer, D., de Wit, E., Klous, P., van de Werken, H. J. G., Simonis, M., Lopez-Jones, M., Eussen, B. J. F. M. M., de Klein, A., Singer, R. H., & de Laat, W. L. (2011) · Nature Cell Biology · doi:10.1038/ncb2278 · Cited by 150 · see citing works

An Integrated Holo-Enhancer Unit Defines Tissue and Gene Specificity of the Fgf8 Regulatory Landscape

Marinić, M., Aktaş, T., Ruf, S., & Spitz, F. (2013) · Developmental Cell · doi:10.1016/j.devcel.2013.01.025 · Cited by 142 · see citing works

Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus

Smith, E. M., Lajoie, B. R., Jain, G., & Dekker, J. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.12.002 · Cited by 142 · see citing works

Complementary Alu sequences mediate enhancer–promoter selectivity

Liang, L., Cao, C., Ji, L., Cai, Z., Wang, D., Ye, R., Chen, J., Yu, X., Zhou, J., Bai, Z., et al. (2023) · Nature · doi:10.1038/s41586-023-06323-x · Cited by 138 · see citing works

The three-dimensional genome: regulating gene expression during pluripotency and development

Andrey, G., & Mundlos, S. (2017) · Development · doi:10.1242/dev.148304 · Cited by 129 · see citing works

Epigenetic Regulation of Gene Expression in Keratinocytes

Botchkarev, V. A., Gdula, M. R., Mardaryev, A. N., Sharov, A. A., & Fessing, M. Y. (2012) · Journal of Investigative Dermatology · doi:10.1038/jid.2012.182 · Cited by 127 · see citing works

<i>Shh</i> and ZRS enhancer colocalisation is specific to the zone of polarising activity

Williamson, I., Lettice, L. A., Hill, R. E., & Bickmore, W. A. (2016) · Development · doi:10.1242/dev.139188 · Cited by 124 · see citing works

A misplaced lncRNA causes brachydactyly in humans

Maass, P. G., Rump, A., Schulz, H., Stricker, S., Schulze, L., Platzer, K., Aydın, A., Tinschert, S., Goldring, M. B., Luft, F. C., et al. (2012) · Journal of Clinical Investigation · doi:10.1172/jci65508 · Cited by 120 · see citing works

Genomic interactions: Chromatin loops and gene meeting points in transcriptional regulation

Sexton, T., Bantignies, F., & Cavalli, G. (2009) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2009.06.004 · Cited by 117 · see citing works

A far downstream enhancer for murine Bcl11b controls its T-cell specific expression

Li, L., Zhang, J. A., Dose, M., Kueh, H. Y., Mosadeghi, R., Gounari, F., & Rothenberg, E. V. (2013) · Blood · doi:10.1182/blood-2012-08-447839 · Cited by 115 · see citing works

Enhancers, enhancers – from their discovery to today’s universe of transcription enhancers

Schaffner, W. (2015) · Biological Chemistry · doi:10.1515/hsz-2014-0303 · Cited by 105 · see citing works

The genomic landscape of cohesin-associated chromatin interactions

DeMare, L. E., Leng, J., Cotney, J., Reilly, S. K., Yin, J., Sarro, R., & Noonan, J. P. (2013) · Genome Research · doi:10.1101/gr.156570.113 · Cited by 114 · see citing works

Cis-regulatory mutations in human disease

Epstein, D. J. (2009) · Briefings in Functional Genomics and Proteomics · doi:10.1093/bfgp/elp021 · Cited by 113 · see citing works

Getting the genome in shape: the formation of loops, domains and compartments

Bouwman, B. A. M., & de Laat, W. L. (2015) · Genome biology · doi:10.1186/s13059-015-0730-1 · Cited by 109 · see citing works

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

Schoenfelder, S., Javierre, B. M., Furlan-Magaril, M., Wingett, S., & Fraser, P. (2018) · Journal of Visualized Experiments · doi:10.3791/57320 · Cited by 114 · see citing works

Large-scale chromatin organization: the good, the surprising, and the still perplexing

Belmont, A. S. (2013) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2013.10.002 · Cited by 104 · see citing works

Chromatin and epigenetic features of long-range gene regulation

Harmston, N., & Lenhard, B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt499 · Cited by 107 · see citing works

Identification of Plant Enhancers and Their Constituent Elements by STARR-seq in Tobacco Leaves

Jores, T., Tonnies, J., Dorrity, M. W., Cuperus, J. T., Fields, S., & Queitsch, C. (2020) · The Plant Cell · doi:10.1105/tpc.20.00155 · Cited by 102 · see citing works

A cluster of three long-range enhancers directs regionalShhexpression in the epithelial linings

Sagai, T., Amano, T., Tamura, M., Mizushina, Y., Sumiyama, K., & Shiroishi, T. (2009) · Development · doi:10.1242/dev.032714 · Cited by 102 · see citing works

Human limb abnormalities caused by disruption of hedgehog signaling

Anderson, E., Peluso, S., Lettice, L. A., & Hill, R. E. (2012) · Trends in Genetics · doi:10.1016/j.tig.2012.03.012 · Cited by 95 · see citing works

Interchromosomal association and gene regulation in trans

Williams, A., Spilianakis, C. G., & Flavell, R. A. (2010) · Trends in Genetics · doi:10.1016/j.tig.2010.01.007 · Cited by 91 · see citing works

Minor Loops in Major Folds: Enhancer–Promoter Looping, Chromatin Restructuring, and Their Association with Transcriptional Regulation and Disease

Matharu, N. K., & Ahituv, N. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005640 · Cited by 88 · see citing works

Cis-ruption mechanisms: disruption of cis-regulatory control as a cause of human genetic disease

Kleinjan, D., & Coutinho, P. (2009) · Briefings in Functional Genomics and Proteomics · doi:10.1093/bfgp/elp022 · Cited by 83 · see citing works

GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data

Harmston, N., Ing-Simmons, E., Perry, M., Barešić, A., & Lenhard, B. (2015) · BMC Genomics · doi:10.1186/s12864-015-2140-x · Cited by 67 · see citing works

The role of 3D chromatin domains in gene regulation: a multi-facetted view on genome organization

Ibrahim, D. M., & Mundlos, S. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.02.015 · Cited by 79 · see citing works

Using transgenic reporter assays to functionally characterize enhancers in animals

Kvon, E. Z. (2015) · Genomics · doi:10.1016/j.ygeno.2015.06.007 · Cited by 73 · see citing works

Mapping the Shh long-range regulatory domain

Anderson, E., Devenney, P. S., Hill, R., & Lettice, L. (2014) · Development · doi:10.1242/dev.108480 · Cited by 86 · see citing works

Transcriptional enhancers and their communication with gene promoters

Ray-Jones, H., & Spivakov, M. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03903-w · Cited by 81 · see citing works

Twist1 activity thresholds define multiple functions in limb development

Krawchuk, D., Weiner, S. J., Chen, Y., Lu, B. C., Costantini, F. D., Behringer, R. R., & Laufer, E. (2010) · Developmental Biology · doi:10.1016/j.ydbio.2010.08.015 · Cited by 74 · see citing works

Enhancers: From Developmental Genetics to the Genetics of Common Human Disease

Williamson, I., Hill, R. E., & Bickmore, W. A. (2011) · Developmental Cell · doi:10.1016/j.devcel.2011.06.008 · Cited by 71 · see citing works

cis‐regulatory mutations are a genetic cause of human limb malformations

VanderMeer, J. E., & Ahituv, N. (2011) · Developmental Dynamics · doi:10.1002/dvdy.22535 · Cited by 73 · see citing works

Gene PositioningPreprint

Ferrai, C., de Castro, I. J., Lavitas, L.-M., Chotalia, M., & Pombo, A. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a000588 · Cited by 72 · see citing works

Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA

Mateo, L. J., Sinnott-Armstrong, N., & Boettiger, A. N. (2021) · Nature Protocols · doi:10.1038/s41596-020-00478-x · Cited by 64 · see citing works

Development of five digits is controlled by a bipartite long-range cis -regulator

Lettice, L. A., Williamson, I., Devenney, P. S., Kilanowski, F. M., Dorin, J. R., & Hill, R. E. (2014) · Development · doi:10.1242/dev.095430 · Cited by 71 · see citing works

Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features

Chen, C., Morris, Q., & Mitchell, J. A. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-152 · Cited by 70 · see citing works

Nipbl and Mediator Cooperatively Regulate Gene Expression to Control Limb Development

Muto, A., Ikeda, S., Lopez‐Burks, M. E., Kikuchi, Y., Calof, A. L., Lander, A. D., & Schilling, T. F. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004671 · Cited by 69 · see citing works

The regulatory landscapes of developmental genes

Bolt, C. C., & Duboule, D. (2020) · Development · doi:10.1242/dev.171736 · Cited by 60 · see citing works

A Genetic Approach to the Transcriptional Regulation ofHoxGene Clusters

Tschopp, P., & Duboule, D. (2011) · Annual Review of Genetics · doi:10.1146/annurev-genet-102209-163429 · Cited by 66 · see citing works

The interdependence of gene-regulatory elements and the 3D genome

Vermunt, M. W., Zhang, D., & Blobel, G. A. (2018) · The Journal of Cell Biology · doi:10.1083/jcb.201809040 · Cited by 65 · see citing works

Activation of Estrogen-Responsive Genes Does Not Require Their Nuclear Co-Localization

Kocanova, S., Kerr, E. A., Rafique, S., Boyle, S., Katz, E., Caze-Subra, S., Bickmore, W. A., & Bystricky, K. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000922 · Cited by 66 · see citing works

Etiology and Morphogenesis of Congenital Heart Disease

Yamagishi, H., Srivastava, D., Keller, B. B., Hs, B., Markwald, R. R., & Nakanishi, T. (2016) · Springer eBooks · doi:10.1007/978-4-431-54628-3 · Cited by 66 · see citing works

Structural variations, the regulatory landscape of the genome and their alteration in human disease.

Spielmann, M., & Mundlos, S. (2013) · Bioessays · doi:10.1002/bies.201200178 · Cited by 69 · 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

Lactogenic Hormonal Induction of Long Distance Interactions between β-Casein Gene Regulatory Elements

Kabotyanski, E. B., Rijnkels, M., Freeman-Zadrowski, C., Buser, A. C., Edwards, D. P., & Rosen, J. M. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.032490 · Cited by 65 · see citing works

Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective

Kumar, S., Kaur, S., Seem, K., Kumar, S., & Mohapatra, T. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.774719 · Cited by 66 · see citing works

Anterior-posterior differences in HoxD chromatin topology in limb development

Williamson, I., Eskeland, R., Lettice, L. A., Hill, A. E., Boyle, S., Grimes, G. R., Hill, R. E., & Bickmore, W. A. (2012) · Development · doi:10.1242/dev.081174 · Cited by 62 · see citing works

Do chromatin loops provide epigenetic gene expression states?

Deng, W., & Blobel, G. A. (2010) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2010.06.007 · Cited by 57 · see citing works

Transcriptional regulation of graded Hedgehog signaling

Falkenstein, K. N., & Vokes, S. A. (2014) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2014.05.010 · Cited by 59 · see citing works

Plant 3D genomics: the exploration and application of chromatin organization

Pei, L., Li, G., Lindsey, K., Zhang, X., & Wang, M. (2021) · New Phytologist · doi:10.1111/nph.17262 · Cited by 56 · see citing works

The temporal dynamics of vertebrate limb development, teratogenesis and evolution

Zeller, R. (2010) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2010.04.014 · Cited by 57 · see citing works

C‐ing the Genome: A Compendium of Chromosome Conformation Capture Methods to Study Higher‐Order Chromatin Organization

Barutcu, A. R., Fritz, A. J., Zaidi, S. K., van Wijnen, A. J., Lian, J. B., Stein, J. L., Nickerson, J. A., Imbalzano, A. N., & Stein, G. S. (2015) · Journal of Cellular Physiology · doi:10.1002/jcp.25062 · Cited by 57 · see citing works

Functional CRISPR screen identifies AP1-associated enhancer regulating FOXF1 to modulate oncogene-induced senescence

Han, R., Li, L., Ugalde, A. P., Tal, A., Manber, Z., Barberà, E. P., Chiara, V. D., Elkon, R., & Agami, R. (2018) · Genome biology · doi:10.1186/s13059-018-1494-1 · Cited by 53 · see citing works

Three-dimensional organization and dynamics of the genome

Szałaj, P., & Plewczyński, D. (2018) · Cell Biology and Toxicology · doi:10.1007/s10565-018-9428-y · Cited by 54 · see citing works

3D genome organization: a role for phase separation and loop extrusion?

Stam, M. E., Tark‐Dame, M., & Fransz, P. F. (2019) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2019.03.008 · Cited by 54 · see citing works

Developmental, genetic, and genomic insights into the evolutionary loss of limbs in snakes

Leal, F., & Cohn, M. J. (2017) · genesis · doi:10.1002/dvg.23077 · Cited by 57 · see citing works

Identification of two novel mutations in Shh long-range regulator associated with familial pre-axial polydactyly

Albuisson, J., Isidor, B., Giraud, M., Pichon, O., Marsaud, T., David, A., Caignec, C. L., & Bezieau, S. (2010) · Clinical Genetics · doi:10.1111/j.1399-0004.2010.01465.x · Cited by 51 · see citing works

Fly Fishing with a Hedgehog

(2009) · Science · doi:10.1126/science.323.5913.439c

3D Chromatin Regulation of Sonic Hedgehog in the Limb Buds

Ferrai, C., & Pombo, A. (2009) · Developmental Cell · doi:10.1016/j.devcel.2008.12.010 · Cited by 6 · see citing works

<i>Shh</i> and ZRS enhancer colocalisation is specific to the zone of polarising activity

Williamson, I., Lettice, L. A., Hill, R. E., & Bickmore, W. A. (2016) · Development · doi:10.1242/dev.139188 · Cited by 124 · see citing works

Chromatin dynamics at the Sonic Hedgehog locus : a study using limb derived Sonic Hedgehog inducible cell lines to investigate chromatin architecture

Douglas, A. (2017) · ERA

Transcriptional dynamics of the Sonic hedgehog gene

Graham, K. A. (2023) · ERA · doi:10.7488/era/3524