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

An intrinsic chromatin timer sets the tempo for developmentPreprint

Catalano, C., Levine, M., & Tullius, T. W. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.28.685222 · Cited by 2

Enhancer buffering protects dosage-sensitive housekeeping genes during vulnerable developmental transitionsPreprint

Ni, C., Ichino, L., Swigut, T., & Wysocka, J. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.07.29.741571 · Cited by 2

Osteogenesis Imperfecta and Split Foot Malformation due to 7q21.2q21.3 Deletion Including COL1A2, DLX5/6 Genes: Review of the Literature

Öztürk, Ö., Bağış, H., & Bolu, S. (2021) · Journal of Pediatric Genetics · doi:10.1055/s-0041-1736613 · Cited by 2

Enhancer-promoter communication in Drosophila developmental gene transcription

Hunt, G., & Mannervik, M. (2024) · The International Journal of Developmental Biology · doi:10.1387/ijdb.230218gh · Cited by 1

The exit from naive pluripotency: a platform for the study of enhancer mechanistics

Jonasson, M., & Buecker, C. (2025) · Biochemical Society Transactions · doi:10.1042/bst20253037 · Cited by 1

Environmental yin-yang: how external cues are processed at the level of cells and at the level of an organism

Afzal, Z., & Kumar, D. (2025) · Developmental Biology · doi:10.1016/j.ydbio.2025.11.013 · Cited by 1

How to build the regulatory genome: a constructionist guide to the cis-regulatory code

Bell, C. C., de Boer, C. G., Camellato, B. R., Delàs, M. J., Ibrahim, D. M., & Montgomery, M. T. (2026) · Development · doi:10.1242/dev.205516 · Cited by 2

Expanding the fly eye gene regulatory network: From Drosophila to the hoverfly Episyrphus balteatus

Navarro, T., Torres, J., Sáez-Moreno, R., Guerrero, G., Almudí, I., Iannini, A., Figueras, J., Wotton, K. R., Aerts, S., & Casares, F. (2026) · PLoS Genetics · doi:10.1371/journal.pgen.1011864 · Cited by 1

Compensatory action of different types of cis -regulatory elements buffers the striped expression of Drosophila pair-rule genes

Fischer, M. D., Au, K. M., Lê, M., Graham, P. L., & Pick, L. (2025) · Development · doi:10.1242/dev.204872 · Cited by 1

New Techniques for Mechanical Measurements in the Superconducting Magnet Models

Guinchard, M., Artoos, K., Gerardin, A., & Kuzmin, A. (2010) · JACOW · doi:10.18429/jacow-ipac2010-mopeb043 · Cited by 1

GOOD AGRICULTURAL PRACTICES: FOOD SAFETY FOR FRESH PRODUCE

Singh, A. (2009) · Cited by 1

Genomic Regulation of the Shox2 Gene during Mouse Limb Development

Abassah‐Oppong, S. (2016) · Libraries and Cultural Resources (University of Calgary) · doi:10.11575/prism/26274 · Cited by 1

Studying enhancer function using the Tbx4 locus as a model

Mihala, A. G. (2014) · Cited by 1

Model-based analysis of polymorphisms in an enhancer reveals cis-regulatory mechanismsPreprint

Khajouei, F., Samper, N., Djabrayan, N., Lunt, B., Jiménez, G., & Sinha, S. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.07.939264 · Cited by 1

Evolution of transposable element-derived enhancer activityPreprint

Du, A. Y., Zhuo, X., Sundaram, V., Jensen, N. O., Chaudhari, H. G., Saccone, N. L., Cohen, B. A., & Wang, T. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.16.483999 · Cited by 1

Decoding the Epigenetics and Chromatin Loop Dynamics of Androgen Receptor-Mediated TranscriptionPreprint

Lack, N. A., Altıntaş, U. B., Seo, J.-H., Giambartolomei, C., Özturan, D., Fortunato, B. J., Nelson, G. M., Goldman, S. R., Adelman, K., Hach, F., et al. (2024) · Research Square · doi:10.21203/rs.3.rs-3854707/v1 · Cited by 1

Neurogenetic evidence that Dilp8 promotes developmental-stability via Lgr3-neuron oscillationPreprint

Zanini, R., Pereirinha, J., Fernandez-Acosta, M., Casimiro, A. P., Pinho, M. G., Lage, L. R., Garelli, A., Herédia, F., & Gontijo, A. M. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.26.625404 · Cited by 1

Evolution of Human Gene Expression Control

Boyd, J. L., & Wray, G. A. (2014) · Wiley eBooks · doi:10.1002/9780470015902.a0020769.pub2

Ancient trans -acting siRNAs Confer Robustness and Sensitivity onto the Auxin ResponsePreprint

Plavskin, Y., Nagashima, A., Perroud, P., Hasebe, M., Quatrano, R. S., Atwal, G. S., & Timmermans, M. C. P. (2015) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/024307

Computational modeling of gene expression from regulatory sequences

Samee, M. A. H. (2015) · Illinois Digital Environment for Access to Learning and Scholarship (University of Illinois at Urbana-Champaign)

OVERLAPPING SEQUENCE FEATURES OF MAMMALIAN ENHANCERS COORDINATELY CONTROL ENGAGEMENT OF TRANSCRIPTION FACTOR CONSENSUS SITES AND NUCLEOSOMAL OCCUPANCY

Barozzi, I. (2014) · Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) · doi:10.13130/barozzi-iros-giacomo_phd2014-03-25

Genetic Mechanisms during Terminal Cell Fate Specification in the Drosophila CNS

Stratmann, J. (2017) · Linköping University medical dissertations · doi:10.3384/diss.diva-133225

Shaping Up the Embryo: The Role of Genome 3D Organization

Jácome-López, K., & Furlan-Magaril, M. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7714-7_15

A Multiplexed Assay for Exon Recognition Reveals That an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Disruptions to SplicingPreprint

Cheung, R., Insigne, K. D., Yao, D., Burghard, C. P., Jones, E. M., Goodman, D. B., & Kosuri, S. (2018) · SSRN Electronic Journal · doi:10.2139/ssrn.3188378

Enhancer-Promoter Interactions and Their Role in the Control of Epidermal Differentiation

Oh, I. Y., & Strong, C. D. G. (2018) · Contributions to management science · doi:10.1007/978-3-319-16769-5_10

Functional analysis of human enhancers using the zebrafish embryo

Miguel-Escalada, I. (2014) · University of Birmingham Institutional Research Archive (University of Birmingham)

Shadow Enhancers Provide Precision and Robustness for the Patterning of the Precellular Drosophila Embryo

Perry, M. (2011) · eScholarship (California Digital Library)

Faculty Opinions recommendation of Assessing constraints on the path of regulatory sequence evolution.

Furlong, E. E. M., & Garfield, D. (2014) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.718173682.793490897

Faculty Opinions recommendation of Enhancer redundancy provides phenotypic robustness in mammalian development.

Skok, J. A. (2018) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.732585246.793545860

In Brief

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

Faculty Opinions recommendation of Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers.

Zaugg, J. B. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.726338707.793567308

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

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Primary and Shadow Enhancers of Dorsal - Ventral Patterning Genes in Drosophila melanogaster

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Epigenetic Control of Cell Fate Decisions by Enhancer-Derived Long Noncoding RNAs

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Conservation and Evolution of Gene Networks Driving Development

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Distinct mechanisms decommission redundant enhancers to facilitate phenotypic evolution

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Evolution of repressive sequences within an enhancer contributed to morphological diversity in crucifer plants

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Additional file 2 of Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns

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Additional file 1 of Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns

Wu, C., & Huang, J. (2024) · Figshare · doi:10.6084/m9.figshare.26721306

Inferring chromatin architecture at a single locus through probabilistic in situ DNA localization

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Evolution of regulation of ascidian species

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Dynamique chromatinienne lors de l'activation des enhancers au cours de la différenciation cellulaire

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Analyse d'interactions Hox/Cofacteur à l'échelle super-résolutive et contrôle transcriptionnel de l'autophagie chez la drosophile

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Study of the role of the gene ovo/svb in the maintenance and the differentiation of intestinal stem cells in Drosophila

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L’hétérochromatine duale H3K9me3/H3K36me3 dépendante de SETDB1 et des NSDs assure l’expression des gènes en maintenant les enhancers inactifs

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Comprehensive mapping of human genetic variation at Epromoters

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Mathematical modeling of gene expression in space and time

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Mitotic reactivation and transcriptional bursting govern transcriptional noise in the early Drosophila embryo

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Regulatory changes underlying the evolution of skylight navigation

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Transcription factor clusters enhance gene expression in vivo without modulating bursting dynamics

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Temporal regulation of a spatial patterning factor in Drosophila neurogenesisPreprint

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Editing cis-regulatory elements to enhance desired traits in plants

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Two distributed enhancers of Sox17 additively regulate the developmental fate of bipotential ventral pancreato-biliary progenitor cells

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Cells are computational entities specialized in statistical learning

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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

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

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