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Recent advances in high-throughput approaches to dissect enhancer function

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Enhancer architecture and chromatin accessibility constrain phenotypic space during Drosophila development

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Krüppel Expression Levels Are Maintained through Compensatory Evolution of Shadow Enhancers

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Altered Chromatin Occupancy of Master Regulators Underlies Evolutionary Divergence in the Transcriptional Landscape of Erythroid Differentiation

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The appeasement of Doug: a synthetic approach to enhancer biology

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Deep homology in the age of next-generation sequencing

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Decoding enhancer complexity with machine learning and high-throughput discovery

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Rate variation in the evolution of non-coding DNA associated with social evolution in bees

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On the Regulatory Evolution of New Genes Throughout Their Life History

Zhang, J., & Zhou, Q. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy206 · Cited by 36 · see citing works

The origins of developmental gene regulation

Arenas‐Mena, C. (2017) · Evolution & Development · doi:10.1111/ede.12217 · Cited by 35 · see citing works

Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for Evolutionary Studies

Buchberger, E., Reis, M., Lu, T.-H., & Posnien, N. (2019) · Genes · doi:10.3390/genes10070492 · Cited by 32 · see citing works

Recent advances in genomics and transcriptomics of cnidarians

Technau, U., & Schwaiger, M. (2015) · Marine Genomics · doi:10.1016/j.margen.2015.09.007 · Cited by 35 · see citing works

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 30 · see citing works

Identifying Novel Enhancer Elements with CRISPR-Based Screens

Klein, J. C., Chen, W., Gasperini, M. J., & Shendure, J. (2018) · ACS Chemical Biology · doi:10.1021/acschembio.7b00778 · Cited by 29 · see citing works

Computational and experimental methods for classifying variants of unknown clinical significance.Preprint

Spielmann, M., & Kircher, M. (2022) · PubMed Central · doi:10.1101/mcs.a006196 · Cited by 28 · see citing works

Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine

Lange, M., Begolli, R., & Giakountis, A. (2021) · Non-Coding RNA · doi:10.3390/ncrna7030047 · Cited by 26 · see citing works

Genetic Dissection of Dual Roles for the Transcription Factor six7 in Photoreceptor Development and Patterning in Zebrafish

Sotolongo-Lopez, M., Álvarez-Delfín, K., Saade, C. J., Vera, D. L., & Fadool, J. M. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1005968 · Cited by 25 · see citing works

Enhancers display constrained sequence flexibility and context-specific modulation of motif functionPreprint

Reiter, F., de Almeida, B. P., & Stark, A. (2023) · Genome Research · doi:10.1101/gr.277246.122 · Cited by 24 · see citing works

Conservation of peripheral nervous system formation mechanisms in divergent ascidian embryos

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What Does It Take to Evolve an Enhancer? A Simulation-Based Study of Factors Influencing the Emergence of Combinatorial Regulation

Duque, T. S. P. C., & Sinha, S. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv080 · Cited by 21 · see citing works

Transcriptional enhancers: from prediction to functional assessment on a genome-wide scale

Tobias, I. C., Abatti, L. E., Moorthy, S. D., Mullany, S., Taylor, T., Khader, N., Filice, M., & Mitchell, J. A. (2020) · Genome · doi:10.1139/gen-2020-0104 · Cited by 20 · see citing works

Human gene regulatory evolution is driven by the divergence of regulatory element function in both cis and trans

Hansen, T. J., Fong, S., Day, J. K., Capra, J. A., & Hodges, E. C. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100536 · Cited by 20 · see citing works

Evolution of New cis-Regulatory Motifs Required for Cell-Specific Gene Expression in Caenorhabditis

Barkoulas, M., Velazquez, A. M. V., Peluffo, A. E., & Félix, M. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006278 · Cited by 18 · see citing works

Genomic Loss and Silencing on the Y Chromosomes of Rumex

Beaudry, F. E. G., Barrett, S. C. H., & Wright, S. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx254 · Cited by 19 · see citing works

The Interplay Between Developmental Stage and Environment Underlies the Adaptive Effect of a Natural Transposable Element Insertion

Merenciano, M., & González, J. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad044 · Cited by 18 · see citing works

Predicting Ancestral Segmentation Phenotypes from Drosophila to Anopheles Using In Silico Evolution

Rothschild, J., Tsimiklis, P., Siggia, E. D., & François, P. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006052 · Cited by 18 · see citing works

Diverse Cis-Regulatory Mechanisms Contribute to Expression Evolution of Tandem Gene Duplicates

Baudouin-Gonzalez, L., Santos, M. A., Tempesta, C., Sucena, É., Roch, F., & Tanaka, K. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx237 · Cited by 18 · see citing works

Three topological features of regulatory networks control life-essential and specialized subsystems

Wolf, I. R., Simões, R. P., & Valente, G. T. (2021) · Scientific Reports · doi:10.1038/s41598-021-03625-w · Cited by 16 · see citing works

Beyond modular enhancers: new questions in cis-regulatory evolution

McDonald, J. M. C., & Reed, R. D. (2024) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2024.07.005 · Cited by 15 · see citing works

The Role of Chromatin Accessibility in cis-Regulatory Evolution

Peng, P.-C., Khoueiry, P., Girardot, C., Reddington, J. P., Garfield, D. A., Furlong, E. E. M., & Sinha, S. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz103 · Cited by 16 · see citing works

Functional regulatory evolution outside of the minimal even-skipped stripe 2 enhancer

Crocker, J., & Stern, D. L. (2017) · Development · doi:10.1242/dev.149427 · Cited by 16 · see citing works

Cis-regulatory variants affect gene expression dynamics in yeast

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Whole-genome functional characterization of RE1 silencers using a modified massively parallel reporter assay

Mouri, K., Dewey, H. B., Castro, R., Berenzy, D., Kales, S., & Tewhey, R. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100234 · Cited by 16 · see citing works

Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila

Carl, S. H., & Russell, S. R. H. (2015) · BMC Genomics · doi:10.1186/s12864-015-1495-3 · Cited by 13 · see citing works

Influence of genetic polymorphism on transcriptional enhancer activity in the malaria vector Anopheles coluzzii

Nardini, L., Holm, I., Pain, A., Bischoff, E., Gohl, D. M., Zongo, S., Guelbeogo, M. W., Sagnon, N., Vernick, K. D., & Riehle, M. M. (2019) · Scientific Reports · doi:10.1038/s41598-019-51730-8 · Cited by 15 · see citing works

The transcription factor Traffic jam orchestrates the somatic piRNA pathway in Drosophila ovaries

Alizada, A., Martins, A., Mouniée, N., Suarez, J. V. R., Bertin, B., Gueguen, N., Mirouse, V., Papameletiou, A. M., Rivera, A. J., Lau, N. C., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115453 · Cited by 14 · see citing works

Accelerated evolution at chaperone promoters among Antarctic notothenioid fishes

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Filtering the Junk: Assigning Function to the Mosquito Non-Coding Genome

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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 14 · see citing works

Mutational scans reveal differential evolvability of Drosophila promoters and enhancers

Li, X., Fuqua, T., van Breugel, M. E., & Crocker, J. (2023) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2022.0054 · Cited by 12 · see citing works

Divergent MLS1 Promoters Lie on a Fitness Plateau for Gene Expression

Bergen, A. C., Olsen, G. M., & Fay, J. C. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw010 · Cited by 14 · see citing works

Decoding transcriptional enhancers: Evolving from annotation to functional interpretation

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Decoding transcriptional states in cancer

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Proformer: a hybrid macaron transformer model predicts expression values from promoter sequences

Kwak, I., Kim, B.-C., Lee, J., Kang, T., Garry, D. J., Zhang, J. J., & Gong, W. (2024) · BMC Bioinformatics · doi:10.1186/s12859-024-05645-5 · Cited by 10 · see citing works

Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq

Zhou, W., Shi, H., Wang, Z., Huang, Y., Ni, L., Chen, X., Liu, Y., Li, C., Liu, Y., & Liu, Y. (2024) · Genomics Proteomics & Bioinformatics · doi:10.1093/gpbjnl/qzae012 · Cited by 10 · see citing works

Systematic identification and characterization of repressive domains in Drosophila transcription factors

Klaus, L., de Almeida, B. P., Vlasova, A. V., Nemčko, F., Schleiffer, A., Bergauer, K., Hofbauer, L., Rath, M., & Stark, A. (2022) · The EMBO Journal · doi:10.15252/embj.2022112100 · Cited by 11 · see citing works

A systematic evaluation of the design, orientation, and sequence context dependencies of massively parallel reporter assaysPreprint

Klein, J. C., Agarwal, V., Inoue, F., Keith, A., Martin, B., Kircher, M., Ahituv, N., & Shendure, J. (2020) · doi:10.21203/rs.3.pex-1065/v1 · Cited by 11 · see citing works

The evolution of gene regulation on sex chromosomes

Shaw, D. E., & White, M. A. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.04.004 · Cited by 10 · see citing works

Traffic Jam activates the Flamenco piRNA cluster locus and the Piwi pathway to ensure transposon silencing and Drosophila fertility

Rivera, A. J., Lee, J.-H. R., Gupta, S., Yang, L. G., Goel, R. K., Zaia, J., & Lau, N. C. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115354 · Cited by 11 · see citing works

Integrative Approaches to Understanding the Pathogenic Role of Genetic Variation in Rheumatic Diseases

Laufer, V. A., Chen, J. Y., Langefeld, C. D., & Bridges, S. L. (2017) · Rheumatic Disease Clinics of North America · doi:10.1016/j.rdc.2017.04.012 · Cited by 10 · see citing works

Enhancers as potential targets for engineering salinity stress tolerance in crop plants

Jain, M., & Garg, R. (2021) · Physiologia Plantarum · doi:10.1111/ppl.13421 · Cited by 9 · see citing works

Conservation and divergence of enhancer function across five Drosophila species

Spies, D. (2014) · University of Vienna · doi:10.25365/thesis.33438

STARR-seq: genome-wide quantitative enhancer activity maps and the evolution of cis-regulatory elements

Arnold, C. D. (2013)

Analysis of the genomic conservation of the pleiotropic activity of enhancers between Drosophila melanogaster and Drosophila virilis

Altamirano, A. (2024) · Repositorio Digital Institucional de la Universidad de Buenos Aires (Universidad de Buenos Aires)

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

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Gene Regulatory Enhancers with Evolutionarily Conserved Activity Are More Pleiotropic than Those with Species-Specific Activity

Fish, A. E., Chen, L., & Capra, J. A. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx194 · Cited by 42 · see citing works