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

Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation

Brennan, K., Weilert, M., Krueger, S., Pampari, A., Liu, H., Yang, A. W. H., Morrison, J. A., Hughes, T. R., Rushlow, C. A., Kundaje, A. B., et al. (2023) · Developmental Cell · doi:10.1016/j.devcel.2023.07.007 · Cited by 79

Buffering and Amplifying Transcriptional Noise During Cell Fate Specification

Urban, E., & Johnston, R. J. (2018) · Frontiers in Genetics · doi:10.3389/fgene.2018.00591 · Cited by 75

Enhancer and super‐enhancer: Positive regulators in gene transcription

Peng, Y., & Zhang, Y. (2018) · Animal Models and Experimental Medicine · doi:10.1002/ame2.12032 · Cited by 78

Composite Effects of Polymorphisms near Multiple Regulatory Elements Create a Major-Effect QTL

Bickel, R. D., Kopp, A., & Nuzhdin, S. V. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001275 · Cited by 73

Odd-paired controls frequency doubling in Drosophila segmentation by altering the pair-rule gene regulatory network

Clark, E., & Akam, M. E. (2016) · eLife · doi:10.7554/elife.18215 · Cited by 71

The chromatin signatures of enhancers and their dynamic regulation

Barral, A., & Déjardin, J. (2023) · Nucleus · doi:10.1080/19491034.2022.2160551 · Cited by 78

Quantitative Analysis of the Drosophila Segmentation Regulatory Network Using Pattern Generating Potentials

Kazemian, M., Blatti, C. A., Richards, A., McCutchan, M., Wakabayashi-Ito, N., Hammonds, A. S., Celniker, S., Kumar, S., Wolfe, S. A., Brodsky, M. H., et al. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000456 · Cited by 73

Shared Enhancer Activity in the Limbs and Phallus and Functional Divergence of a Limb-Genital cis-Regulatory Element in Snakes

Infante, C. R., Mihala, A. G., Park, S., Wang, J. S., Johnson, K. K., Lauderdale, J. D., & Menke, D. B. (2015) · Developmental Cell · doi:10.1016/j.devcel.2015.09.003 · Cited by 71

Functional cis -regulatory genomics for systems biology

Nam, J., Dong, P., Tarpine, R., Istrail, S., & Davidson, E. H. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000147107 · Cited by 68

Synthetic regulatory genomics uncovers enhancer context dependence at the Sox2 locus

Brosh, R., Coelho, C., Ribeiro-dos-Santos, A. M., Ellis, G., Hogan, M. S., Ashe, H. J., Somogyi, N., Ordóñez, R., Luther, R. D., Huang, E., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.02.027 · Cited by 75

Global transcriptome analysis and enhancer landscape of human primary T follicular helper and T effector lymphocytes

Weinstein, J. S., Lezon-Geyda, K., Maksimova, Y. D., Craft, S., Zhang, Y., Su, M. Y., Schulz, V., Craft, J. E., & Gallagher, P. G. (2014) · Blood · doi:10.1182/blood-2014-06-582700 · Cited by 71

Shadow Enhancers Mediate Dynamic Shifts of Gap Gene Expression in the Drosophila Embryo

El‐Sherif, E., & Levine, M. (2016) · Current Biology · doi:10.1016/j.cub.2016.02.054 · Cited by 71

Studying Transcriptional Enhancers: The Founder Fallacy, Validation Creep, and Other Biases

Halfon, M. S. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.11.004 · Cited by 66

Ancient trans-Acting siRNAs Confer Robustness and Sensitivity onto the Auxin Response

Plavskin, Y., Nagashima, A., Perroud, P., Hasebe, M., Quatrano, R. S., Atwal, G. S., & Timmermans, M. C. P. (2016) · Developmental Cell · doi:10.1016/j.devcel.2016.01.010 · Cited by 66

Targeting Of Somatic Hypermutation By immunoglobulin Enhancer And Enhancer-Like Sequences

Buerstedde, J.-M., Alinikula, J., Arakawa, H., McDonald, J. J., & Schatz, D. G. (2014) · PLoS Biology · doi:10.1371/journal.pbio.1001831 · Cited by 65

Gene Regulation in and out of Equilibrium

Wong, F. J., & Gunawardena, J. (2020) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-121219-081542 · Cited by 68

Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis

Koenecke, N., Johnston, J., Gaertner, B., Natarajan, M., & Zeitlinger, J. (2016) · Genome Biology · doi:10.1186/s13059-016-1057-2 · Cited by 65

Structural Redundancy in Supracellular Actomyosin Networks Enables Robust Tissue Folding

Yevick, H. G., Miller, P. W., Dunkel, J., & Martin, A. C. (2019) · Developmental Cell · doi:10.1016/j.devcel.2019.06.015 · Cited by 68

Functional characterization of tissue-specific enhancers in the DLX5/6 locus

Birnbaum, R. Y., Everman, D. B., Murphy, K. K., Gurrieri, F., Schwartz, C. E., & Ahituv, N. (2012) · Human Molecular Genetics · doi:10.1093/hmg/dds336 · Cited by 63

A dynamic interplay of enhancer elements regulates Klf4 expression in naïve pluripotencyPreprint

Xie, L., Torigoe, S. E., Xiao, J., Mai, D. H., Li, L., Davis, F. P., Dong, P., Marie-Nelly, H., Grimm, J. B., Lavis, L. D., et al. (2017) · Genes & Development · doi:10.1101/gad.303321.117 · Cited by 65

Rapid Transcription Fosters Coordinate snail Expression in the Drosophila Embryo

Boettiger, A. N., & Levine, M. (2013) · Cell Reports · doi:10.1016/j.celrep.2012.12.015 · Cited by 62

Subtle Changes in Motif Positioning Cause Tissue-Specific Effects on Robustness of an Enhancer's Activity

Erceg, J., Saunders, T. E., Girardot, C., Devos, D. P., Hufnagel, L., & Furlong, E. E. M. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004060 · Cited by 63

Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development

Watts, J. A., Zhang, C., Klein–Szanto, A. J., Kormish, J. D., Fu, J., Zhang, M. Q., & Zaret, K. S. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002277 · Cited by 63

SET1A/COMPASS and shadow enhancers in the regulation of homeotic gene expressionPreprint

Cao, K., Collings, C. K., Marshall, S. A., Morgan, M. A., Rendleman, E. J., Wang, L., Sze, C. C., Sun, T., Bartom, E. T., & Shilatifard, A. (2017) · Genes & Development · doi:10.1101/gad.294744.116 · Cited by 61

Rearrangements of 2.5 Kilobases of Noncoding DNA from the Drosophila even-skipped Locus Define Predictive Rules of Genomic cis-Regulatory Logic

Kim, A.-R., Martinez, C., Ionides, J., Ramos, A. F., Ludwig, M. Z., Ogawa, N., Sharp, D. H., & Reinitz, J. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003243 · Cited by 62

Conserved non-coding elements and cis regulation: actions speak louder than words

Nelson, A. C., & Wardle, F. C. (2013) · Development · doi:10.1242/dev.084459 · Cited by 63

Information processing at the foxa node of the sea urchin endomesoderm specification network

de‐Leon, S. B., & Davidson, E. H. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1004824107 · Cited by 59

Challenges for modeling global gene regulatory networks during development: Insights from Drosophila

Wilczyński, B., & Furlong, E. E. M. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2009.10.032 · Cited by 60

Enhancer-promoter communication at theDrosophila engrailedlocus

Kwon, D. Y., Mucci, D., Langlais, K. K., Americo, J. L., DeVido, S. K., Cheng, Y., & Kassis, J. A. (2009) · Development · doi:10.1242/dev.036426 · Cited by 58

Maternal control of the Drosophila dorsal–ventral body axis

Stein, D. S., & Stevens, L. M. (2014) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.138 · Cited by 58

Shadow enhancers flanking the HoxB cluster direct dynamic Hox expression in early heart and endoderm development

Nolte, C., Jinks, T., Wang, X., Martínez‐Pastor, M. T., & Krumlauf, R. K. (2013) · Developmental Biology · doi:10.1016/j.ydbio.2013.09.016 · Cited by 56

Conservation of enhancer location in divergent insects

Cande, J., Goltsev, Y., & Levine, M. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0905754106 · Cited by 57

Identifying noncoding risk variants using disease-relevant gene regulatory networks

Gao, L., Uzun, Y., Gao, P., He, B., Ma, X., Wang, J., Han, S., & Tan, K. (2018) · Nature Communications · doi:10.1038/s41467-018-03133-y · Cited by 55

Enhancer identification and activity evaluation in the red flour beetle, Tribolium castaneum

Lai, Y., Deem, K. D., Borràs-Castells, F., Sambrani, N., Rudolf, H., Suryamohan, K., El‐Sherif, E., Halfon, M. S., McKay, D. J., & Tomoyasu, Y. (2018) · Development · doi:10.1242/dev.160663 · Cited by 57

A Mammalian Conserved Element Derived from SINE Displays Enhancer Properties Recapitulating Satb2 Expression in Early-Born Callosal Projection Neurons

Tashiro, K., Teissier, A., Kobayashi, N., Nakanishi, A., Sasaki, T., Yan, K., Tarabykin, V. S., Vigier, L., Sumiyama, K., Hirakawa, M., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028497 · Cited by 53

Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development

Yuan, X., Song, M., Devine, P., Bruneau, B. G., Scott, I. C., & Wilson, M. D. (2018) · Nature Communications · doi:10.1038/s41467-018-07451-z · Cited by 55

VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers

Kosicki, M., Baltoumas, F. A., Kelman, G., Boverhof, J., Ong, Y., Cook, L., Dickel, D. E., Pavlopoulos, G. A., Pennacchio, L. A., & Visel, A. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae940 · Cited by 54

Functions of noncoding sequences in mammalian genomes

Patrushev, L. I., & Kovalenko, T. F. (2014) · Biochemistry (Moscow) · doi:10.1134/s0006297914130021 · Cited by 51

Shadow enhancers can suppress input transcription factor noise through distinct regulatory logic

Waymack, R., Fletcher, A., Enciso, G., & Wunderlich, Z. (2020) · eLife · doi:10.7554/elife.59351 · Cited by 53

Nomadic Enhancers: Tissue-Specific cis-Regulatory Elements of yellow Have Divergent Genomic Positions among Drosophila Species

Kalay, G., & Wittkopp, P. J. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001222 · Cited by 53

Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers

Wunderlich, Z., Bragdon, M. D. J., Vincent, B. J., White, J. A., Estrada, J., & DePace, A. H. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.08.021 · Cited by 55

The architecture of gene expression: integrating dispersed cis-regulatory modules into coherent regulatory domains

Schwarzer, W., & Spitz, F. (2014) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2014.03.014 · Cited by 52

Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic periodPreprint

Jj, González-Aguilera, Fernández-Miñán, Vázquez-Marín, Parra-Acero, Cross, Jw, Rigby, Pwj, Carvajal, et al. (2014) · Genome Research · doi:10.1101/gr.163915.113 · Cited by 49

Developmental Regulation of Chromatin Conformation by Hox Proteins in Drosophila

Agelopoulos, M., McKay, D. J., & Mann, R. S. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.03.003 · Cited by 50

Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization

Menoret, D., Santolini, M., Fernandes, I., Spokony, R. F., Zanet, J., Gonzalez, I., Latapie, Y., Ferrer, P., Rouault, H., White, K. P., et al. (2013) · Genome biology · doi:10.1186/gb-2013-14-8-r86 · Cited by 52

Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions

Luo, R., Yan, J., Oh, J. W., Wang, X., Shigaki, D., Wong, W., Cho, H., Murphy, D., Cutler, R. R., Rosen, B. P., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01450-7 · Cited by 50

Identification of Biologically Relevant Enhancers in Human Erythroid Cells

Su, M. Y., Steiner, L. A., Bogardus, H. H., Mishra, T., Schulz, V., Hardison, R. C., & Gallagher, P. G. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.413260 · Cited by 49

On the specificity of gene regulatory networks: How does network co-option affect subsequent evolution?

McQueen, E. W., & Rebeiz, M. (2020) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2020.03.002 · Cited by 51

Predicting Spatial and Temporal Gene Expression Using an Integrative Model of Transcription Factor Occupancy and Chromatin State

Wilczyński, B., Liu, Y.-H., Yeo, Z. X., & Furlong, E. E. M. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002798 · Cited by 46

Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos

Koromila, T., Gao, F., Iwasaki, Y., He, P., Pachter, L. S., Gergen, J. P., & Stathopoulos, A. (2020) · eLife · doi:10.7554/elife.59610 · Cited by 48

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

Landscapes and archipelagos: spatial organization of gene regulation in vertebrates

Montavon, T., & Duboule, D. (2012) · Trends in Cell Biology · doi:10.1016/j.tcb.2012.04.003 · Cited by 50

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

Whole-Embryo Modeling of Early Segmentation in Drosophila Identifies Robust and Fragile Expression Domains

Bieler, J., Pozzorini, C., & Naef, F. (2011) · Biophysical Journal · doi:10.1016/j.bpj.2011.05.060 · Cited by 44

The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development

Miesfeld, J. B., Ghiasvand, N. M., Marsh-Armstrong, B. P., Marsh‐Armstrong, N., Miller, E. B., Zhang, P., Manna, S. K., Zawadzki, R. J., Brown, N. L., & Glaser, T. M. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2006888117 · Cited by 44

Program Specificity for Ptf1a in Pancreas versus Neural Tube Development Correlates with Distinct Collaborating Cofactors and Chromatin Accessibility

Meredith, D. M., Borromeo, M. D., Deering, T. G., Casey, B. H., Savage, T. K., Mayer, P. R., Hoang, C. Q., Tung, K.-C., Kumar, M., Shen, C., et al. (2013) · Molecular and Cellular Biology · doi:10.1128/mcb.00364-13 · Cited by 45

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

Neurogenin 1 expression in the ventral neural tube is mediated by a distinct enhancer and preferentially marks ventral interneuron lineages

Quiñones, H. I., Savage, T. K., Battiste, J., & Johnson, J. E. (2010) · Developmental Biology · doi:10.1016/j.ydbio.2010.02.012 · Cited by 43

Divergent Transcriptional Regulatory Logic at the Intersection of Tissue Growth and Developmental Patterning

Slattery, M. G., Voutev, R., Ma, L., Nègre, N., White, K. P., & Mann, R. S. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003753 · Cited by 43

Transcriptional Enhancers in Drosophila

Small, S., & Arnosti, D. N. (2020) · Genetics · doi:10.1534/genetics.120.301370 · Cited by 44

Cis-regulation and chromosomal rearrangement of the fgf8 locus after the teleost/tetrapod split

Komisarczuk, A. Z., Kawakami, K., & Becker, T. S. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2009.09.029 · Cited by 41

Distinct Regulatory Mechanisms Act to Establish and Maintain Pax3 Expression in the Developing Neural Tube

Moore, S., Ribes, V., Terriente, J., Wilkinson, D. G., Relaix, F., & Briscoe, J. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003811 · Cited by 42

Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences

Bhatia, S., & Kleinjan, D. A. (2014) · Human Genetics · doi:10.1007/s00439-014-1424-6 · Cited by 42

Salivary gland branching morphogenesis: a quantitative systems analysis of the Eda/Edar/NFκB paradigm

Melnick, M., Phair, R. D., Lapidot, S. A., & Jaskoll, T. F. (2009) · BMC Developmental Biology · doi:10.1186/1471-213x-9-32 · Cited by 44

Integration of the transcriptional networks regulating limb morphogenesis

Rabinowitz, A. H., & Vokes, S. A. (2012) · Developmental Biology · doi:10.1016/j.ydbio.2012.05.035 · Cited by 41

Evidence for Deep Regulatory Similarities in Early Developmental Programs across Highly Diverged Insects

Kazemian, M., Suryamohan, K., Chen, J., Zhang, Y., Samee, M. A. H., Halfon, M. S., & Sinha, S. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu184 · Cited by 41

Genome-wide analysis of cis-regulatory changes underlying metabolic adaptation of cavefish

Krishnan, J., Seidel, C. W., Zhang, N., Singh, N. P., VanCampen, J., Peuß, R., Xiong, S., Kenzior, A., Li, H., Conaway, J. W., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01049-4 · Cited by 47

Shear stress switches the association of endothelial enhancers from ETV/ETS to KLF transcription factor binding sites

Tsaryk, R., Yucel, N. D., Leonard, E. V., Díaz, N., Bondareva, O., Odenthal-Schnittler, M., Arany, Z. P., Vaquerizas, J. M., Schnittler, H., & Siekmann, A. F. (2022) · Scientific Reports · doi:10.1038/s41598-022-08645-8 · Cited by 39

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

A SINE-Derived Element Constitutes a Unique Modular Enhancer for Mammalian Diencephalic Fgf8

Nakanishi, A., Kobayashi, N., Suzuki‐Hirano, A., Nishihara, H., Sasaki, T., Hirakawa, M., Sumiyama, K., Shimogori, T., & Okada, N. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043785 · Cited by 39

Evolution of a tissue-specific silencer underlies divergence in the expression of pax2 and pax8 paralogues

Ochi, H., Tamai, T., Nagano, H., Kawaguchi, A., Sudou, N., & Ogino, H. (2012) · Nature Communications · doi:10.1038/ncomms1851 · Cited by 40

Molecular and functional genetics of the proopiomelanocortin gene, food intake regulation and obesity

Rubinstein, M., & Low, M. J. (2017) · FEBS Letters · doi:10.1002/1873-3468.12776 · Cited by 40

Enhancers compete with a long non-coding RNA for regulation of the Kcnq1 domain

Schultz, B. M., Gallicio, G. A., Cesaroni, M., Lupey-Green, L. N., & Engel, N. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1324 · Cited by 37

Cis-regulatory Mutations in the Caenorhabditis elegans Homeobox Gene Locus cog-1 Affect Neuronal Development

O’Meara, M., Bigelow, H., Flibotte, S., Etchberger, J. F., Moerman, D. G., & Hobert, O. (2009) · Genetics · doi:10.1534/genetics.108.097832 · Cited by 37

p63 cooperates with CTCF to modulate chromatin architecture in skin keratinocytes

Qu, J., Yi, G., & Zhou, H. (2019) · Epigenetics & Chromatin · doi:10.1186/s13072-019-0280-y · Cited by 38

Zebrafish as a genomics model for human neurological and polygenic disorders

Becker, T. S., & Rinkwitz, S. (2011) · Developmental Neurobiology · doi:10.1002/dneu.20888 · Cited by 38

Transcription factor-dependent ‘anti-repressive’ mammalian enhancers exclude H3K27me3 from extended genomic domainsPreprint

Saxena, M., Roman, A. K. S., O’Neill, N. K., Sulahian, R., Jadhav, U., & Shivdasani, R. A. (2017) · Genes & Development · doi:10.1101/gad.308536.117 · Cited by 37

Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices

Racioppi, C., Wiechecki, K., & Christiaen, L. (2019) · eLife · doi:10.7554/elife.49921 · Cited by 36

Autoregulatory Feedback Controls Sequential Action of cis-Regulatory Modules at the brinker Locus

Dunipace, L., Saunders, A., Ashe, H. L., & Stathopoulos, A. (2013) · Developmental Cell · doi:10.1016/j.devcel.2013.08.010 · Cited by 36

Transcriptional activators and activation mechanisms

Ma, J. (2011) · Protein & Cell · doi:10.1007/s13238-011-1101-7 · Cited by 40

Sexual Back Talk With Evolutionary Implications: Stimulation of the Drosophila Sex-Determination Gene Sex-lethal by Its Target transformer

Siera, S. G., & Cline, T. W. (2008) · Genetics · doi:10.1534/genetics.108.093898 · Cited by 37

Transcriptional repression via antilooping in the Drosophila embryo

Chopra, V. S., Kong, N. R., & Levine, M. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1102625108 · Cited by 34

Multiple layers of complexity in cis‐regulatory regions of developmental genes

Frankel, N. (2012) · Developmental Dynamics · doi:10.1002/dvdy.23871 · Cited by 34

Modular tissue-specific regulation of doublesex underpins sexually dimorphic development in Drosophila

Rice, G. R., Barmina, O. Y., Luecke, D. M., Hu, K., Arbeitman, M. N., & Kopp, A. (2019) · Development · doi:10.1242/dev.178285 · Cited by 35

Gene Regulation: Enhancers Stepping Out of the Shadow

Hobert, O. (2010) · Current Biology · doi:10.1016/j.cub.2010.07.035 · Cited by 35

Dynamic evolution of precise regulatory encodings creates the clustered site signature of enhancers

Crocker, J., Potter, N., & Erives, A. J. (2010) · Nature Communications · doi:10.1038/ncomms1102 · Cited by 33

Identification and function of enhancers in the human genome

Coppola, C. J., Ramaker, R. C., & Mendenhall, E. M. (2016) · Human Molecular Genetics · doi:10.1093/hmg/ddw216 · Cited by 34

Spatial regulation by multiple Gremlin1 enhancers provides digit development with cis-regulatory robustness and evolutionary plasticity

Malkmus, J., Martins, L. R., Jhanwar, S., Kircher, B. K., Palacio, V., Sheth, R., Leal, F., Duchesne, A., López-Rı́os, J., Peterson, K. A., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-25810-1 · Cited by 32

Deep conservation of cis -regulatory elements in metazoans

Maeso, I., Irimia, M., Tena, J. J., Casares, F., & Gómez-Skármeta, J. L. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0020 · Cited by 35

The Relationship Between Long-Range Chromatin Occupancy and Polymerization of theDrosophilaETS Family Transcriptional Repressor Yan

Webber, J. L., Zhang, J., Cote, L. E., Vivekanand, P., Ni, X., Zhou, J. H. S., Nègre, N., Carthew, R. W., White, K. P., & Rebay, I. (2012) · Genetics · doi:10.1534/genetics.112.146647 · Cited by 34

Enhancer Talk

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Understanding developmental system drift

McColgan, Á., & DiFrisco, J. (2024) · Development · doi:10.1242/dev.203054 · Cited by 37

Quantitative Modeling of a Gene's Expression from Its Intergenic Sequence

Samee, M. A. H., & Sinha, S. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003467 · Cited by 34

When needles look like hay: How to find tissue-specific enhancers in model organism genomes

Haeussler, M., & Joly, J. (2010) · Developmental Biology · doi:10.1016/j.ydbio.2010.11.026 · Cited by 32

Sequence signatures extracted from proximal promoters can be used to predict distal enhancers

Taher, L., Smith, R. P., Kim, M. J., Ahituv, N., & Ovcharenko, I. (2013) · Genome biology · doi:10.1186/gb-2013-14-10-r117 · Cited by 32

Perturbing Enhancer Activity in Cancer Therapy

Hamdan, F. H., & Johnsen, S. A. (2019) · Cancers · doi:10.3390/cancers11050634 · Cited by 31

Ancient cis-regulatory constraints and the evolution of genome architecture

Irimia, M., Maeso, I., Roy, S. W., & Fraser, H. B. (2013) · Trends in Genetics · doi:10.1016/j.tig.2013.05.008 · Cited by 31

Distinct Functional Constraints Partition Sequence Conservation in a cis-Regulatory Element

Barrière, A., Gordon, K. L., & Ruvinsky, I. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002095 · Cited by 30

A Systematic Enhancer Screen Using Lentivector Transgenesis Identifies Conserved and Non-Conserved Functional Elements at the Olig1 and Olig2 Locus

Friedli, M., Barde, I., Arcangeli, M., Verp, S., Quazzola, A., Zákány, J., Lin-Marq, N., Robyr, D., Attanasio, C., Spitz, F., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015741 · Cited by 30

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