Enhancer loops appear stable during development and are associated with paused polymerase

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482

Differential expression analysis for sequence count data

Anders, S., & Huber, W. (2010) · Genome Biology · doi:10.1186/gb-2010-11-10-r106 · Cited by 15,581

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

Genetic Transformation of Drosophila with Transposable Element Vectors

Rubin, G. M., & Spradling, A. C. (1982) · Science · doi:10.1126/science.6289436 · Cited by 2,996

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

Ross-Innes, C. S., Stark, R., Teschendorff, A. E., Holmes, K. A., Ali, H. R., Dunning, M., Brown, G. D., Gojiš, O., Ellis, I. O., Green, A. R., et al. (2012) · Nature · doi:10.1038/nature10730 · Cited by 2,182

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

The developmental transcriptome of Drosophila melanogaster

Graveley, B. R., Brooks, A. N., Carlson, J. W., Duff, M. O., Landolin, J. M., Yang, L. C., Artieri, C. G., van Baren, M. J., Boley, N. P., Booth, B. W., et al. (2010) · Nature · doi:10.1038/nature09715 · Cited by 1,504

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

Differential Oestrogen Receptor Binding is Associated with Clinical Outcome in Breast Cancer

Stark, R. (2012) · Lecture notes in computer science · doi:10.1007/978-3-642-29627-7_30 · Cited by 1,403

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

Promoter architectures and developmental gene regulation

Haberle, V., & Lenhard, B. (2016) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2016.01.014 · Cited by 94

Conserved Higher-Order Chromatin Regulates NMDA Receptor Gene Expression and Cognition

Bharadwaj, R., Peter, C. J., Jiang, Y., Roussos, P., Vogel-Ciernia, A., Shen, E. Y., Mitchell, A. C., Mao, W., Whittle, C., Dincer, A., et al. (2014) · Neuron · doi:10.1016/j.neuron.2014.10.032 · Cited by 84

Increased enhancer–promoter interactions during developmental enhancer activation in mammals

Chen, Z., Snetkova, V., Bower, G., Jacinto, S. H., Clock, B., Dizehchi, A., Barozzi, I., Mannion, B. J., Alcaina‐Caro, A., López-Ríos, J., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01681-2 · Cited by 98

Combined Cohesin–RUNX1 Deficiency Synergistically Perturbs Chromatin Looping and Causes Myelodysplastic Syndromes

Ochi, Y., Kon, A., Sakata, T., Nakagawa, M. M., Nakazawa, N., Kakuta, M., Kataoka, K., Koseki, H., Nakayama, M., Morishita, D., et al. (2020) · Cancer Discovery · doi:10.1158/2159-8290.cd-19-0982 · Cited by 86

Enhancer–promoter interactions become more instructive in the transition from cell-fate specification to tissue differentiation

Pollex, T., Rabinowitz, A. H., Gambetta, M. C., Marco-Ferreres, R., Viales, R. R., Jankowski, A., Schaub, C., & Furlong, E. E. M. (2024) · Nature Genetics · doi:10.1038/s41588-024-01678-x · Cited by 90

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 87

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

An autonomous CEBPA enhancer specific for myeloid-lineage priming and neutrophilic differentiation

Avellino, R., Havermans, M., Erpelinck-Verschueren, C. A. J., Sanders, M. A., Hoogenboezem, R. M., van de Werken, H. J. G., Rombouts, E. J. C., van Lom, K., van Strien, P. M. H., Gebhard, C., et al. (2016) · Blood · doi:10.1182/blood-2016-01-695759 · Cited by 87

Forces driving the three‐dimensional folding of eukaryotic genomes

Rada-Iglesias, Á., Grosveld, F. G., & Papantonis, A. (2018) · Molecular Systems Biology · doi:10.15252/msb.20188214 · Cited by 84

Transcriptional reprogramming at the intersection of the heat shock response and proteostasis

Pessa, J. C., Joutsen, J., & Sistonen, L. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.11.024 · Cited by 85

From genetic associations to genes: methods, applications, and challenges

Qi, T., Song, L., Guo, Y., Chen, C., & Yang, J. (2024) · Trends in Genetics · doi:10.1016/j.tig.2024.04.008 · Cited by 85

Molecular mechanisms of floral organ specification by MADS domain proteins

Yan, W., Chen, D., & Kaufmann, K. (2016) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2015.12.004 · Cited by 82

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

RNA polymerase II clusters form in line with surface condensation on regulatory chromatin

Pancholi, A., Klingberg, T., Zhang, W., Prizak, R., Mamontova, I., Noa, A., Sobucki, M., Kobitski, A. Y., Nienhaus, G. U., Zaburdaev, V., et al. (2021) · Molecular Systems Biology · doi:10.15252/msb.202110272 · Cited by 85

Chromosome-level organization of the regulatory genome in the Drosophila nervous system

Mohana, G., Dorier, J., Li, X., Mouginot, M., Smith, R. C., Malek, H., Leleu, M., Rodríguez, D., Khadka, J., Rosa, P., et al. (2023) · Cell · doi:10.1016/j.cell.2023.07.008 · Cited by 81

Topologically associated domains: a successful scaffold for the evolution of gene regulation in animals

Acemel, R. D., Maeso, I., & Gómez-Skármeta, J. L. (2017) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.265 · Cited by 82

HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization

Wei, X., Yu, X., Peters, D., Marius, C., Sun, T., Shan, R., Ou, J., Lin, X., Yue, F., Li, W., et al. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.01.023 · Cited by 84

Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler

Noack, F., Vangelisti, S., Raffl, G., Carido, M., Diwakar, J., Chong, F., & Bonev, B. (2022) · Nature Neuroscience · doi:10.1038/s41593-021-01002-4 · Cited by 76

Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long-range interactions inDrosophila

Zolotarev, N., Fedotova, A., Kyrchanova, O., Bonchuk, A. N., Penin, A. A., Lando, A. S., Eliseeva, I. A., Kulakovskiy, I. V., Maksimenko, O. G., & Georgiev, P. G. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw371 · Cited by 76

Three-Dimensional Genome Organization and Function in Drosophila

Schwartz, Y. B., & Cavalli, G. (2017) · Genetics · doi:10.1534/genetics.115.185132 · Cited by 77

Genetic Tailors: CTCF and Cohesin Shape the Genome During Evolution

Rudan, M. V., & Hadjur, S. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.09.004 · Cited by 70

Order and disorder: abnormal 3D chromatin organization in human disease

Anania, C., & Lupiáñez, D. G. (2019) · Briefings in Functional Genomics · doi:10.1093/bfgp/elz028 · Cited by 74

3D chromatin architecture and transcription regulation in cancer

Deng, S., Feng, Y., & Pauklin, S. (2022) · Journal of Hematology & Oncology · doi:10.1186/s13045-022-01271-x · Cited by 79

Perspectives: using polymer modeling to understand the formation and function of nuclear compartments

Haddad, N., Jost, D., & Vaillant, C. (2017) · Chromosome Research · doi:10.1007/s10577-016-9548-2 · Cited by 75

TRIM33 switches off Ifnb1 gene transcription during the late phase of macrophage activation

Ferri, F., Parcelier, A., Petit, V., Gallouet, A.-S., Lewandowski, D., Dalloz, M., van den Heuvel, A., Kolovos, P., Soler, E., Squadrito, M. L., et al. (2015) · Nature Communications · doi:10.1038/ncomms9900 · Cited by 70

Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum

Lu, X. M., Batugedara, G., Lee, M., Prudhomme, J. G., Bunnik, E. M., & Roch, K. G. L. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx464 · Cited by 64

Mechanisms of Transcription Elongation Factor DSIF (Spt4–Spt5)

Decker, T.-M. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.09.016 · Cited by 71

Functional characterization of Alzheimer’s disease genetic variants in microglia

Yang, X., Wen, J., Yang, H., Jones, I. R., Zhu, X., Liu, W., Li, B., Clelland, C. D., Luo, W., Wong, M. Y., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01506-8 · Cited by 71

HIV Tat controls RNA Polymerase II and the epigenetic landscape to transcriptionally reprogram target immune cells

Reeder, J. E., Kwak, Y.-T., McNamara, R. P., Forst, C. V., & D’Orso, I. (2015) · eLife · doi:10.7554/elife.08955 · Cited by 74

Mechanisms of Enhancer-Promoter Interactions in Higher Eukaryotes

Georgiev, P. G., & Kyrchanova, O. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22020671 · Cited by 72

REDfly: the transcriptional regulatory element database for Drosophila

Rivera, J., Keränen, S. V. E., Gallo, S. M., & Halfon, M. S. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky957 · Cited by 67

Reprogramming: identifying the mechanisms that safeguard cell identity

Brumbaugh, J., Stefano, B. D., & Hochedlinger, K. (2019) · Development · doi:10.1242/dev.182170 · Cited by 66

Alterations in promoter interaction landscape and transcriptional network underlying metabolic adaptation to diet

Qin, Y., Grimm, S. A., Roberts, J. D., Chrysovergis, K., & Wade, P. A. (2020) · Nature Communications · doi:10.1038/s41467-020-14796-x · Cited by 67

A Discrete Transition Zone Organizes the Topological and Regulatory Autonomy of the Adjacent Tfap2c and Bmp7 Genes

Tsujimura, T., Klein, F. A., Langenfeld, K., Glaser, J., Huber, W. K., & Spitz, F. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1004897 · Cited by 64

Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency

Atlasi, Y., Megchelenbrink, W., Peng, T., Habibi, E., Joshi, O., Wang, S.-Y., Wang, C., Logie, C., Poser, I., Marks, H., et al. (2019) · Nature Cell Biology · doi:10.1038/s41556-019-0310-9 · Cited by 62

Identifying transcriptional cis‐regulatory modules in animal genomes

Suryamohan, K., & Halfon, M. S. (2014) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.168 · Cited by 70

Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity

Pancaldi, V., Pau, E. C. D. S., Javierre, B. M., Juan, D., Fraser, P., Spivakov, M., Valencia, A., & Rico, D. (2016) · Genome biology · doi:10.1186/s13059-016-1003-3 · Cited by 66

Determining chromatin architecture with Micro Capture-C

Hamley, J. C., Li, H., Denny, N., Downes, D. J., & Davies, J. O. J. (2023) · Nature Protocols · doi:10.1038/s41596-023-00817-8 · Cited by 62

An Integrative Breakage Model of genome architecture, reshuffling and evolution

Farré, M., Robinson, T. J., & Ruiz‐Herrera, A. (2015) · BioEssays · doi:10.1002/bies.201400174 · Cited by 70

Single-cell profiling reveals that eRNA accumulation at enhancer–promoter loops is not required to sustain transcription

Rahman, S., Zorca, C. E., Traboulsi, T., Noutahi, E., Krause, M. R., Mader, S., & Zenklusen, D. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1220 · Cited by 63

A β-catenin-driven switch in TCF/LEF transcription factor binding to DNA target sites promotes commitment of mammalian nephron progenitor cells

Guo, Q., Kim, A., Li, B., Ransick, A., Bugacov, H., Chen, X., Lindström, N. O., Brown, A. C., Oxburgh, L. H., Ren, B., et al. (2021) · eLife · doi:10.7554/elife.64444 · Cited by 62

Chromatin Conformation in Development and Disease

Boltsis, I., Grosveld, F. G., Giraud, G., & Kolovos, P. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.723859 · Cited by 59

Mesoscale structure–function relationships in mitochondrial transcriptional condensates

Feric, M., Sarfallah, A., Dar, F., Temiakov, D., Pappu, R. V., & Misteli, T. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2207303119 · Cited by 57

CTCF, BEAF-32, and CP190 are not required for the establishment of TADs in early Drosophila embryos but have locus-specific roles

Cavalheiro, G. R., Girardot, C., Viales, R. R., Feng, S., Pollex, T., Cao, T. B. N., Lacour, P., Rabinowitz, A. H., & Furlong, E. E. M. (2023) · Science Advances · doi:10.1126/sciadv.ade1085 · Cited by 59

Understanding Spatial Genome Organization: Methods and Insights

Ramani, V., Shendure, J., & Duan, Z. (2016) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2016.01.002 · Cited by 66

Enhancer Sharing Promotes Neighborhoods of Transcriptional Regulation Across Eukaryotes

Quintero-Cadena, P., & Sternberg, P. W. (2016) · G3 Genes Genomes Genetics · doi:10.1534/g3.116.036228 · Cited by 55

Epigenetics/Programming in the HPA Axis

Buschdorf, J. P., & Meaney, M. J. (2015) · Comprehensive physiology · doi:10.1002/cphy.c140027 · Cited by 64

Topologically Associating Domains and Regulatory Landscapes in Development, Evolution and Disease

Tena, J. J., & Santos-Pereira, J. M. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.702787 · Cited by 65

CTCF-mediated chromatin loops enclose inducible gene regulatory domains

Oti, M., Falck, J., Huynen, M. A., & Zhou, H. (2016) · BMC Genomics · doi:10.1186/s12864-016-2516-6 · Cited by 62

Genome-Wide Regulatory Adaptation Shapes Population-Level Genomic Landscapes in Heliconius

Lewis, J. J., & Reed, R. D. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy209 · Cited by 55

Chromatin architecture reorganization during neuronal cell differentiation in Drosophila genomePreprint

Chathoth, K. T., & Zabet, N. R. (2019) · Genome Research · doi:10.1101/gr.246710.118 · Cited by 56

Genetic variants regulating expression levels and isoform diversity during embryogenesis

Cannavò, E., Koelling, N., Harnett, D., Garfield, D., Casale, F. P., Ciglar, L., Gustafson, E. H., Viales, R. R., Marco-Ferreres, R., Degner, J. F., et al. (2016) · Nature · doi:10.1038/nature20802 · Cited by 57

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 59

The control of transcriptional memory by stable mitotic bookmarking

Bellec, M., Dufourt, J., Hunt, G., Hasse, H. L., Trullo, A., Aabidine, A. Z. E., Lamarque, M., Gaskill, M. M., Faure-Gautron, H., Mannervik, M., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28855-y · Cited by 59

Genome‐wide association and multi‐omics studies identify MGMT as a novel risk gene for Alzheimer's disease among women

Chung, J., Das, A., Sun, X., Sobreira, D. R., Leung, Y. Y., Igartua, C., Mozaffari, S. V., Chou, Y., Thiagalingam, S., Mez, J., et al. (2022) · Alzheimer s & Dementia · doi:10.1002/alz.12719 · Cited by 51

The boundary paradox in the Bithorax complex

Kyrchanova, O., Mogila, V., Wolle, D. G., Magbanua, J. P., White, R. A., Georgiev, P. G., & Schedl, P. D. (2015) · Mechanisms of Development · doi:10.1016/j.mod.2015.07.002 · Cited by 52

Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities

Rennie, S., Dalby, M., Lloret-Llinares, M., Bakoulis, S., Vaagensø, C. D., Jensen, T. H., & Andersson, R. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky244 · Cited by 59

Towards genome-wide prediction and characterization of enhancers in plants

Marand, A. P., Zhang, T., Zhu, B., & Jiang, J. (2016) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2016.06.006 · Cited by 53

A class of circadian long non-coding RNAs mark enhancers modulating long-range circadian gene regulation

Fan, Z., Zhao, M. L., Joshi, P. D., Li, P., Zhang, Y., Guo, W., Xu, Y., Wang, H., Zhao, Z., & Yan, J. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx156 · Cited by 50

Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate

Raviram, R., Rocha, P. P., Luo, V. M., Swanzey, E., Miraldi, E. R., Chuong, E. B., Feschotte, C., Bonneau, R., & Skok, J. A. (2018) · Genome biology · doi:10.1186/s13059-018-1598-7 · Cited by 50

Nuclear pores in genome architecture and enhancer function

Pascual‐García, P., & Capelson, M. (2019) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2019.04.001 · Cited by 50

In the loop: how chromatin topology links genome structure to function in mechanisms underlying learning and memory

Watson, L. A., & Tsai, L. (2016) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2016.12.002 · Cited by 52

International Union of Basic and Clinical Pharmacology CXIII: Nuclear Receptor Superfamily—Update 2023

Burris, T. P., de Vera, I. M. S., Côté, I., Flaveny, C. A., Wanninayake, U. S., Chatterjee, A., Walker, J. K., Steinauer, N., Zhang, J., Coons, L. A., et al. (2023) · Pharmacological Reviews · doi:10.1124/pharmrev.121.000436 · Cited by 54

Eukaryotic enhancers: common features, regulation, and participation in diseases

Erokhin, M., Vassetzky, Y. S., Georgiev, P. G., & Chetverina, D. (2015) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-015-1871-9 · Cited by 54

Dynamic 3D genome architecture of cotton fiber reveals subgenome-coordinated chromatin topology for 4-staged single-cell differentiation

Pei, L., Huang, X., Liu, Z., Tian, X., You, J., Li, J., Fang, D. D., Lindsey, K., Zhu, L., Zhang, X., et al. (2022) · Genome biology · doi:10.1186/s13059-022-02616-y · Cited by 50

Extensive co-binding and rapid redistribution of NANOG and GATA6 during emergence of divergent lineages

Thompson, J. J., Lee, D. J., Mitra, A., Frail, S., Dale, R., & Rocha, P. P. (2022) · Nature Communications · doi:10.1038/s41467-022-31938-5 · Cited by 48

From single genes to entire genomes: the search for a function of nuclear organization

Pueschel, R., Coraggio, F., & Meister, P. (2016) · Development · doi:10.1242/dev.129007 · Cited by 52

The Role of Insulation in Patterning Gene Expression

Özdemir, I., & Gambetta, M. C. (2019) · Genes · doi:10.3390/genes10100767 · Cited by 50

3D genome evolution and reorganization in the Drosophila melanogaster species group

Torosin, N. S., Anand, A., Golla, T. R., Cao, W., & Ellison, C. E. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1009229 · Cited by 46

The role of insulators and transcription in 3D chromatin organization of fliesPreprint

Chathoth, K. T., Mikheeva, L. A., Crevel, G., Wolfe, J. C., Hunter, I., Beckett-Doyle, S., Cotterill, S., Dai, H., Harrison, A., & Zabet, N. R. (2022) · Genome Research · doi:10.1101/gr.275809.121 · Cited by 46

Enhancers reside in a unique epigenetic environment during early zebrafish development

Kaaij, L. J. T., Mokrý, M., Zhou, M., Musheev, M. U., Geeven, G., Melquiond, A. S. J., Domingues, A. M. D. J., de Laat, W. L., Niehrs, C., Smith, A. D., et al. (2016) · Genome biology · doi:10.1186/s13059-016-1013-1 · Cited by 46

Chromatin topology in development and disease

Bompadre, O., & Andrey, G. (2019) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2019.04.007 · Cited by 47

Formation of a Polycomb-Domain in the Absence of Strong Polycomb Response Elements

De, S., Mitra, A., Cheng, Y., Pfeifer, K. E., & Kassis, J. A. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006200 · Cited by 46

Transcriptional Regulation and Implications for Controlling Hox Gene Expression

Afzal, Z., & Krumlauf, R. K. (2022) · Journal of Developmental Biology · doi:10.3390/jdb10010004 · Cited by 51

Decoding enhancer complexity with machine learning and high-throughput discovery

Smith, G. D., Ching, W. H., Cornejo‐Páramo, P., & Wong, E. S. W. (2023) · Genome biology · doi:10.1186/s13059-023-02955-4 · Cited by 48

Chromatin gene-gene loops support the cross-regulation of genes with related function

Pollex, T., Marco-Ferreres, R., Ciglar, L., Ghavi-Helm, Y., Rabinowitz, A. H., Viales, R. R., Schaub, C., Jankowski, A., Girardot, C., & Furlong, E. E. M. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.12.023 · Cited by 45

Chromatin Architecture of the Pitx2 Locus Requires CTCF- and Pitx2-Dependent Asymmetry that Mirrors Embryonic Gut Laterality

Welsh, I. C., Kwak, H., Chen, F. L., Werner, M., Shopland, L. S., Danko, C. G., Lis, J. T., Zhang, M., Martin, J. F., & Kurpios, N. A. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.08.075 · Cited by 46

Dynamic 3D Chromatin Reorganization during Establishment and Maintenance of Pluripotency

Pelham‐Webb, B., Murphy, D., & Apostolou, E. (2020) · Stem Cell Reports · doi:10.1016/j.stemcr.2020.10.012 · Cited by 45

Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity

Khoueiry, P., Girardot, C., Ciglar, L., Peng, P.-C., Gustafson, E. H., Sinha, S., & Furlong, E. E. (2017) · eLife · doi:10.7554/elife.28440 · Cited by 44

Signal Integration by Shadow Enhancers and Enhancer Duplications Varies across the Drosophila Embryo

Scholes, C., Biette, K. M., Harden, T. T., & DePace, A. H. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.01.115 · Cited by 44

The multiscale effects of polycomb mechanisms on 3D chromatin folding

Cheutin, T., & Cavalli, G. (2019) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2019.1679082 · Cited by 43

SRC-3 Coactivator Governs Dynamic Estrogen-Induced Chromatin Looping Interactions during Transcription

Panigrahi, A. K., Foulds, C. E., Lanz, R. B., Hamilton, R. A., Yi, P., Lonard, D. M., Tsai, M., Tsai, S. Y., & O’Malley, B. W. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.04.014 · Cited by 41

Local Chromatin Motion and Transcription

Babokhov, M., Hibino, K., Itoh, Y., & Maeshima, K. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.10.018 · Cited by 42

N-terminal domain of the architectural protein CTCF has similar structural organization and ability to self-association in bilaterian organisms

Bonchuk, A. N., Kamalyan, S., Mariasina, S. S., Boyko, K. M., Popov, V. O., Maksimenko, O. G., & Georgiev, P. G. (2020) · Scientific Reports · doi:10.1038/s41598-020-59459-5 · Cited by 42

Designing Cell-Type-Specific Genome-wide Experiments

Handley, A., Schauer, T., Ladurner, A. G., & Margulies, C. E. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.04.024 · Cited by 42

Transcriptional precision and accuracy in development: from measurements to models and mechanisms

Bentovim, L., Harden, T. T., & DePace, A. H. (2017) · Development · doi:10.1242/dev.146563 · Cited by 41

Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers

Bejjani, F., Tolza, C., Boulanger, M., Downes, D. J., Romero, R., Maqbool, M. A., Aabidine, A. Z. E., Andrau, J., Lèbre, S., Bréhélin, L., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab053 · Cited by 44

Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures

Comoglio, F., Park, H. J., Schoenfelder, S., Barozzi, I., Bode, D., Fraser, P., & Green, A. R. (2018) · Genome Research · doi:10.1101/gr.227272.117 · Cited by 41

Coupling 1D modifications and 3D nuclear organization: data, models and function

Jost, D., Vaillant, C., & Meister, P. (2016) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2016.12.001 · Cited by 42

Chromosome topology guides the Drosophila Dosage Compensation Complex for target gene activation

Schauer, T., Ghavi-Helm, Y., Sexton, T., Albig, C., Regnard, C., Cavalli, G., Furlong, E. E. M., & Becker, P. B. (2017) · EMBO Reports · doi:10.15252/embr.201744292 · Cited by 46

Combinatorial Action of Temporally Segregated Transcription Factors

Charest, J., Daniele, T., Wang, J., Bykov, A., Mandlbauer, A., Asparuhova, M., Roehsner, J., Gutiérrez‐Pérez, P., & Cochella, L. (2020) · Developmental Cell · doi:10.1016/j.devcel.2020.09.002 · Cited by 37

Enhancer-associated RNAs as therapeutic targets

Léveillé, N., Melo, C. A., & Agami, R. (2015) · Expert Opinion on Biological Therapy · doi:10.1517/14712598.2015.1029452 · Cited by 38

Opbp is a new architectural/insulator protein required for ribosomal gene expression

Zolotarev, N., Maksimenko, O. G., Kyrchanova, O., Sokolinskaya, E. L., Osadchiy, I. S., Girardot, C., Bonchuk, A. N., Ciglar, L., Furlong, E. E. M., & Georgiev, P. G. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx840 · Cited by 40

Enhancer–promoter interactions can form independently of genomic distance and be functional across TAD boundaries

Balasubramanian, D., Pinto, P. B., Grasso, A., Vincent, S., Tarayre, H., Lajoignie, D., & Ghavi-Helm, Y. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad1183 · Cited by 45

3D hotspots of recurrent retroviral insertions reveal long-range interactions with cancer genes

Babaei, S., Akhtar, W., de Jong, J., Reinders, M., & de Ridder, J. (2015) · Nature Communications · doi:10.1038/ncomms7381 · Cited by 37

An epigenetic perspective on tumorigenesis: Loss of cell identity, enhancer switching, and NamiRNA network

Liang, Y. J., Xu, P., Zou, Q., Luo, H., & Yu, W. (2018) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2018.09.004 · Cited by 37

Chromatin interactions in differentiating keratinocytes reveal novel atopic dermatitis– and psoriasis-associated genes

Sahlén, P., Spalinskas, R., Asad, S., Mahapatra, K. D., Höjer, P., Anil, A., Eisfeldt, J., Srivastava, A., Nikamo, P., Mukherjee, A., et al. (2020) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2020.09.035 · Cited by 38

3D spatial genome organization in the nervous system: From development and plasticity to disease

Fujita, Y., Pather, S. R., Ming, G., & Song, H. (2022) · Neuron · doi:10.1016/j.neuron.2022.06.004 · Cited by 37

Uncovering Enhancer Functions Using the α-Globin Locus

Vernimmen, D. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004668 · Cited by 36

Nuclear Compartments, Genome Folding, and Enhancer-Promoter Communication

Ulianov, S. V., Gavrilov, A. A., & Razin, S. V. (2015) · International review of cytology · doi:10.1016/bs.ircmb.2014.11.004 · Cited by 37

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

Kvon, E. Z., Kazmar, T., Stampfel, G., Yáñez-Cuna, J. O., Pagani, M., Schernhuber, K., Dickson, B. J., & Stark, A. (2014) · Nature · doi:10.1038/nature13395 · Cited by 461

Loop the loop with your partner

Skipper, M. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1541

Transcriptional enhancers in development

Sakabe, N. J., Savic, D., & Nobrega, M. A. (2013)

Enhancer contacts during embryonic development show diverse interaction modes and modest yet significant increases upon gene activation

Ibrahim, D. M. (2024) · Nature Genetics · doi:10.1038/s41588-024-01700-2 · Cited by 2

3D dynamics of trans enhancer-promoter interactions in living Drosophila embryos reveals spatiotemporal thresholds for transcription activationPreprint

Deng, H., Valenti, P., Payre, F., & Lim, B. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.03.17.643800 · Cited by 3