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

The Functionality and Evolution of Eukaryotic Transcriptional Enhancers

Buffry, A. D., Mendes, C. C., & McGregor, A. P. (2016) · Advances in genetics · doi:10.1016/bs.adgen.2016.08.004 · Cited by 34

Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters

Bass, J. I. F., Tamburino, A. M., Mori, A., Beittel, N., Weirauch, M. T., Reece-Hoyes, J. S., & Walhout, A. J. M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt858 · Cited by 30

Shared regulation and functional relevance of local gene co-expression revealed by single cell analysis

Ribeiro, D. M., Ziyani, C., & Delaneau, O. (2022) · Communications Biology · doi:10.1038/s42003-022-03831-w · Cited by 30

Single-cell chromatin accessibility identifies enhancer networks driving gene expression during spinal cord development in mouse

Shu, M., Hong, D., Lin, H., Zhang, J., Luo, Z., Du, Y., Sun, Z., Yin, M., Yin, Y., Liu, L., et al. (2022) · Developmental Cell · doi:10.1016/j.devcel.2022.11.011 · Cited by 28

Secondary enhancers synergise with primary enhancers to guarantee fine-tuned muscle gene expression

Guerrero, L., Marco-Ferreres, R., Serrano, A. L., Arredondo, J. J., & Cervera, M. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2009.10.006 · Cited by 29

Cis -acting variation is common across regulatory layers but is often buffered during embryonic developmentPreprint

Floc’hlay, S., Wong, E. S. W., Zhao, B., Viales, R. R., Thomas‐Chollier, M., Thieffry, D., Garfield, D. A., & Furlong, E. E. M. (2020) · Genome Research · doi:10.1101/gr.266338.120 · Cited by 30

Cis-Regulatory Mechanisms for Robust Olfactory Sensory Neuron Class-restricted Odorant Receptor Gene Expression in Drosophila

Jafari, S., & Alenius, M. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005051 · Cited by 30

Lineage-affiliated transcription factors bind the Gata3 Tce1 enhancer to mediate lineage-specific programs

Hosoya-Ohmura, S., Mizuno, S., Oishi, H., Ku, C.-J., Hermann, M., Hosoya, T., Takahashi, S., & Engel, J. D. (2016) · Journal of Clinical Investigation · doi:10.1172/jci83894 · Cited by 29

Integrative view on how erythropoietin signaling controls transcription patterns in erythroid cells

Perreault, A. A., & Venters, B. J. (2018) · Current Opinion in Hematology · doi:10.1097/moh.0000000000000415 · Cited by 27

Extreme restructuring of cis-regulatory regions controlling a deeply conserved plant stem cell regulator

Ciren, D., Zebell, S. G., & Lippman, Z. B. (2024) · PLoS Genetics · doi:10.1371/journal.pgen.1011174 · Cited by 26

Peak-valley-peak pattern of histone modifications delineates active regulatory elements and their directionality

Pundhir, S., Bagger, F. O., Lauridsen, F. B., Rapin, N., & Porse, B. T. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw250 · Cited by 26

Enhancer Dysfunction in 3D Genome and Disease

Xia, J., & Wei, G. (2019) · Cells · doi:10.3390/cells8101281 · Cited by 26

A complex regulatory landscape involved in the development of mammalian external genitals

Amândio, A. R., Lopez‐Delisle, L., Bolt, C. C., Mascrez, B., & Duboule, D. (2020) · eLife · doi:10.7554/elife.52962 · Cited by 26

Regulatory Principles Governing Tissue Specificity of Developmental EnhancersPreprint

Farley, E. K., Olson, K. M., & Levine, M. (2015) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2015.80.027227 · Cited by 26

Neuronal cell fate specification by the molecular convergence of different spatio-temporal cues on a common initiator terminal selector gene

Stratmann, J., & Thor, S. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006729 · Cited by 25

Modularity and hierarchy in biological systems: Using gene regulatory networks to understand evolutionary change

Hatleberg, W. L., & Hinman, V. F. (2021) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2020.11.004 · Cited by 28

Functional analysis of limb transcriptional enhancers in the mouse

Nolte, M. J., Wang, Y., Deng, J. M., Swinton, P. G., Wei, C., Guindani, M., Schwartz, R. J., & Behringer, R. R. (2014) · Evolution & Development · doi:10.1111/ede.12084 · Cited by 26

The intriguing complexities of mammalian gene regulation: How to link enhancers to regulated genes. Are we there yet?

Dániel, B., Nagy, G., & Nagy, L. (2014) · FEBS Letters · doi:10.1016/j.febslet.2014.05.041 · Cited by 25

Human genetic variation within neural crest enhancers: molecular and phenotypic implications

Rada-Iglesias, A., Prescott, S. L., & Wysocka, J. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2012.0360 · Cited by 24

Three-dimensional genome: developmental technologies and applications in precision medicine

Li, Y., Tao, T., Du, L., & Zhu, X. M. (2020) · Journal of Human Genetics · doi:10.1038/s10038-020-0737-7 · Cited by 24

Setting the stage for development: the maternal-to-zygotic transition in Drosophila

Harrison, M. M., Marsh, A. J., & Rushlow, C. A. (2023) · Genetics · doi:10.1093/genetics/iyad142 · Cited by 25

Notch regulates numb: integration of conditional and autonomous cell fate specification

Rebeiz, M., Miller, S. W., & Posakony, J. W. (2010) · Development · doi:10.1242/dev.050161 · Cited by 26

Evolution of Shh endoderm enhancers during morphological transition from ventral lungs to dorsal gas bladder

Sagai, T., Amano, T., Maeno, A., Kimura, T., Nakamoto, M., Takehana, Y., Naruse, K., Okada, N., Kiyonari, H., & Shiroishi, T. (2017) · Nature Communications · doi:10.1038/ncomms14300 · Cited by 24

Repressive interactions in gene regulatory networks: When you have no other choice

Delàs, M. J., & Briscoe, J. (2020) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2020.03.003 · Cited by 25

Decoding the epigenetics and chromatin loop dynamics of androgen receptor-mediated transcription

Altıntaş, U. B., Seo, J.-H., Giambartolomei, C., Özturan, D., Fortunato, B. J., Nelson, G. M., Goldman, S. R., Adelman, K., Hach, F., Freedman, M. L., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-53758-5 · Cited by 24

Identifying Coopted Networks and Causative Mutations in the Origin of Novel Complex Traits

Monteiro, A., & Gupta, M. D. (2016) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2016.03.003 · Cited by 23

Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements

Thierion, E., Men, J. L., Collombet, S., Hernandez, C., Coulpier, F., Torbey, P., Thomas‐Chollier, M., Noordermeer, D., Charnay, P., & Gilardi‐Hebenstreit, P. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006903 · Cited by 24

Evolutionary emergence of the rac3b / rfng / sgca regulatory cluster refined mechanisms for hindbrain boundaries formation

Letelier, J., Terriente, J., Belzunce, I., Voltes, A., Undurraga, C. A., Polvillo, R., Devos, L., Tena, J. J., Maeso, I., Rétaux, S., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1719885115 · Cited by 24

Broadening primate genomics: new insights into the ecology and evolution of primate gene regulation

Anderson, J. A., Vilgalys, T. P., & Tung, J. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.05.009 · Cited by 23

Independent Transposon Exaptation Is a Widespread Mechanism of Redundant Enhancer Evolution in the Mammalian Genome

Barth, N. K. H., Li, L., & Taher, L. (2020) · Genome Biology and Evolution · doi:10.1093/gbe/evaa004 · Cited by 24

Control of Distal-less expression in the Drosophila appendages by functional 3′ enhancers

Galindo, M. I., Fernández-Garza, D., Phillips, R. J., & Couso, J. P. (2011) · Developmental Biology · doi:10.1016/j.ydbio.2011.02.005 · Cited by 23

Favorable genomic environments for cis-regulatory evolution: A novel theoretical framework

Maeso, I., & Tena, J. J. (2015) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2015.12.003 · Cited by 25

A Distalless-responsive enhancer of the Hox gene Sex combs reduced is required for segment- and sex-specific sensory organ development in Drosophila

Eksi, S. E., Barmina, O. Y., McCallough, C. L., Kopp, A., & Orenic, T. V. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007320 · Cited by 23

Diversification of transcription factor–DNA interactions and the evolution of gene regulatory networks

Rogers, J. M., & Bulyk, M. L. (2018) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1423 · Cited by 22

Mitosis-associated repression in developmentPreprint

Esposito, E., Lim, B., Guessous, G., Falahati, H., & Levine, M. (2016) · Genes & Development · doi:10.1101/gad.281188.116 · Cited by 22

Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells

Bakoulis, S., Krautz, R., Alcaraz, N., Salvatore, M., & Andersson, R. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac088 · Cited by 23

Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient

Álamos, S., Reimer, A. E., Westrum, C., Turner, M. A., Talledo, P., Zhao, J., Luu, E., & García, H. G. (2023) · Cell Systems · doi:10.1016/j.cels.2022.12.008 · Cited by 26

Modular Organization ofCis-regulatory Control Information of Neurotransmitter Pathway Genes inCaenorhabditis elegans

Serrano‐Saiz, E., Gülez, B., Pereira, L., Gendrel, M., Kerk, S. Y., Vidal, B., Feng, W., Wang, C., Kratsios, P., Rand, J. B., et al. (2020) · Genetics · doi:10.1534/genetics.120.303206 · Cited by 21

Super-enhancers require a combination of classical enhancers and novel facilitator elements to drive high levels of gene expressionPreprint

Blayney, J., Francis, H. S., Camellato, B. R., MITCHELL, L. A., Stolper, R. J., Boeke, J. D., Higgs, D. R., & Kassouf, M. T. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.20.496856 · Cited by 21

Use of a Drosophila genome‐wide conserved sequence database to identify functionally related cis‐regulatory enhancers

Brody, T., Yavatkar, A. S., Kuzin, A., Kundu, M., Tyson, L. J., Ross, J., Lin, T., Lee, C., Awasaki, T., Lee, T., et al. (2011) · Developmental Dynamics · doi:10.1002/dvdy.22728 · Cited by 21

The search for cis-regulatory driver mutations in cancer genomes

Poulos, R. C., Sloane, M. A., Hesson, L. B., & Wong, J. W. H. (2015) · Oncotarget · doi:10.18632/oncotarget.5085 · Cited by 21

Regulatory logic driving stable levels of defective proventriculus expression during terminal photoreceptor specification in flies

Yan, J. J., Anderson, C., Viets, K., Tran, S., Goldberg, G. W., Small, S., & Johnston, R. J. (2017) · Development · doi:10.1242/dev.144030 · Cited by 20

Cooperation, cis-interactions, versatility and evolutionary plasticity of multiple cis-acting elements underlie krox20 hindbrain regulation

Torbey, P., Thierion, E., Collombet, S., Cian, A. D., Dinh, C. D., Dura, M., Concordet, J., Charnay, P., & Gilardi‐Hebenstreit, P. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007581 · Cited by 21

Functional Consequences of Chromosomal Rearrangements on Gene Expression: Not So Deleterious After All?

Ghavi-Helm, Y. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.09.010 · Cited by 20

Transcriptional regulation of neuronal identity

Sousa, E., & Flames, N. (2021) · European Journal of Neuroscience · doi:10.1111/ejn.15551 · Cited by 19

From shavenbaby to the naked valley: trichome formation as a model for evolutionary developmental biology

Arif, S., Kittelmann, S., & McGregor, A. P. (2015) · Evolution & Development · doi:10.1111/ede.12113 · Cited by 23

Stripy Ftz target genes are coordinately regulated by Ftz-F1

Hou, H. Y., Heffer, A. M., Anderson, W. R., Liu, J., Bowler, T. G., & Pick, L. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2009.08.004 · Cited by 19

Redundant and Cryptic Enhancer Activities of the Drosophila yellow Gene

Kalay, G., Lachowiec, J., Rosas, U., Dome, M. R., & Wittkopp, P. J. (2019) · Genetics · doi:10.1534/genetics.119.301985 · Cited by 20

A regulatory sub-circuit downstream of Wnt signaling controls developmental transitions in neural crest formation

Azambujá, A. P., & Simões-Costa, M. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009296 · Cited by 19

Study of Cis-regulatory Elements in the Ascidian Ciona intestinalis

Irvine, S. Q. (2013) · Current Genomics · doi:10.2174/138920213804999192 · Cited by 19

An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes

Arunachalam, M., Jayasurya, K., Tomančák, P., & Ohler, U. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq358 · Cited by 20

Disrupting the three-dimensional regulatory topology of the Pitx1 locus results in overtly normal development

Sarro, R., Kocher, A. A., Emera, D., Uebbing, S., Dutrow, E. V., Weatherbee, S. D., Nottoli, T., & Noonan, J. P. (2018) · Development · doi:10.1242/dev.158550 · Cited by 20

Evolution of Insect Dorsoventral Patterning MechanismsPreprint

Perry, M., Cande, J., Boettiger, A. N., & Levine, M. (2009) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2009.74.021 · Cited by 19

Mechanisms of Enhancer-Mediated Gene Activation in the Context of the 3D Genome

Papantonis, A., & Oudelaar, A. M. (2025) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-120423-012301 · Cited by 19

Gene regulatory networks: from correlative models to causal explanations

Maizels, R. J., & Briscoe, J. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-026-00939-1 · Cited by 21

Dynamic patterning by morphogens illuminated by cis-regulatory studies

Irizarry, J., & Stathopoulos, A. (2021) · Development · doi:10.1242/dev.196113 · Cited by 19

Copy number variants in patients with intellectual disability affect the regulation of ARX transcription factor gene

Ishibashi, M., Manning, E., Shoubridge, C., Krecsmarik, M., Hawkins, T. A., Giacomotto, J., Zhao, T., Mueller, T., Bader, P. I., Cheung, S. W., et al. (2015) · Human Genetics · doi:10.1007/s00439-015-1594-x · Cited by 19

Genomic context sensitizes regulatory elements to genetic disruption

Ordóñez, R., Zhang, W., Ellis, G., Zhu, Y., Ashe, H. J., Ribeiro-dos-Santos, A. M., Brosh, R., Huang, E., Hogan, M. S., Boeke, J. D., et al. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.04.013 · Cited by 22

The case against simplistic genetic explanations of evolution

Cooper, K. L. (2024) · Development · doi:10.1242/dev.203077 · Cited by 17

Neural precursor-specific expression of multiple Drosophila genes is driven by dual enhancer modules with overlapping function

Miller, S. W., Rebeiz, M., Atanasov, J. E., & Posakony, J. W. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1415308111 · Cited by 18

Direct Interactions BetweenGli3,Wnt8b, andFgfsUnderlie Patterning of the Dorsal Telencephalon

Hasenpusch‐Theil, K., Watson, J. A., & Theil, T. (2015) · Cerebral Cortex · doi:10.1093/cercor/bhv291 · Cited by 18

Quantitative modeling of gene expression using DNA shape features of binding sites

Peng, P.-C., & Sinha, S. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw446 · Cited by 17

Chromatin looping and organization at developmentally regulated gene loci

Noordermeer, D., & Duboule, D. (2013) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.103 · Cited by 17

Coacting enhancers can have complementary functions within gene regulatory networks and promote canalization

Dunipace, L., Ákos, Z., & Stathopoulos, A. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008525 · Cited by 17

The logic of native enhancer-promoter compatibility and cell-type-specific gene expression variationPreprint

Narita, T., Higashijima, Y., Kilic, S., Maskey, E., Neumann, K., & Choudhary, C. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.18.500456 · Cited by 17

Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth

Zhang, Y., Chen, K., Tang, S. C., Cai, Y., Niibori-Nambu, A., See, Y. X., Fu, C., Raju, A., Lebeau, B., Ling, Z., et al. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01391-7 · Cited by 16

Biological roles of enhancer RNA m6A modification and its implications in cancer

Han, Y., Sun, J., Yao, M., Miao, L., & Li, M. (2025) · Cell Communication and Signaling · doi:10.1186/s12964-025-02254-4 · Cited by 19

Epo reprograms the epigenome of erythroid cells

Perreault, A. A., Benton, M. L., Koury, M. J., Brandt, S. J., & Venters, B. J. (2017) · Experimental Hematology · doi:10.1016/j.exphem.2017.03.004 · Cited by 18

Gene silencing dynamics are modulated by transiently active regulatory elements

Vermunt, M. W., Luan, J. Y., Zhang, Z., Thrasher, A. J., Huang, A., Saari, M. S., Khandros, E., Beagrie, R. A., Zhang, S., Vemulamada, P., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.02.006 · Cited by 16

Conserved enhancers control notochord expression of vertebrate Brachyury

Kemmler, C. L., Smolikova, J., Moran, H. R., Mannion, B. J., Knapp, D., Lim, F., Czarkwiani, A., Hermosilla, V. E., Rapp, V., Fitch, O. E., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-42151-3 · Cited by 16

Chromosomal organization at the level of gene complexes

Chopra, V. S. (2010) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-010-0585-2 · Cited by 16

Temporal regulation of epithelium formation mediated by FoxA, MKLP1, MgcRacGAP, and PAR-6

Stetina, S. E. V., Liang, J., Marnellos, G., & Mango, S. E. (2017) · Molecular Biology of the Cell · doi:10.1091/mbc.e16-09-0644 · Cited by 15

Diverse logics and grammar encode notochord enhancers

Song, B. P., Ragsac, M. F., Tellez, K., Jindal, G. A., Grudzien, J. L., Le, S. H., & Farley, E. K. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112052 · Cited by 15

Localized and Temporal Gene Regulation in Heart Development

Barnett, P., van den Boogaard, M., & Christoffels, V. M. (2012) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/b978-0-12-387786-4.00004-x · Cited by 15

Unique N-terminal sequences in two Runx1 isoforms are dispensable for Runx1 function

Nieke, S., Yasmin, N., Kakugawa, K., Yokomizo, T., Muroi, S., & Taniuchi, I. (2017) · BMC Developmental Biology · doi:10.1186/s12861-017-0156-y · Cited by 15

Frequent fetal heart-rate monitoring for early detection of abruptio placentae in severe proteinuric hypertension.

Odendaal, H. J., Pattinson, R., Toit, R. D., & Grove, D. (1988) · PubMed · Cited by 15

Cross-species analysis of melanoma enhancer logic using deep learningPreprint

Minnoye, L., Taskiran, I. I., Mauduit, D., Fazio, M., Aerschot, L. V., Hulsemans, G., Christiaens, V., Makhzami, S., Seltenhammer, M. H., Karras, P., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2019.12.21.885715 · Cited by 15

Identification of new Anopheles gambiae transcriptional enhancers using a cross‐species prediction approach

Schember, I., & Halfon, M. S. (2021) · Insect Molecular Biology · doi:10.1111/imb.12705 · Cited by 14

Stepwise Progression of Embryonic Patterning

Sandler, J. E., & Stathopoulos, A. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.04.004 · Cited by 14

Transcriptional autoregulation of zebrafish tbx6 is required for somite segmentation

Ban, H., Yokota, D., Otosaka, S., Kikuchi, M., Kinoshita, H., Fujino, Y., Yabe, T., Ovara, H., Izuka, A., Akama, K., et al. (2019) · Development · doi:10.1242/dev.177063 · Cited by 14

The anterior Hox gene ceh-13 and elt-1/GATA activate the posterior Hox genes nob-1 and php-3 to specify posterior lineages in the C. elegans embryo

Murray, J. I., Preston, E. A., Crawford, J. P., Rumley, J. D., Amom, P., Anderson, B. D., Sivaramakrishnan, P., Patel, S. D., Bennett, B. A., Lavon, T. D., et al. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010187 · Cited by 15

Phenotypic suppression of the Drosophila mitochondrial disease-like mutant tko25t by duplication of the mutant gene in its natural chromosomal context

Kemppainen, E., Fernández‐Ayala, D. J. M., Galbraith, L. C. A., O’Dell, K. M. C., & Jacobs, H. T. (2009) · Mitochondrion · doi:10.1016/j.mito.2009.07.002 · Cited by 14

Augmentation of a wound response element accompanies the origin of a Hox-regulated Drosophila abdominal pigmentation trait

Grover, S., Williams, M. E., Kaiser, R. E., Hughes, J. T., Gresham, L., Rebeiz, M., & Williams, T. M. (2018) · Developmental Biology · doi:10.1016/j.ydbio.2018.07.001 · Cited by 14

Distinct Roles of Broadly Expressed Repressors Support Dynamic Enhancer Action and Change in Time

Koromila, T., & Stathopoulos, A. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.06.063 · Cited by 14

Loss-of-function tolerance of enhancers in the human genome

Xu, D., Gökçümen, Ö., & Khurana, E. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008663 · Cited by 14

Tissue context determines the penetrance of regulatory DNA variation

Halow, J. M., Byron, R., Hogan, M. S., Ordóñez, R., Groudine, M. T., Bender, M. A., Stamatoyannopoulos, J. A., & Maurano, M. T. (2021) · Nature Communications · doi:10.1038/s41467-021-23139-3 · Cited by 15

Functional characterization of enhancer activity during a long terminal repeat's evolutionPreprint

Du, A. Y., Zhuo, X., Sundaram, V., Jensen, N. O., Chaudhari, H. G., Saccone, N. L., Cohen, B. A., & Wang, T. (2022) · Genome Research · doi:10.1101/gr.276863.122 · Cited by 16

Widespread cis ‐ and trans ‐regulatory evolution underlies the origin, diversification, and loss of a sexually dimorphic fruit fly pigmentation trait

Hughes, J. T., Williams, M. E., Rebeiz, M., & Williams, T. M. (2021) · Journal of Experimental Zoology Part B Molecular and Developmental Evolution · doi:10.1002/jez.b.23068 · Cited by 13

Enhancing Gene Regulation

Wray, G. A., & Babbitt, C. C. (2008) · Science · doi:10.1126/science.1163568 · Cited by 13

Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution

Sakabe, N. J., & Nóbrega, M. A. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0022 · Cited by 13

Functional characterization ofSIM1-associated enhancers

Kim, M. J., Oksenberg, N., Hoffmann, T. J., Vaisse, C., & Ahituv, N. (2013) · Human Molecular Genetics · doi:10.1093/hmg/ddt559 · Cited by 13

Transcriptional control of transglutaminase 2 expression in mouse apoptotic thymocytes

Sándor, K., Dániel, B., Kiss, B., Kovács, F., & Szondy, Z. (2016) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2016.05.011 · Cited by 13

A shared ancient enhancer element differentially regulates the bric-a-brac tandem gene duplicates in the developing Drosophila leg

Bourbon, H.-M. G., Benetah, M. H., Guillou, E., Mojica-Vázquez, L. H., Baanannou, A., Bernat-Fabre, S., Loubière, V., Bantignies, F., Cavalli, G., & Boube, M. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010083 · Cited by 14

Assessing constraints on the path of regulatory sequence evolution

Glassford, W. J., & Rebeiz, M. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0026 · Cited by 14

Deletion of Pax1 scoliosis-associated regulatory elements leads to a female-biased tail abnormality

Ushiki, A., Sheng, R. R., Zhang, Y., Zhao, J., Nobuhara, M., Murray, E., Ruan, X., Rios, J. J., Wise, C. A., & Ahituv, N. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.113907 · Cited by 13

BMP-dependent gene repression cascade in Drosophila eggshell patterning

Charbonnier, E., Fuchs, A., Cheung, L. S., Chayengia, M., Veikkolainen, V., Seyfferth, J., Shvartsman, S. Y., & Pyrowolakis, G. (2015) · Developmental Biology · doi:10.1016/j.ydbio.2015.02.004 · Cited by 12

The regulatory control of Cebpa enhancers and silencers in the myeloid and red-blood cell lineages

Repele, A., Krueger, S., Bhattacharyya, T., Tuineau, M. Y., & Manu (2019) · PLoS ONE · doi:10.1371/journal.pone.0217580 · Cited by 13

Intrinsic control of muscle attachment sites matching

Carayon, A., Bataillé, L., Lebreton, G., Dubois, L., Pelletier, A., Carrier, Y., Wystrach, A., Vincent, A., & Frendo, J. (2020) · eLife · doi:10.7554/elife.57547 · Cited by 13

The Drosophila Transcription Factors Tinman and Pannier Activate and Collaborate with Myocyte Enhancer Factor-2 to Promote Heart Cell Fate

Lovato, T. L., Sensibaugh, C. A., Swingle, K. L., Martinez, M. M., & Cripps, R. M. (2015) · PLoS ONE · doi:10.1371/journal.pone.0132965 · Cited by 12

RARβ2 is required for vertebrate somitogenesis

Janesick, A., Tang, W., Nguyen, T. T. L., & Blumberg, B. (2017) · Development · doi:10.1242/dev.144345 · Cited by 12

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