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

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Potential impact of gene regulatory mechanisms on the evolution of multicellularity in the volvocine algae

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Multi-Species Comparative Analysis of the Equine ACE Gene Identifies a Highly Conserved Potential Transcription Factor Binding Site in Intron 16

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The structural properties of DNA regulate gene expression

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Prediction and identification of transcriptional regulatory elements at the lung cancer‑specific DKK1 locus

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Unexpected variability of allelic imbalance estimates from RNA sequencingPreprint

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Genome-wide analysis of cis -regulatory changes in the metabolic adaptation of cavefishPreprint

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A novel enhancer of Agouti contributes to parallel evolution of cryptically colored beach micePreprint

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Functional similarity of non-coding regions is revealed in phylogenetic average motif score representationsPreprint

Alam, A., Duncan, A. G., Mitchell, J. A., & Moses, A. M. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.04.09.536185 · Cited by 5

Predicting gene expression responses to environment in Arabidopsis thaliana using natural variation in DNA sequencePreprint

Takou, M., Bellis, E. S., & Lasky, J. R. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.25.591174 · Cited by 4

Differential Expression Pattern of Brassica juncea MIR160 Paralogs and Homeologs and In Silico Analysis of Brassicaceae Promoters Uncover Evolutionary Distinctness of MIR160a

Singh, S. D., Chattopadhyay, S., Kaur, S., Das, S., & Singh, A. (2025) · Plant Molecular Biology Reporter · doi:10.1007/s11105-025-01526-0 · Cited by 3

Identification of the U-box gene family in peach (Prunus persica) and functional analysis of PpPUB20 in response to salt stress

Zhang, H., Guo, R., Zhang, X., Zhao, C., Wu, J., Xiao, X., Shen, Y., Liu, C., Li, G., Su, K., et al. (2025) · Frontiers in Genetics · doi:10.3389/fgene.2025.1549981 · Cited by 3

Genome-wide identification of zinc finger-homeodomain (ZF-HD) gene family and expression analysis during abiotic stress in rye

Li, Q., Ren, Y., Long, J., Wang, Z., Dou, F., Wang, S., Liu, C., Wang, X., Liu, C., Liu, F., et al. (2025) · Genetic Resources and Crop Evolution · doi:10.1007/s10722-025-02550-5 · Cited by 3

DNA polymerase β suppresses somatic indels at CpG dinucleotides in developing cortical neurons

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Enhancer regulation in cancer: from epigenetics to m6A RNA modification

Vasukutty, A., Bhattarai, P. Y., & Choi, H. S. (2025) · Archives of Pharmacal Research · doi:10.1007/s12272-025-01561-1 · Cited by 5

Genome-wide evolution and function analysis of ALOG gene family in cotton

Liu, Z., Shen, S., Cui, Z., Wang, T., Li, P., Wei, Y., & Peng, R. (2025) · Frontiers in Genetics · doi:10.3389/fgene.2025.1625634 · Cited by 3

Conserved regions upstream of BRC1B regulate bud dormancy in tomato

Hatinoğlu, G., van der Wal, F., Angenent, G. C., de Maagd, R. A., & Immink, R. G. H. (2025) · Frontiers in Plant Science · doi:10.3389/fpls.2025.1702139 · Cited by 4

Genome-wide analysis of the WRKY transcription factor family in Perilla frutescens and the positive role of PfWRKY38, PfWRKY59, and PfWRKY78 in regulating rosmarinic acid biosynthesis

Zhang, X., Wang, P., Zhang, L., Xu, J., Lian, J., Chen, J., Wang, Y., Wei, H., Wang, Y., Yan, Y., et al. (2025) · Industrial Crops and Products · doi:10.1016/j.indcrop.2025.122338 · Cited by 3

A novel CsbZIP26–CsSEP4–CsSPL18 regulatory module governs gynostemium morphology and floral architecture in Cymbidium sinense

Lin, Z., Lu, C., Wang, Y., Wei, Y., Gao, J., Li, J., Xie, Q., Jin, J., Sun, Y., Zhu, W., et al. (2025) · Horticulture Research · doi:10.1093/hr/uhaf329 · Cited by 3

Systematic genomic characterization of β-glucosidase genes in tobacco reveals NtBGLU50 as a multifunctional regulator of glycoside metabolism and defense-associated pathways

Liu, J., Liu, H., Li, Z., Gao, J., Cao, P., Yang, J., & Xie, X. (2026) · Industrial Crops and Products · doi:10.1016/j.indcrop.2026.122643 · Cited by 3

Genomic perplexity and the evolution of context-dependent function

McInerney, J. O. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag041 · Cited by 4

MUTE drives asymmetric divisions to form stomatal subsidiary cells in Crassulaceae succulents

Cheng, X., Lindner, H., Hoffmann, L., Filho, A. A. P. G., Duarte, P. R., Boxall, S. F., Gündoğmuş, Y. B., Pritchard, J. H., Haldenby, S. T., Gemmell, M., et al. (2026) · Science Advances · doi:10.1126/sciadv.aeb8145 · Cited by 3

A digital twin reproducing gene regulatory network dynamics of early Ciona embryos indicates robust buffers in the network

Tokuoka, M., & Satou, Y. (2023) · PLoS Genetics · doi:10.1371/journal.pgen.1010953 · Cited by 4

Genome-wide identification of the walnut MYC gene family and functional characterization of Xinjiang wild walnut under low-temperature stress

Song, Y., Ma, K., Zhao, Y. Q., Han, L.-Q., & Liu, L. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2024.1399721 · Cited by 3

Genome-Wide Analysis of the Histone Modification Gene (HM) Family and Expression Investigation during Anther Development in Rice (Oryza sativa L.)

Huang, Y., Liu, J., Cheng, L., Xu, D., Liu, S., Hu, H., Ling, Y., Yang, R., & Zhang, Y. (2024) · Plants · doi:10.3390/plants13172496 · Cited by 3

Vascular bundle cell-specific expression of a phosphate transporter improves phosphate use efficiency of transgenic Arabidopsis without detrimental effects

Tada, Y., & Shimizu, A. (2024) · Scientific Reports · doi:10.1038/s41598-024-78500-5 · Cited by 3

Genome-wide identification, characterization and expression profiles of FORMIN gene family in cotton (Gossypium Raimondii L.)

Shing, P., Islam, M. S. U., Khatun, M. S., Zohra, F. T., Hasan, N., Rahman, S. M., & Sarkar, M. A. R. (2024) · BMC Genomic Data · doi:10.1186/s12863-024-01285-z · Cited by 3

Integrative Genomics Refines Tissues, Candidate Genes and Putative Regulatory Links Involved in the Humic Adaptation of Keystone Freshwater Fish

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Identification of nuclear factor YA6 genes in sorghum and characterization of their involvement in drought tolerance

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Unravelling the regulatory network underlying divergent expression of the key lipid metabolism transcription factor SREBP in two congeneric oyster species

Du, M., Bu, T., Wang, C., Chen, J., Jiang, Z., Wang, M., Pang, M., Cong, R., Wang, W., Zhang, G., et al. (2025) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.145808 · Cited by 3

Pattern recognition in living cells through the lens of machine learning

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Integrated genomic analysis and CRISPRi implicates EGFR in Alzheimer’s disease risk

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Differences in LEA-like 11-24 gene expression in desiccation tolerant and sensitive species of Linderniaceae are due to variations in gene promoter sequences

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In silico identification of transcription factors associated with the biosynthesis of carotenoids in corn (Zea mays L.)

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Overexpressed somatic alleles are enriched in functional elements in Breast Cancer

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Integration of Multi-omics Data for Expression Quantitative Trait Loci (eQTL) Analysis and eQTL Epistasis

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Functional Identification of EjGIF1 in Arabidopsis and Preliminary Analysis of Its Regulatory Mechanisms in the Formation of Triploid Loquat Leaf Heterosis

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Optimized barley phytase gene expression by focused FIND-IT screening for mutations in cis-acting regulatory elements

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Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches in Anolis lizards

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How to scan naked DNA using promiscuous recognition and no clamping: a model for pioneer transcription factors

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Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita

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Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat

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Effective Quality Breeding Directions—Comparison and Conservative Analysis of Hepatic Super-Enhancers between Chinese and Western Pig Breeds

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Of mice and men

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Molecular Mechanisms of Larval Color Pattern Switch in the Swallowtail Butterfly

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Modulation of Gene Expression by Gene Architecture and Promoter Structure

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Allele-specific expression elucidates cis-regulatory logic

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Borders of Cis-Regulatory DNA Sequences Preferentially Harbor the Divergent Transcription Factor Binding Motifs in the Human Genome

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Analysis of γ-Tocopherol methyl transferase3 promoter activity and study of methylation patterns of the promoter and its gene body

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Regulatory DNA in A . thaliana can tolerate high levels of sequence divergencePreprint

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Cis acting variation is common, can propagates across multiple regulatory layers, but is often buffered in developmental programsPreprint

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Bioinformatic analysis based genome-wide identification, characterization, diversification and regulatory transcription components of RNA silencing machinery genes in wheat ( Triticum aestivum L.)Preprint

Akond, Z., Rahman, H., Ahsan, M. A., Mosharaf, M. P., Alam, M., & Mollah, M. N. H. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.21.108100 · Cited by 3

Multi-locus interactions and the build-up of reproductive isolationPreprint

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Function and constraint in enhancers with multiple evolutionary originsPreprint

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The Promise of eQTL Studies in Dissecting Crop Genetic Basis and Evolution

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Genome-wide identification and characterization of major RNAi genes highlighting their regulatory factors in Cowpea ( Vigna unguiculata (L.) Walp.)Preprint

Hasan, M. N., Mosharaf, M. P., Uddin, K. S., Das, K. R., Sultana, N., Noorunnahar, M., Naim, D., & Mollah, M. N. H. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.02.15.528631 · Cited by 3

Evolved and plastic gene expression in adaptation to a novel nichePreprint

Steward, R., Ortega, J., Choudhary, S., Su, Y., Aken, O. V., & Runemark, A. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.02.583104 · Cited by 3

Adaptive cellular evolution in the intestinal tracts of hyperdiverse African cichlid fishesPreprint

Fages, A., Luxey, M., Ronco, F., Huyghe, C. E. T., Menon, P. N. K., Indermaur, A., Salzburger, W., & Tschopp, P. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.28.625862 · Cited by 3

DeepReGraph co-clusters temporal gene expression and cis-regulatory elements through heterogeneous graph representation learning

Moreno, J. F. C., Zarrineh, P., Sánchez‐Rodríguez, A., & Mecella, M. (2022) · F1000Research · doi:10.12688/f1000research.114698.1 · Cited by 2

A combination of transcriptomics and epigenomics identifies genes and regulatory elements involved in embryonic tail development in the mouse

Chen, Y.-X., Zhang, X., Cooper, D. N., Wu, D., & Bao, W.-D. (2025) · BMC Biology · doi:10.1186/s12915-025-02192-0 · Cited by 2

Editing multiple genes in Physalis pubescens provides valuable lessons and implications for creating new germplasm and varieties of Physalis crops

Liu, Q., Wu, L., Liu, P., & He, C. (2025) · Plant and Cell Physiology · doi:10.1093/pcp/pcaf036 · Cited by 2

Divergent Cardiovascular Adaptations and Gene Regulation in High-Elevation Natives and Recent Colonizers of the Qinghai-Tibetan Plateau

She, H., Scott, G. R., Fang, Y., Zhao, Q., Meng, F., & Qu, Y. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf103 · Cited by 2

Characterization of the WD40 gene family in Pyrus bretschneideri and functional analysis of PbrWD40–60 in pollen tube growth

Li, M., Yan, Y., Zhou, J., Dai, Y., Wu, J., Zhang, S., & Kou, X. (2025) · Scientia Horticulturae · doi:10.1016/j.scienta.2025.114183 · Cited by 2

Gene network topology drives the mutational landscape of gene expression

Pouzet, S., & Rouzic, A. L. (2025) · Evolution · doi:10.1093/evolut/qpaf068 · Cited by 3

Disentangling cell-intrinsic and cell-extrinsic factors underlying evolution

Starr, A. L., Nishimura, T., Igarashi, K. J., Funamoto, C., Nakauchi, H., & Fraser, H. B. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.100891 · Cited by 3

ZxSAUR15 regulates root growth and abiotic stress tolerance: from genome-wide characterization of SAUR genes in Zygophyllum xanthoxylum to functional validation

Liu, C., Li, M., Yang, Y., Chai, R., Li, W., & Yin, H. (2025) · Plant and Soil · doi:10.1007/s11104-025-07718-7 · Cited by 2

Genome-Wide Characterization of SNAC Gene Family in Ten Cotton Species and Function Analysis of GhSNAC3D Under Cold Stress

Fan, J., Meng, L., Zhu, F., Niu, J., Zhang, G., Wang, J., Li, Z., Wang, F., & Li, H. (2025) · Plants · doi:10.3390/plants14182894 · Cited by 2

Dissecting the genomic landscape of ERD genes in alfalfa (Medicago sativa): the effect of melatonin and low selenium under salt stress

Qadir, M., Nabi, F., Shi, J., Ahmed, Z. F. R., & Sabir, I. A. (2025) · Functional & Integrative Genomics · doi:10.1007/s10142-025-01703-0 · Cited by 2

Predicting Gene Expression Responses to Cold in Arabidopsis thaliana Using Natural Variation in DNA Sequence

Takou, M., Bellis, E. S., & Lasky, J. R. (2025) · Genes · doi:10.3390/genes16091108 · Cited by 2

Rapid promoter evolution of male accessory gland genes is accompanied by divergent expression in closely related Drosophila species

McQuarrie, D. W. J., Stephens, F. H. S., Ferguson, A. D., Arnold, R. R., Civetta, A., & Soller, M. (2025) · Genetics · doi:10.1093/genetics/iyaf226 · Cited by 2

A deep learning model leveraging semantic features fusion for DNase I hypersensitive sites identification in the human genome

Alarfaj, F. K., Tahir, M., & Srivastava, G. (2025) · Computer Methods and Programs in Biomedicine · doi:10.1016/j.cmpb.2025.109127 · Cited by 2

Genome-Wide Identification of the Litchi BBX Gene Family and Analysis of Its Potential Role in Pericarp Coloring

Liu, T., Chen, Y., Song, W., Zhang, H., & Wei, Y. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms262210834 · Cited by 2

Genome-Wide Identification and Expression Profiling of MYC Transcription Factor Family in Toona sinensis Under Abiotic and Hormonal Stresses

Zhou, G., Zeng, S., Cui, X., Liao, Y., Zhang, W., Xu, F., & Jiang, D. (2025) · Forests · doi:10.3390/f16121756 · Cited by 2

Pan-cancer epigenetic landscape of human tumor-associated macrophages reveals crucial enhancers governing their heterogenous formation by Pol II pausing modulation

Xiong, C., Ning, H., Wang, X., Xie, Y., Liu, Z., Hu, D., & Gao, X. (2026) · Journal of Advanced Research · doi:10.1016/j.jare.2026.01.048 · Cited by 2

Prenatal and postnatal effects of gestational immune activation on synaptic and neurodevelopmental pathways via epigenetic mechanisms

Zhu, B., Li, G., Saunders, J. M., Naler, L. B., Hadlock, T. M., Wang, C., García‐Sastre, A., González‐Maeso, J., & Lu, C. (2026) · Translational Psychiatry · doi:10.1038/s41398-026-03884-z · Cited by 4

Chromatin accessibility landscapes define stromal cell identities across tissues

Nooranikhojasteh, A., Tavallaee, G., Khuu, N., Shen, S. Y., Ouladan, S., Raman, A., & Orouji, E. (2026) · Communications Biology · doi:10.1038/s42003-026-09720-w · Cited by 2

Transposable element-driven expansion of enhancer RNA repertoires underlies regulatory innovation and polyploid adaptation in cereal crops

Liu, J., Li, Z., Zhao, S., Li, H., Zhang, B., Liu, C., Zhang, W., Mao, H., Huang, L., Dong, Z., et al. (2026) · Plant Communications · doi:10.1016/j.xplc.2026.101887 · Cited by 2

Computational Design of DNA-Binding Proteins

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Genome Editing Technologies for Plant Improvement: Advances, Applications and Challenges

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Gnocis: An integrated system for interactive and reproducible analysis and modelling of cis-regulatory elements in Python 3

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In silico analysis of steviol glycoside biosynthesis related genes of Helianthus annuus shows its potential for sweetener production

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EIN3/EIL (Ethylene Insensitive3 / Ethylene Insensitive3 Like) Protein Family in Phaseolus vulgaris: Identification, Evolution and Expression Analysis within the Genome

Akbulut, S. E., Şafak, Z., Okay, A., Amirina, K., & Büyük, İ. (2023) · Turkish Journal of Agriculture - Food Science and Technology · doi:10.24925/turjaf.v11i2.215-226.5172 · Cited by 2

Intraspecific Comparative Analysis Reveals Genomic Variation of Didymella arachidicola and Pathogenicity Factors Potentially Related to Lesion Phenotype

Li, S., Wang, Z., Gao, M., Li, T., Cui, X., Zu, J., Sang, S., Fan, W., & Zhang, H. (2023) · Biology · doi:10.3390/biology12030476 · Cited by 2

Interdisciplinary approaches to predicting evolutionary biology

Crocker, J., Payne, J. L., Walczak, A. M., & Wittkopp, P. J. (2023) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2022.0042 · Cited by 2

Evolution of a new form of haploid-specific gene regulation appearing in a limited clade of ascomycete yeast species

Frate, F. D., Garber, M. E., & Johnson, A. D. (2023) · Genetics · doi:10.1093/genetics/iyad053 · Cited by 2

Naturally Occurring Disruptive Genetic Variants Affect Expression of Populus trichocarpa Secondary Cell Wall Deposition Genes and Associated Wood Traits

Piot, A., El-Kassaby, Y. A., & Porth, I. M. (2024) · Compendium of plant genomes · doi:10.1007/978-3-031-50787-8_7 · Cited by 2

regLM: Designing Realistic Regulatory DNA with Autoregressive Language Models

Lal, A., Garfield, D., Biancalani, T., & Eraslan, G. (2024) · Lecture notes in computer science · doi:10.1007/978-1-0716-3989-4_24 · Cited by 2

Genome-wide identification and characterization of DTX family genes highlighting their locations, functions, and regulatory factors in banana (Musa acuminata)

Amin, A., Naim, M. D., Islam, M. N., & Mollah, M. N. H. (2024) · PLoS ONE · doi:10.1371/journal.pone.0303065 · Cited by 2

Genome-Wide Analysis of the PERK Gene Family in Brassica napus L. and Their Potential Roles in Clubroot Disease

Zhang, Z., Fu, T., Zhou, C., Liu, F., Zeng, L., Ren, L., Tong, C., Liú, L., & Li, X. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26062685 · Cited by 2

Gene-by-environment Interactions and Adaptive Body Size Variation in Mice From the Americas

Mack, K. L., Landino, N. P., Tertyshnaia, M., Longo, T. C., Vera, S. A., Crew, L., McDonald, K., & Phifer‐Rixey, M. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf078 · Cited by 2

Identification of superior haplotype and haplotype combinations for UV-B stress-related genes in Rice (Oryza sativa L.)

Zeng, Y., Lee, D., Kim, B., & Kwon, S.-W. (2025) · Plant Biotechnology Reports · doi:10.1007/s11816-025-00963-3 · Cited by 2

Fitness landscapes of simple regulatory genetic interactions show pervasive heterozygote advantage and support stable polymorphism

Porter, A. H., Johnson, N., & Tulchinsky, A. Y. (2025) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2025.112233 · Cited by 2

Genome-Wide Identification and Characterization of BPC Transcription Factors in Tobacco (Nicotiana tabacum)

Zhang, Y., Jia, S., Wang, S., Ji, X., & Liu, Z. (2025) · Agronomy · doi:10.3390/agronomy15092084 · Cited by 2

SVCROWS: a user-defined tool for interpreting significant structural variants in heterogeneous datasets

Brown, N., Danis, C., Ahmedjanova, V., & Güler, J. L. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1440 · Cited by 2

Fast and Efficient Cloning of Cis-Regulatory Sequences for High-Throughput Yeast One-Hybrid Analyses of Transcription Factors

Kelemen, Z., Przybyla‐Toscano, J., Tissot, N., Lepiniec, L., & Dubos, C. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6396-6_9 · Cited by 2

eQTL Mapping Study via Regularized Sparse Canonical Correlation Analysis

Kang, M., Li, S., Kim, D., Liu, C., Zhang, B., Wu, X., & Gao, J. (2013) · International Conference on Machine Learning and Applications · doi:10.1109/icmla.2013.29 · Cited by 2

Regulation of mRNA expression in breast cancer - a cis-tematic trans-action

Verhaak, R. G. W., & Mills, G. B. (2012) · Breast Cancer Research · doi:10.1186/bcr3227 · Cited by 2

The Zebrafish as Model for Deciphering the Regulatory Architecture of Vertebrate Genomes

Rastegar, S., & Strähle, U. (2016) · Advances in genetics · doi:10.1016/bs.adgen.2016.04.003 · Cited by 2

Systematic Discovery of Chromatin-Bound Protein Complexes from ChIP-seq Datasets

Γιαννοπούλου, Ε., & Elemento, O. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6518-2_4 · Cited by 2

Association analysis of rice grain traits with single nucleotide polymorphisms in a Brassinosteroid-insensitive 1 (BRI1)-associated receptor kinase 1-like gene

Teh, C.-Y., Kasim, N. A. M., Rafii, M. Y., Namasivayam, P., Hanafi, M. M., & Ho, C. (2019) · Plant Gene · doi:10.1016/j.plgene.2019.100188 · Cited by 2

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

Methods to Detect and Associate Divergence in Cis-Regulatory Elements to Phenotypic Divergence

Roscito, J. G., & Hiller, M. (2019) · Springer eBooks · doi:10.1007/978-3-030-30363-1_6 · Cited by 2

Transforming our understanding of species-specific gene regulation

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www.nature.com/hdy Evolution of cis-regulatory sequence and function

Diptera, I. (2013)

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