Shadow Enhancers as a Source of Evolutionary Novelty

Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo

Markstein, M., Markstein, P., Markstein, V., & Levine, M. S. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.012591199 · Cited by 375

Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo.

Stathopoulos, A., Drenth, M. V., Erives, A. J., Markstein, M., & Levine, M. (2002) · Cell · doi:10.1016/s0092-8674(02)01087-5 · Cited by 310

The Evolution of Gene Regulation Underlies a Morphological Difference between Two Drosophila Sister Species

Jeong, S., Rebeiz, M., Andolfatto, P., Werner, T., True, J., & Carroll, S. B. (2008) · Cell · doi:10.1016/j.cell.2008.01.014 · Cited by 309

Whole-genome ChIP–chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo

Zeitlinger, J., Zinzen, R. P., Stark, A., Kellis, M., Zhang, H., Young, R. A., & Levine, M. (2007) · Genes & Development · doi:10.1101/gad.1509607 · Cited by 286

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 238

Redundant and Unique Roles of Two Enhancer Elements in the TCRγ Locus in Gene Regulation and γδ T Cell Development

Xiong, N., Kang, C., & Raulet, D. H. (2002) · Immunity · doi:10.1016/s1074-7613(02)00285-6 · Cited by 65

Comprehensive identification of Drosophila dorsal–ventral patterning genes using a whole-genome tiling array

Biemar, F., Nix, D. A., Piel, J., Peterson, B., Ronshaugen, M., Sementchenko, V., Bell, I., Manak, J. R., & Levine, M. S. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0604484103 · Cited by 53

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

Cis-regulatory elements: Molecular mechanisms and evolutionary processes underlying divergence

Wittkopp, P. J., & Kalay, G. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3095 · Cited by 1,231

Control of the Embryonic Stem Cell State

Young, R. A. (2011) · Cell · doi:10.1016/j.cell.2011.01.032 · Cited by 1,246

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

The selection and function of cell type-specific enhancers

Heinz, S., Romanoski, C. E., Benner, C., & Glass, C. K. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3949 · Cited by 1,010

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

Long, H. K., Prescott, S. L., & Wysocka, J. (2016) · Cell · doi:10.1016/j.cell.2016.09.018 · Cited by 945

Enhancer redundancy provides phenotypic robustness in mammalian development

Osterwalder, M., Barozzi, I., Tissières, V., Fukuda-Yuzawa, Y., Mannion, B. J., Afzal, S. Y., Lee, E. A., Zhu, Y., Plajzer-Frick, I., Pickle, C. S., et al. (2018) · Nature · doi:10.1038/nature25461 · Cited by 642

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

Gasperini, M., Hill, A. J., McFaline-Figueroa, J. L., Martin, B., Kim, S., Zhang, M. D., Jackson, D., Leith, A., Schreiber, J., Noble, W. S., et al. (2019) · Cell · doi:10.1016/j.cell.2018.11.029 · Cited by 613

Morphogen Gradients: From Generation to Interpretation

Rogers, K. W., & Schier, A. F. (2011) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-092910-154148 · Cited by 627

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

Frankel, N., Davis, G. K., Vargas, D., Wang, S., Payre, F., & Stern, D. L. (2010) · Nature · doi:10.1038/nature09158 · Cited by 510

Morphogen rules: design principles of gradient-mediated embryo patterning

Briscoe, J., & Small, S. (2015) · Development · doi:10.1242/dev.129452 · Cited by 497

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

Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers

Hnisz, D., Schuijers, J., Lin, C. Y., Weintraub, A. S., Abraham, B. J., Lee, T. I., Bradner, J. E., & Young, R. A. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.02.014 · Cited by 476

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

Schoenfelder, S., Furlan-Magaril, M., Mifsud, B., Tavares-Cadete, F., Sugar, R., Javierre, B.-M., Nagano, T., Katsman, Y., Sakthidevi, M., Wingett, S. W., et al. (2015) · Genome Research · doi:10.1101/gr.185272.114 · Cited by 460

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

Transcriptional Enhancers in Animal Development and Evolution

Levine, M. (2010) · Current Biology · doi:10.1016/j.cub.2010.06.070 · Cited by 468

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

Towards a comprehensive catalogue of validated and target-linked human enhancers

Gasperini, M., Tome, J. M., & Shendure, J. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-019-0209-0 · Cited by 396

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

Perry, M. W., Boettiger, A. N., Bothma, J. P., & Levine, M. (2010) · Current Biology · doi:10.1016/j.cub.2010.07.043 · Cited by 396

The Genetics of Transcription Factor DNA Binding Variation

Deplancke, B., Alpern, D., & Gardeux, V. (2016) · Cell · doi:10.1016/j.cell.2016.07.012 · Cited by 390

Genetic dissection of the α-globin super-enhancer in vivo

Hay, D., Hughes, J. R., Babbs, C., Davies, J. O. J., Graham, B. J., Hanssen, L. L. P., Kassouf, M. T., Oudelaar, A. M., Sharpe, J. A., Suciu, M. C., et al. (2016) · Nature Genetics · doi:10.1038/ng.3605 · Cited by 385

The cis-Regulatory Atlas of the Mouse Immune System

Yoshida, H., Lareau, C. A., Ramírez, R. N., Rose, S. A., Maier, B. B., Wroblewska, A., Desland, F. A., Chudnovskiy, A., Mortha, A., Dominguez, C. X., et al. (2019) · Cell · doi:10.1016/j.cell.2018.12.036 · Cited by 385

Gene regulatory networks and the role of robustness and stochasticity in the control of gene expressionPreprint

MacNeil, L. T., & Walhout, A. J. M. (2011) · Genome Research · doi:10.1101/gr.097378.109 · Cited by 371

Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest

Prescott, S. L., Srinivasan, R., Marchetto, M. C., Grishina, I., Narvaiza, I., Selleri, L., Gage, F. H., Swigut, T., & Wysocka, J. (2015) · Cell · doi:10.1016/j.cell.2015.08.036 · Cited by 364

Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells

Xie, S., Duan, J., Li, B., Zhou, P., & Hon, G. C. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.03.007 · Cited by 334

Enhancer biology and enhanceropathies

Smith, E. R., & Shilatifard, A. (2014) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2784 · Cited by 326

Deciphering the multi-scale, quantitative cis-regulatory code

Kim, S., & Wysocka, J. (2023) · Molecular Cell · doi:10.1016/j.molcel.2022.12.032 · Cited by 302

Global view of enhancer–promoter interactome in human cells

He, B., Chen, C., Teng, L., & Tan, K. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1320308111 · Cited by 263

A High-Resolution Enhancer Atlas of the Developing Telencephalon

Visel, A., Taher, L., Girgis, H., May, D., Golonzhka, O., Hoch, R. V., McKinsey, G. L., Pattabiraman, K., Silberberg, S. N., Blow, M. J., et al. (2013) · Cell · doi:10.1016/j.cell.2012.12.041 · Cited by 257

Synchronous and Stochastic Patterns of Gene Activation in the Drosophila Embryo

Boettiger, A. N., & Levine, M. (2009) · Science · doi:10.1126/science.1173976 · Cited by 256

Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks

Cannavò, E., Khoueiry, P., Garfield, D. A., Geeleher, P., Zichner, T., Gustafson, E. H., Ciglar, L., Korbel, J. O., & Furlong, E. E. M. (2016) · Current Biology · doi:10.1016/j.cub.2015.11.034 · Cited by 235

Chromatin-associated RNAs as facilitators of functional genomic interactions

Li, X., & Fu, X. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0135-1 · Cited by 236

Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo

Perry, M. W., Boettiger, A. N., & Levine, M. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1109873108 · Cited by 228

Enhancer redundancy in development and disease

Kvon, E. Z., Waymack, R., Gad, M., & Wunderlich, Z. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-020-00311-x · Cited by 247

CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors

Corbo, J. C., Lawrence, K. A., Karlstetter, M., Myers, C. A., Abdelaziz, M., Dirkes, W., Weigelt, K., Seifert, M., Benes, V., Fritsche, L. G., et al. (2010) · Genome Research · doi:10.1101/gr.109405.110 · Cited by 219

Diet-Induced Circadian Enhancer Remodeling Synchronizes Opposing Hepatic Lipid Metabolic Processes

Guan, D., Xiong, Y., Borck, P. C., Jang, C., Doulias, P., Papazyan, R., Fang, B., Jiang, C., Zhang, Y., Briggs, E. R., et al. (2018) · Cell · doi:10.1016/j.cell.2018.06.031 · Cited by 225

Disentangling the Many Layers of Eukaryotic Transcriptional Regulation

Lelli, K. M., Slattery, M. G., & Mann, R. S. (2012) · Annual Review of Genetics · doi:10.1146/annurev-genet-110711-155437 · Cited by 237

A unified architecture of transcriptional regulatory elements

Andersson, R., Sandelin, A., & Danko, C. G. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.05.007 · Cited by 225

Noncanonical Compensation of Zygotic X Transcription in Early Drosophila melanogaster Development Revealed through Single-Embryo RNA-Seq

Lott, S. E., Villalta, J. E., Schroth, G. P., Luo, S. J., Tonkin, L. A., & Eisen, M. B. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1000590 · Cited by 204

Spatially resolved epigenomic profiling of single cells in complex tissues

Lu, T., Ang, C. E., & Zhuang, X. (2022) · Cell · doi:10.1016/j.cell.2022.09.035 · Cited by 197

Super-enhancers include classical enhancers and facilitators to fully activate gene expression

Blayney, J. W., Francis, H., Rampasekova, A., Camellato, B., Mitchell, L., Stolper, R., Cornell, L., Babbs, C., Boeke, J. D., Higgs, D. R., et al. (2023) · Cell · doi:10.1016/j.cell.2023.11.030 · Cited by 196

Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo

Bothma, J. P., Garcia, H. G., Ng, S., Perry, M. W., Gregor, T., & Levine, M. (2015) · eLife · doi:10.7554/elife.07956 · Cited by 192

Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genesPreprint

Moorthy, S. D., Davidson, S., Shchuka, V. M., Singh, G., Malek-Gilani, N., Langroudi, L., Martchenko, A., So, V., Macpherson, N. N., & Mitchell, J. A. (2016) · Genome Research · doi:10.1101/gr.210930.116 · Cited by 202

Evolutionary conservation of the eumetazoan gene regulatory landscapePreprint

Schwaiger, M., Schönauer, A., Rendeiro, A. F., Pribitzer, C., Schauer, A., Gilles, A. F., Schinko, J. B., Renfer, E., Fredman, D., & Technau, U. (2014) · Genome Research · doi:10.1101/gr.162529.113 · Cited by 191

Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activationPreprint

Sun, Y., Nien, C.-Y., Chen, K., Liu, H.-Y., Johnston, J. J., Zeitlinger, J., & Rushlow, C. A. (2015) · Genome Research · doi:10.1101/gr.192542.115 · Cited by 178

STAT3, STAT4, NFATc1, and CTCF Regulate PD-1 through Multiple Novel Regulatory Regions in Murine T Cells

Austin, J. W., Lu, P., Majumder, P., Ahmed, R., & Boss, J. M. (2014) · The Journal of Immunology · doi:10.4049/jimmunol.1302750 · Cited by 171

Enhancer Logic and Mechanics in Development and Disease

Rickels, R. A., & Shilatifard, A. (2018) · Trends in Cell Biology · doi:10.1016/j.tcb.2018.04.003 · Cited by 171

Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells

Freire-Pritchett, P., Schoenfelder, S., Várnai, C., Wingett, S. W., Cairns, J., Collier, A. J., García-Vílchez, R., Furlan-Magaril, M., Osborne, C. S., Fraser, P., et al. (2017) · eLife · doi:10.7554/elife.21926 · Cited by 161

Epigenomic Comparison Reveals Activation of “Seed” Enhancers during Transition from Naive to Primed Pluripotency

Factor, D. C., Corradin, O., Zentner, G. E., Saiakhova, A., Song, L., Chenoweth, J. G., McKay, R. D. G., Crawford, G. E., Scacheri, P. C., & Tesar, P. J. (2014) · Cell stem cell · doi:10.1016/j.stem.2014.05.005 · Cited by 159

Extensive conservation of ancient microsynteny across metazoans due to cis -regulatory constraints

Irimia, M., Tena, J. J., Alexis, M. S., Fernandez-Miñan, A., Maeso, I., Bogdanović, O., de la Calle-Mustienes, E., Roy, S. W., Gómez-Skarmeta, J. L., & Fraser, H. B. (2012) · Genome Research · doi:10.1101/gr.139725.112 · Cited by 146

Regulatory Logic of Pan-Neuronal Gene Expression in C. elegans

Stefanakis, N., Carrera, I., & Hobert, O. (2015) · Neuron · doi:10.1016/j.neuron.2015.07.031 · Cited by 155

Evolution of Alu Elements toward Enhancers

Su, M., Han, D., Boyd-Kirkup, J. D., Yu, X., & Han, J.-D. J. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.03.011 · Cited by 157

Deletion of a remote enhancer near ATOH7 disrupts retinal neurogenesis, causing NCRNA disease

Ghiasvand, N. M., Rudolph, D. D., Mashayekhi, M., Brzezinski, J. A., Goldman, D. J., & Glaser, T. M. (2011) · Nature Neuroscience · doi:10.1038/nn.2798 · Cited by 150

Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers

Farley, E. K., Olson, K. M., Zhang, W., Rokhsar, D. S., & Levine, M. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1605085113 · Cited by 147

Enhancer grammar in development, evolution, and disease: dependencies and interplay

Jindal, G. A., & Farley, E. K. (2021) · Developmental Cell · doi:10.1016/j.devcel.2021.02.016 · Cited by 152

Mechanisms of transcriptional precision in animal development

Lagha, M., Bothma, J. P., & Levine, M. (2012) · Trends in Genetics · doi:10.1016/j.tig.2012.03.006 · Cited by 151

3D enhancer-promoter interactions and multi-connected hubs: Organizational principles and functional roles

Uyehara, C. M., & Apostolou, E. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112068 · Cited by 143

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 149

How the Dorsal gradient works: Insights from postgenome technologies

Hong, J.-W., Hendrix, D. A., Papatsenko, D., & Levine, M. S. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0806476105 · Cited by 137

Transcriptional enhancers in development and disease

Sakabe, N. J., Savic, D., & Nóbrega, M. A. (2012) · Genome biology · doi:10.1186/gb-2012-13-1-238 · Cited by 143

Shadow enhancers: Frequently asked questions about distributed cis‐regulatory information and enhancer redundancy

Barolo, S. (2012) · BioEssays · doi:10.1002/bies.201100121 · Cited by 136

Enhancer Variants Synergistically Drive Dysfunction of a Gene Regulatory Network In Hirschsprung Disease

Chatterjee, S., Kapoor, A., Akiyama, J. A., Auer, D. R., Lee, D., Gabriel, S., Berrios, C., Pennacchio, L. A., & Chakravarti, A. (2016) · Cell · doi:10.1016/j.cell.2016.09.005 · Cited by 135

A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions

Chong, R., Insigne, K. D., Yao, D., Burghard, C. P., Wang, J., Hsiao, Y.-H. E., Jones, E. M., Goodman, D. B., Xiao, X., & Kosuri, S. (2019) · Molecular Cell · doi:10.1016/j.molcel.2018.10.037 · Cited by 130

Zelda Potentiates Morphogen Activity by Increasing Chromatin Accessibility

Foo, S. M., Sun, Y., Lim, B., Ziukaite, R., O’Brien, K. M., Nien, C.-Y., Kirov, N., Shvartsman, S. Y., & Rushlow, C. A. (2014) · Current Biology · doi:10.1016/j.cub.2014.04.032 · Cited by 134

Promoter or enhancer, what’s the difference? Deconstruction of established distinctions and presentation of a unifying model

Andersson, R. (2015) · BioEssays · doi:10.1002/bies.201400162 · Cited by 127

Composition and dosage of a multipartite enhancer cluster control developmental expression of Ihh (Indian hedgehog)

Will, A. J., Cova, G., Osterwalder, M., Chan, W.-L., Wittler, L., Brieske, N., Heinrich, V., de Villartay, J., Vingron, M., Klopocki, E., et al. (2017) · Nature Genetics · doi:10.1038/ng.3939 · Cited by 126

Epigenomic annotation of gene regulatory alterations during evolution of the primate brain

Bank, N. B., Vermunt, M. W., Tan, S., Castelijns, B., Geeven, G., Reinink, P., de Bruijn, E., Kondova, I. I., Persengiev, S. P., Bontrop, R. E., et al. (2016) · Nature Neuroscience · doi:10.1038/nn.4229 · Cited by 125

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species

He, Q., Bardet, A. F., Patton, B., Purvis, J., Johnston, J. J., Paulson, A., Gogol, M., Stark, A., & Zeitlinger, J. (2011) · Nature Genetics · doi:10.1038/ng.808 · Cited by 128

Cross-species analysis of enhancer logic using deep learning

Minnoye, L., Taskiran, I. I., Mauduit, D., Fazio, M., Van Aerschot, L., Hulselmans, G., Christiaens, V., Makhzami, S., Seltenhammer, M., Karras, P., et al. (2020) · Genome Research · doi:10.1101/gr.260844.120 · Cited by 116

A computational pipeline for comparative ChIP-seq analyses

Bardet, A. F., He, Q., Zeitlinger, J., & Stark, A. (2011) · Nature Protocols · doi:10.1038/nprot.2011.420 · Cited by 118

Partially Redundant Enhancers Cooperatively Maintain Mammalian Pomc Expression Above a Critical Functional Threshold

Lam, D. D., de Souza, F. S. J., Nasif, S., Yamashita, M., López‐Leal, R., Otero-Corchón, V., Meece, K., Sampath, H., Mercer, A. J., Wardlaw, S. L., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1004935 · Cited by 120

Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor α-Bound Enhancers

Carleton, J. B., Berrett, K. C., & Gertz, J. (2017) · Cell Systems · doi:10.1016/j.cels.2017.08.011 · Cited by 113

Super-enhancers: critical roles and therapeutic targets in hematologic malignancies

Jia, Y., Chng, W. J., & Zhou, J. (2019) · Journal of Hematology & Oncology · doi:10.1186/s13045-019-0757-y · Cited by 120

Hold out the genome: a roadmap to solving the cis-regulatory code

de Boer, C. G., & Taipale, J. (2024) · Nature · doi:10.1038/s41586-023-06661-w · Cited by 107

Chromatin and epigenetic features of long-range gene regulation

Harmston, N., & Lenhard, B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt499 · Cited by 113

Constrained vertebrate evolution by pleiotropic genes

Hu, H., Uesaka, M., Guo, S., Shimai, K., Lu, T.-M., Li, F., Fujimoto, S., Ishikawa, M., Liu, S., Sasagawa, Y., et al. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0318-0 · Cited by 106

Enhancer Domains Predict Gene Pathogenicity and Inform Gene Discovery in Complex Disease

Wang, X., & Goldstein, D. B. (2020) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2020.01.012 · Cited by 106

Affinity-optimizing enhancer variants disrupt development

Lim, F., Solvason, J. J., Ryan, G. E., Le, S. H., Jindal, G. A., Steffen, P., Jandu, S. K., & Farley, E. K. (2024) · Nature · doi:10.1038/s41586-023-06922-8 · Cited by 102

Dense and pleiotropic regulatory information in a developmental enhancer

Fuqua, T., Jordan, J., van Breugel, M. E., Halavatyi, A. A., Tischer, C., Polidoro, P., Abe, N., Tsai, A., Mann, R. S., Stern, D. L., et al. (2020) · Nature · doi:10.1038/s41586-020-2816-5 · Cited by 98

Mechanisms of mutational robustness in transcriptional regulation

Payne, J. L., & Wagner, A. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00322 · Cited by 97

Testing the super-enhancer concept

Blobel, G. A., Higgs, D. R., Mitchell, J. A., Notani, D., & Young, R. A. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00398-w · Cited by 98

The Drosophila Pioneer Factor Zelda Modulates the Nuclear Microenvironment of a Dorsal Target Enhancer to Potentiate Transcriptional Output

Yamada, S., Whitney, P. H., Huang, S.-K., Eck, E. C., Garcia, H. G., & Rushlow, C. A. (2019) · Current Biology · doi:10.1016/j.cub.2019.03.019 · Cited by 88

How to make stripes: deciphering the transition from non-periodic to periodic patterns in Drosophila segmentation

Schroeder, M. D., Greer, C., & Gaul, U. (2011) · Development · doi:10.1242/dev.062141 · Cited by 88

Neural progenitors adopt specific identities by directly repressing all alternative progenitor transcriptional programs

Kutejova, E., Sasai, N., Shah, A., Gouti, M., & Briscoe, J. (2016) · Developmental Cell · doi:10.1016/j.devcel.2016.02.013 · Cited by 87

Multi-enhancer transcriptional hubs confer phenotypic robustness

Tsai, A., Alves, M. R. P., & Crocker, J. (2019) · eLife · doi:10.7554/elife.45325 · Cited by 88

McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes

Hafez, D., Calviello, A. K., Krueger, S., Hwang, Y.-C., Wang, L., Zinzen, R. P., & Ohler, U. (2017) · Genome biology · doi:10.1186/s13059-017-1316-x · Cited by 86

Complex interactions between cis-regulatory modules in native conformation are critical for Drosophila snail expression

Dunipace, L., Özdemir, A., & Stathopoulos, A. (2011) · Development · doi:10.1242/dev.069146 · Cited by 86

Unraveling the Tangled Skein: The Evolution of Transcriptional Regulatory Networks in Development

Rebeiz, M., Patel, N. H., & Hinman, V. F. (2015) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-091212-153423 · Cited by 89

A chromatin insulator mediates transgene homing and very long-range enhancer-promoter communication

Fujioka, M., Wu, X., & Jaynes, J. B. (2009) · Development · doi:10.1242/dev.036467 · 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

An Enhancer Polymorphism at the Cardiomyocyte Intercalated Disc Protein NOS1AP Locus Is a Major Regulator of the QT Interval

Kapoor, A., Sekar, R. B., Hansen, N. F., Fox-Talbot, K., Morley, M. P., Pihur, V., Chatterjee, S., Brandimarto, J., Moravec, C. S., Pulit, S. L., et al. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.05.001 · Cited by 85

Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profilesPreprint

Wang, S., Zang, C., Xiao, T., Fan, J., Mei, S., Qin, Q., Wu, Q., Li, X., Xu, K., He, H. H., et al. (2016) · Genome Research · doi:10.1101/gr.201574.115 · Cited by 81

The Gene Regulatory Network of Lens Induction Is Wired through Meis-Dependent Shadow Enhancers of Pax6

Antosova, B., Smolikova, J., Klimova, L., Láchová, J., Michaela, B., Kozmiková, I., Machoň, O., & Kozmík, Z. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006441 · Cited by 83

Comparative genomics of gene regulation—conservation and divergence of cis-regulatory information

Meireles-Filho, A. C. A., & Stark, A. (2009) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2009.10.006 · Cited by 83

The mystery of extreme non-coding conservation

Harmston, N., Barešić, A., & Lenhard, B. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0021 · Cited by 80

Convergent evolution of two mammalian neuronal enhancers by sequential exaptation of unrelated retroposons

Franchini, L. F., López‐Leal, R., Nasif, S., Beati, P., Gelman, D. M., Low, M. J., de Souza, F. S. J., & Rubinstein, M. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1104997108 · Cited by 79

Evolution of transcriptional enhancers and animal diversity

Rubinstein, M., & de Souza, F. S. J. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0017 · Cited by 79

Chromatin organization and global regulation of Hox gene clusters

Montavon, T., & Duboule, D. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2012.0367 · Cited by 83

Current challenges in understanding the role of enhancers in disease

Zaugg, J. B., Sahlén, P., Andersson, R., Alberich-Jordà, M., de Laat, W. L., Deplancke, B., Ferrer, J. P., Mandrup, S., Natoli, G., Plewczyński, D., et al. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00896-3 · Cited by 86

Design flexibility in cis-regulatory control of gene expression: Synthetic and comparative evidence

Liberman, L. M., & Stathopoulos, A. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2008.12.020 · Cited by 76

E D B

(2008)

Shadow enhancers' objective seems to be to establish robust growth patterns independent of genetic or environmental stressPreprint

Dowaidar, M. (2021) · doi:10.31219/osf.io/qfnkp · Cited by 2

Enhancer redundancy in development and disease

Kvon, E. Z., Waymack, R., Gad, M., & Wunderlich, Z. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-020-00311-x · Cited by 247

In Brief

(2008) · Nature Reviews Genetics · doi:10.1038/nrg2463

Shadow enhancers: Frequently asked questions about distributed cis‐regulatory information and enhancer redundancy

Barolo, S. (2012) · BioEssays · doi:10.1002/bies.201100121 · Cited by 136