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

Evolutionary divergence and convergence in proteins.

ZUCKERKANDL, E., & PAULING, L. (1965) · Evolving Genes and Proteins · doi:10.1016/b978-1-4832-2734-4.50017-6 · Cited by 3,020

Evolution at Two Levels in Humans and Chimpanzees: Their macromolecules are so alike that regulatory mutations may account for their biological differences

King, M.-C., & Wilson, A. C. (1975) · Science · doi:10.1126/science.1090005 · Cited by 2,815

Gene Regulation for Higher Cells: A Theory

Britten, R. J., & Davidson, E. H. (1969) · Science · doi:10.1126/science.165.3891.349 · Cited by 2,078

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

Carroll, S. B. (2008) · Cell · doi:10.1016/j.cell.2008.06.030 · Cited by 2,067

TRANSFAC(R): transcriptional regulation, from patterns to profiles

Matys, V. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg108 · Cited by 1,985

The UCSC Genome Browser database: update 2011

Fujita, P. A., Rhead, B., Zweig, A. S., Hinrichs, A. S., Karolchik, D., Cline, M., Goldman, M. J., Barber, G. P., Clawson, H., Coelho, A., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq963 · Cited by 1,843

Effective population size and patterns of molecular evolution and variation

Charlesworth, B. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2526 · Cited by 1,743

ChIP-seq accurately predicts tissue-specific activity of enhancers

Visel, A., Blow, M. J., Li, Z., Zhang, T., Akiyama, J. A., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., Chen, F., et al. (2009) · Nature · doi:10.1038/nature07730 · Cited by 1,639

The evolutionary significance of cis-regulatory mutations

Wray, G. A. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2063 · Cited by 1,521

Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles.

Colosimo, P. F., Hosemann, K. E., Balabhadra, S., Villarreal, G., Dickson, M., Grimwood, J., Schmutz, J., Myers, R. M., Schluter, D., & Kingsley, D. M. (2005) · Science · doi:10.1126/science.1107239 · Cited by 1,448

Adaptive evolution and functional innovation of Populus‐specific recently evolved micro RNA s

Xie, J., Yang, X., Song, Y., Du, Q., Li, Y., Chen, J., & Zhang, D. (2016) · New Phytologist · doi:10.1111/nph.14046 · Cited by 46

Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes

Ringel, A. R., Szabo, Q., Chiariello, A. M., Chudzik, K., Schöpflin, R., Rothe, P., Mattei, A. L., Zehnder, T., Harnett, D., Laupert, V., et al. (2022) · Cell · doi:10.1016/j.cell.2022.09.006 · Cited by 50

Architecture design of cucurbit crops for enhanced productivity by a natural allele

Wang, S., Wang, K., Li, Z., Li, Y., He, J., Li, H., Wang, B., Xin, T., Tian, H., Tian, J., et al. (2022) · Nature Plants · doi:10.1038/s41477-022-01297-6 · Cited by 46

Hybrid Incompatibility Arises in a Sequence-Based Bioenergetic Model of Transcription Factor Binding

Tulchinsky, A. Y., Johnson, N., Watt, W. B., & Porter, A. (2014) · Genetics · doi:10.1534/genetics.114.168112 · Cited by 44

High-throughput evaluation of T7 promoter variants using biased randomization and DNA barcoding

Komura, R., Aoki, W., Motone, K., Satomura, A., & Ueda, M. (2018) · PLoS ONE · doi:10.1371/journal.pone.0196905 · Cited by 47

Hominin-specific regulatory elements selectively emerged in oligodendrocytes and are disrupted in autism patients

Castelijns, B., Baak, M. L., Timpanaro, I. S., Wiggers, C. R. M., Vermunt, M. W., Shang, P., Kondova, I. I., Geeven, G., Bianchi, V., de Laat, W. L., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-14269-w · Cited by 46

Cis - and Trans -variations of Stearoyl-CoA Desaturase Provide New Insights into the Mechanisms of Diverged Pattern of Phenotypic Plasticity for Temperature Adaptation in Two Congeneric Oyster Species

Wang, C., Li, A., Cong, R., Qi, H., Wang, W., Zhang, G., & Li, L. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad015 · Cited by 42

Gain of An Auto-regulatory Site Led to Divergence of the Arabidopsis APETALA1 and CAULIFLOWER Duplicate Genes in the Time, Space and Level of Expression and Regulation of One Paralog by the Other

Ye, L., Wang, B., Zhang, W., Shan, H., & Kong, H. (2016) · PLANT PHYSIOLOGY · doi:10.1104/pp.16.00320 · Cited by 49

SHH signaling directed by two oral epithelium-specific enhancers controls tooth and oral development

Sagai, T., Amano, T., Maeno, A., Kiyonari, H., Seo, H.-J., Cho, S. W., & Shiroishi, T. (2017) · Scientific Reports · doi:10.1038/s41598-017-12532-y · Cited by 44

Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana

Alexandre, C. M., Urton, J. R., Jean-Baptiste, K., Huddleston, J., Dorrity, M. W., Cuperus, J. T., Sullivan, A. M., Bemm, F., Jolić, D., Arsovski, A. A., et al. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx326 · Cited by 44

LncRNA‐MAP3K4 regulates vascular inflammation through the p38 MAPK signaling pathway and cis ‐modulation of MAP3K4

Zhou, H., Simion, V., Pierce, J. B., Haemmig, S., Chen, A. F., & Feinberg, M. W. (2020) · The FASEB Journal · doi:10.1096/fj.202001654rr · Cited by 44

A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut

Lourenço, M., Ramiro, R. S., Güleresi, D., Barroso-Batista, J., Xavier, K. B., Gordo, I., & Sousa, A. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006420 · Cited by 44

DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories

Lutz, S., Brion, C., Kliebhan, M., & Albert, F. W. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008375 · Cited by 46

Genome-Wide Characterization of DNase I-Hypersensitive Sites and Cold Response Regulatory Landscapes in Grasses

Han, J., Wang, P., Wang, Q., Lin, Q., Chen, Z., Yu, G., Miao, C., Dao, Y., Wu, R., Schnable, J. C., et al. (2020) · The Plant Cell · doi:10.1105/tpc.19.00716 · Cited by 41

The chromatin landscape of Drosophila: comparisons between species, sexes, and chromosomesPreprint

Brown, E. J., & Bachtrog, D. (2014) · Genome Research · doi:10.1101/gr.172155.114 · Cited by 43

Learning the Regulatory Code of Gene Expression

Zrimec, J., Buric, F., Kokina, M., García, V., & Zelezniak, A. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.673363 · Cited by 45

Advances in AAV technology for delivering genetically encoded cargo to the nonhuman primate nervous system

Campos, L., Arokiaraj, C. M., Chuapoco, M. R., Chen, X., Goeden, N., Gradinaru, V., & Fox, A. S. (2023) · Current Research in Neurobiology · doi:10.1016/j.crneur.2023.100086 · Cited by 42

Evolution of gene network activity by tuning the strength of negative-feedback regulation

Peng, W., Liu, P., Xue, Y., & Açar, M. (2015) · Nature Communications · doi:10.1038/ncomms7226 · Cited by 41

Principles and methods of in-silico prioritization of non-coding regulatory variants

Lee, P. H., Lee, C. R., Li, X., Wee, B., Dwivedi, T., & Daly, M. J. (2017) · Human Genetics · doi:10.1007/s00439-017-1861-0 · Cited by 46

Hierarchical and Dynamic Regulation of Defense-Responsive Specialized Metabolism by WRKY and MYB Transcription Factors

Barco, B., & Clay, N. K. (2020) · Frontiers in Plant Science · doi:10.3389/fpls.2019.01775 · Cited by 43

A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish

Jimenez, E., Slevin, C. C., Song, W., Chen, Z., Frederickson, S. C., Gildea, D. E., Wu, W., ELKAHLOUN, A. G., Ovcharenko, I., & Burgess, S. M. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100170 · Cited by 44

Evolutionary Dynamics of Floral Homeotic Transcription Factor Protein–Protein Interactions

Bartlett, M. E., Thompson, B. E., Brabazon, H., Gizzi, R. D., Zhang, T., & Whipple, C. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw031 · Cited by 41

RepeatFiller newly identifies megabases of aligning repetitive sequences and improves annotations of conserved non-exonic elements

Osipova, E., Hecker, N., & Hiller, M. (2019) · GigaScience · doi:10.1093/gigascience/giz132 · Cited by 40

Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family in Medicago truncatula Under a Broad Range of Heavy Metal Stress

El‐Sappah, A. H., Elbaiomy, R. G., Elrys, A. S., Wang, Y., Zhu, Y., Huang, Q., Yan, K., Xianming, Z., Abbas, M., El-Tarabily, K. A., et al. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.713224 · Cited by 41

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

Genetic variation and expression diversity between grain and sweet sorghum lines

Jiang, S., Ma, Z., Vanitha, J., & Ramachandran, S. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-18 · Cited by 40

Development and evolution of character displacement

Pfennig, D. W., & Pfennig, K. S. (2012) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.2011.06381.x · Cited by 42

Allele-specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato.

Albert, E., Duboscq, R., Latreille, M., Santoni, S., Beukers, M., Bouchet, J., Bitton, F., Gricourt, J., Poncet, C., Gautier, V., et al. (2018) · The Plant Journal · doi:10.1111/tpj.14057 · Cited by 32

Embryo polarity in moth flies and mosquitoes relies on distinct old genes with localized transcript isoforms

Yoon, Y., Klomp, J. A., Martín-Martín, I., Criscione, F., Calvo, E., Ribeiro, J. M. C., & Schmidt‐Ott, U. (2019) · eLife · doi:10.7554/elife.46711 · Cited by 37

piEnPred: a bi-layered discriminative model for enhancers and their subtypes via novel cascade multi-level subset feature selection algorithm

Khan, Z. U., Pi, D., Yao, S., Nawaz, A., Ali, F., & Ali, S. (2021) · Frontiers of Computer Science · doi:10.1007/s11704-020-9504-3 · Cited by 40

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

Modern biology of extrachromosomal DNA: A decade-long voyage of discovery

Yang, Q., Xie, Y., Qiao, K., Lim, J. Y. S., & Wu, S. (2025) · Cell Research · doi:10.1038/s41422-024-01054-8 · Cited by 41

Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris)

Kryvokhyzha, D., Milesi, P., Duan, T., Orsucci, M., Wright, S., Glémin, S., & Lascoux, M. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008131 · Cited by 37

Genomic identification and characterization of MYC family genes in wheat (Triticum aestivum L.)

Bai, J., Wang, Y., Guo, L., Guo, X., Guo, H., Yuan, S., Duan, W., Liu, Z., Zhao, C., Zhang, F., et al. (2019) · BMC Genomics · doi:10.1186/s12864-019-6373-y · Cited by 39

Hybrid male sterility and genome-wide misexpression of male reproductive proteases

Gomes, S., & Civetta, A. (2015) · Scientific Reports · doi:10.1038/srep11976 · Cited by 39

Pleiotropy constrains the evolution of protein but not regulatory sequences in a transcription regulatory network influencing complex social behaviors

Molodtsova, D., Harpur, B. A., Kent, C. F., Seevananthan, K., & Zayed, A. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00431 · Cited by 38

Genetic architecture of retinal and macular degenerative diseases: the promise and challenges of next-generation sequencing

Ratnapriya, R., & Swaroop, A. (2013) · Genome Medicine · doi:10.1186/gm488 · Cited by 38

A Phylogenetic Study of the ANT Family Points to a preANT Gene as the Ancestor of Basal and euANT Transcription Factors in Land Plants

Dipp-Álvarez, M., & Cruz‐Ramírez, A. (2019) · Frontiers in Plant Science · doi:10.3389/fpls.2019.00017 · Cited by 38

Environmentally robust cis -regulatory changes underlie rapid climatic adaptation

Ballinger, M. A., Mack, K. L., Durkin, S. M., Riddell, E. A., & Nachman, M. W. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2214614120 · Cited by 38

Modulation in gene expression and enzyme activity suggested the roles of monodehydroascorbate reductase in development and stress response in bread wheat

Madhu, M., Sharma, A., Kaur, A., Singh, K., & Upadhyay, S. K. (2023) · Plant Science · doi:10.1016/j.plantsci.2023.111902 · Cited by 37

Evolutionary dynamics of metazoan TRP channels

Kadowaki, T. (2015) · Pflügers Archiv - European Journal of Physiology · doi:10.1007/s00424-015-1705-5 · Cited by 37

A Genome-Wide Identification of the WRKY Family Genes and a Survey of Potential WRKY Target Genes in Dendrobium officinale

He, C., da Silva, J. A. T., Tan, J., Zhang, J., Pan, X., Li, M., Luo, J., & Duan, J. (2017) · Scientific Reports · doi:10.1038/s41598-017-07872-8 · Cited by 37

Functional characterization of adaptive variation within a cis-regulatory element influencing Drosophila melanogaster growth

Glaser‐Schmitt, A., & Parsch, J. (2018) · PLoS Biology · doi:10.1371/journal.pbio.2004538 · Cited by 38

Adaptive Mutations in RNA Polymerase and the Transcriptional Terminator Rho Have Similar Effects on Escherichia coli Gene Expression

González‐González, A., Hug, S. M., Rodríguez‐Verdugo, A., Patel, J. S., & Gaut, B. S. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx216 · Cited by 39

New Horizons for Dissecting Epistasis in Crop Quantitative Trait Variation

Soyk, S., Benoit, M., & Lippman, Z. B. (2020) · Annual Review of Genetics · doi:10.1146/annurev-genet-050720-122916 · Cited by 37

Genome-wide identification of DCL, AGO and RDR gene families and their associated functional regulatory elements analyses in banana (Musa acuminata)

Ahmed, F. F., Hossen, M. I., Sarkar, M. A. R., Konak, J. N., Zohra, F. T., Shoyeb, M., & Mondal, S. (2021) · PLoS ONE · doi:10.1371/journal.pone.0256873 · Cited by 37

Hemophilia B Leyden and once mysterious cis-regulatory mutations

Funnell, A. P. W., & Crossley, M. (2013) · Trends in Genetics · doi:10.1016/j.tig.2013.09.007 · Cited by 40

Noncoding regions underpin avian bill shape diversification at macroevolutionary scalesPreprint

Yusuf, L. H., Heatley, M. C., Palmer, J., Barton, H. J., Cooney, C. R., & Gossmann, T. I. (2020) · Genome Research · doi:10.1101/gr.255752.119 · Cited by 39

Natural variation in a K+‐preferring HKT transporter contributes to wheat shoot K+ accumulation and salt tolerance

Du, L., Ding, L., Huang, X., Tang, D., Chen, B., Tian, H., Kang, Z., & Mao, H. (2023) · Plant Cell & Environment · doi:10.1111/pce.14746 · Cited by 36

Identification and expression analysis of ATP-binding cassette (ABC) transporters revealed its role in regulating stress response in pear (Pyrus bretchneideri)

Kou, X., Zhao, Z., Xu, X., Li, C., Wu, J., & Zhang, S. (2024) · BMC Genomics · doi:10.1186/s12864-024-10063-1 · Cited by 37

Transcriptional regulation of early T‐cell development in the thymus

Seo, W., & Taniuchi, I. (2016) · European Journal of Immunology · doi:10.1002/eji.201545821 · Cited by 42

Expression of a carotenoid‐modifying gene and evolution of red coloration in weaverbirds (Ploceidae)

Twyman, H., Prager, M., Mundy, N. I., & Andersson, S. (2017) · Molecular Ecology · doi:10.1111/mec.14451 · Cited by 36

Application of CRISPR/Cas to Understand Cis- and Trans-Regulatory Elements in Plants

Wolter, F., & Puchta, H. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8657-6_2 · Cited by 35

Lessons from natural variations: artificially induced heading date variations for improvement of regional adaptation in rice

Hu, Y., Li, S., & Xing, Y. (2018) · Theoretical and Applied Genetics · doi:10.1007/s00122-018-3225-0 · Cited by 36

Polygenic selection drives the evolution of convergent transcriptomic landscapes across continents within a Nearctic sister species complex

Rougeux, C., Gagnaire, P., Præbel, K., D, O. S. C., & Bernatchez, L. (2019) · Molecular Ecology · doi:10.1111/mec.15226 · Cited by 35

iDHS-Deep: an integrated tool for predicting DNase I hypersensitive sites by deep neural network

Dao, F., Lv, H., Su, W., Sun, Z., Huang, Q.-L., & Lin, H. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab047 · Cited by 37

Co-option during the evolution of multicellular and developmental complexity in the volvocine green algae

Olson, B. J. S. C., & Nedelcu, A. M. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.06.003 · Cited by 38

Evolutionary potential of transcription factors for gene regulatory rewiring

Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., & Guet, C. C. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0651-y · Cited by 35

Dominance and Sexual Dimorphism Pervade the Salix purpurea L. Transcriptome

Carlson, C. H., Choi, Y., Chan, A. P.-Y., Serapiglia, M. J., Town, C. D., & Smart, L. B. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx174 · Cited by 35

Functional divergence of paralogous transcription factors supported the evolution of biomineralization in echinoderms

Khor, J. M., & Ettensohn, C. A. (2017) · eLife · doi:10.7554/elife.32728 · Cited by 33

Transcriptional and epigenetic adaptation of maize chromosomes in Oat-Maize addition lines

Dong, Z., Yu, J., Li, H., Huang, W., Xu, L., Zhao, Y., Zhang, T., Xu, W., Jiang, J., Su, Z., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky209 · Cited by 35

Structural, Functional, and Evolutionary Characterization of Major Drought Transcription Factors Families in Maize

Mittal, S., Pooja, B., Mallikarjuna, M. G., Rao, A. R., Jain, P. A., Dash, P. K., & Thirunavukkarasu, N. (2018) · Frontiers in Chemistry · doi:10.3389/fchem.2018.00177 · Cited by 35

Predominant contribution of cis‐regulatory divergence in the evolution of mouse alternative splicing

Gao, Q., Sun, W., Ballegeer, M., Libert, C., & Chen, W. (2015) · Molecular Systems Biology · doi:10.15252/msb.20145970 · Cited by 34

Genetic variation in regulatory DNA elements: the case of OCA 2 transcriptional regulation

Visser, M., Kayser, M., Grosveld, F. G., & Palstra, R.-J. T. S. (2014) · Pigment Cell & Melanoma Research · doi:10.1111/pcmr.12210 · Cited by 35

Direct activation of a mouse Hoxd11 axial expression enhancer by Gdf11/Smad signalling

Gaunt, S. J., George, M., & Paul, Y. (2013) · Developmental Biology · doi:10.1016/j.ydbio.2013.08.025 · Cited by 35

From tradition to innovation: conventional and deep learning frameworks in genome annotation

Chen, Z., Ain, N. U., Zhao, Q., & Zhang, X. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae138 · Cited by 37

Regulatory Divergence in Wound-Responsive Gene Expression between Domesticated and Wild Tomato

Liu, M., Sugimoto, K., Uygun, S., Panchy, N. L., Campbell, M. S., Yandell, M. D., Howe, G. A., & Shiu, S. (2018) · The Plant Cell · doi:10.1105/tpc.18.00194 · Cited by 34

Blue, Black, and Stripes: Evolution and Development of Color Production and Pattern Formation in Lizards and Snakes

Kuriyama, T., Murakami, A., Brandley, M., & Hasegawa, M. (2020) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2020.00232 · Cited by 34

Organ Evolution in Angiosperms Driven by Correlated Divergences of Gene Sequences and Expression Patterns

Yang, R., & Wang, X. (2013) · The Plant Cell · doi:10.1105/tpc.112.106716 · Cited by 32

Experimental evidence for cancer resistance in a bat species

Hua, R., Ma, Y.-S., Yang, L., Hao, J., Hua, Q., Shi, L., Yao, X., Zhi, H.-Y., & Liu, Z. (2024) · Nature Communications · doi:10.1038/s41467-024-45767-1 · Cited by 33

Understanding the Role of the WRKY Gene Family under Stress Conditions in Pigeonpea (Cajanus Cajan L.)

Singh, A. K., Singh, P. K., Sharma, A., Singh, N. K., Sonah, H., Deshmukh, R. K., & Sharma, T. R. (2019) · Plants · doi:10.3390/plants8070214 · Cited by 33

Basic Helix-Loop-Helix (bHLH) transcription factor family in Yellow horn (Xanthoceras sorbifolia Bunge): Genome-wide characterization, chromosome location, phylogeny, structures and expression patterns

Lang, Y., & Liu, Z. (2020) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2020.05.253 · Cited by 33

Epistasis between promoter activity and coding mutations shapes gene evolvability

Cisneros, A. F., Gagnon-Arsenault, I., Dubé, A. K., Després, P. C., Kumar, P., Lafontaine, K., Pelletier, J. N., & Landry, C. R. (2023) · Science Advances · doi:10.1126/sciadv.add9109 · Cited by 33

The Phenome-Wide Distribution of Genetic Variance

Blows, M. W., Allen, S. L., Collet, J. M., Chenoweth, S. F., & McGuigan, K. (2015) · The American Naturalist · doi:10.1086/681645 · Cited by 33

Evolutionary changes in transcription factor coding sequence quantitatively alter sensory organ development and function

Weinberger, S., Topping, M. P., Yan, J., Claeys, A., Geest, N. D., Özbay, D., Hassan, T., He, X., Albert, J. T., Hassan, B. A., et al. (2017) · eLife · doi:10.7554/elife.26402 · Cited by 32

Emerging RUNX2-Mediated Gene Regulatory Mechanisms Consisting of Multi-Layered Regulatory Networks in Skeletal Development

Hojo, H. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24032979 · Cited by 33

Epigenomic insights into common human disease pathology

Bell, C. G. (2024) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-024-05206-2 · Cited by 36

Rice Promoter Editing: An Efficient Genetic Improvement Strategy

Wu, B., Luo, H., Chen, Z., Amin, B., Yang, M., Li, Z., Wu, S., Salmen, S. H., Alharbi, S. A., & Fang, Z. (2024) · Rice · doi:10.1186/s12284-024-00735-7 · Cited by 32

Modular Evolution of DNA-Binding Preference of a Tbrain Transcription Factor Provides a Mechanism for Modifying Gene Regulatory Networks

Jarvela, A. M. C., Brubaker, L., Vedenko, A., Gupta, A., Armitage, B. A., Bulyk, M. L., & Hinman, V. F. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu213 · Cited by 32

Adaptor proteins in long noncoding RNA biology

Dangelmaier, E. A., & Lal, A. (2019) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2019.03.003 · Cited by 32

Transcription Factors AhR/ARNT Regulate the Expression of CYP6CY3 and CYP6CY4 Switch Conferring Nicotine Adaptation

Pan, Y., Peng, T., Xu, P., Zeng, X., Tian, F., Song, J., & Shang, Q. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20184521 · Cited by 31

CRUP: a comprehensive framework to predict condition-specific regulatory units

Ramisch, A., Heinrich, V., Glaser, L. V., Fuchs, A., Yang, X., Benner, P., Schöpflin, R., Li, N., Kinkley, S., Römer-Hillmann, A., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1860-7 · Cited by 29

Evaluating the probability of CRISPR‐based gene drive contaminating another species

Courtier‐Orgogozo, V., Danchin, A., Gouyon, P., & Boëte, C. (2020) · Evolutionary Applications · doi:10.1111/eva.12939 · Cited by 33

Advancing bioinformatics with language models: components, applications, and perspectives

Liu, J., Yang, M., Yu, Y., Xu, H., Wang, T., Li, K., & Zhou, X. (2026) · Briefings in Bioinformatics · doi:10.1093/bib/bbag367 · Cited by 66

Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits

Zhu, T., Xia, C., Yu, R., Zhou, X., Xu, X., Wang, L., Zong, Z., Yang, J., Liu, Y., Ming, L., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-50787-y · Cited by 34

Molecular landscapes of human hematopoietic stem cells in health and leukemia

Vedi, A., Santoro, A., Dunant, C. F., Dick, J. E., & Laurenti, E. (2015) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.12981 · Cited by 32

Inferring the Molecular Mechanisms of Noncoding Alzheimer’s Disease-Associated Genetic Variants

Amlie‐Wolf, A., Tang, M., Way, J., Dombroski, B. A., Ming, J., Vrettos, N., Chou, Y., Zhao, Y., Kuzma, A. B., Mlynarski, E. E., et al. (2019) · Journal of Alzheimer s Disease · doi:10.3233/jad-190568 · Cited by 32

Bacterial contribution to genesis of the novel germ line determinant oskar

Blondel, L., Jones, T. E. M., & Extavour, C. G. M. (2020) · eLife · doi:10.7554/elife.45539 · Cited by 32

Mutation bias interacts with composition bias to influence adaptive evolution

Cano, A. V., & Payne, J. L. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008296 · Cited by 32

Genome-wide identification, characterization and expression analysis of MATE family genes in apple (Malus × domestica Borkh)

Zhang, W., Liao, L., Xu, J., Han, Y., & Li, L. (2021) · BMC Genomics · doi:10.1186/s12864-021-07943-1 · Cited by 31

Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila

Ullastres, A., Merenciano, M., & González, J. (2021) · Genome biology · doi:10.1186/s13059-021-02471-3 · Cited by 38

Transcriptional states and chromatin accessibility during bovine myoblasts proliferation and myogenic differentiation

Li, Q., Wang, Y., Hu, X., Zhang, Y., Li, H., Zhang, Q., Cai, W., Wang, Z., Zhu, B., Xu, L., et al. (2022) · Cell Proliferation · doi:10.1111/cpr.13219 · Cited by 30

Improving yield-related traits by editing the promoter of the heading date gene Ehd1 in rice

Li, S., Luo, Y., Wei, G., Zong, W., Zeng, W., Xiao, D., Zhang, H., Song, Y., Yu, H., Sun, K., et al. (2023) · Theoretical and Applied Genetics · doi:10.1007/s00122-023-04489-6 · Cited by 33

Evolutionary constraints in variable environments, from proteins to networks

Taute, K. M., Gude, S., Nghe, P., & Tans, S. J. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.04.003 · Cited by 30

Prediction and validation of cis-regulatory elements in 5′ upstream regulatory regions of lectin receptor-like kinase gene family in rice

Passricha, N., Saifi, S. K., Ansari, M. W., & Tuteja, N. (2016) · PROTOPLASMA · doi:10.1007/s00709-016-0979-6 · Cited by 31

Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictionsPreprint

Naval-Sánchez, M., Potier, D., Haagen, L., Sánchez, M., Munck, S., de Sande, B. V., Casares, F., Christiaens, V., & Aerts, S. (2012) · Genome Research · doi:10.1101/gr.140426.112 · Cited by 31

Evolution of regulatory signatures in primate cortical neurons at cell-type resolution

Kozlenkov, A., Vermunt, M. W., Apontes, P., Li, J., Hao, K., Sherwood, C. C., Hof, P. R., Ely, J. J., Wegner, M., Mukamel, E. A., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2011884117 · Cited by 30

The Chemical Ecology of Benzoxazinoids

Robert, C. A. M., & Mateo, P. (2022) · CHIMIA International Journal for Chemistry · doi:10.2533/chimia.2022.928 · Cited by 30

Transcriptional factor MdESE3 controls fruit acidity by activating genes regulating malic acid content in apple

Zheng, L., Ma, W., Liu, P., Song, S., Wang, L., Yang, W. C., Ren, H., Wei, X., Zhu, L., Peng, J., et al. (2024) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiae282 · Cited by 30

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

Dennis, M. Y. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100540 · Cited by 1

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