[{"abstract":[{"lang":"eng","text":"Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an individual TF binds arbitrary DNA sequences and how individual binding events on the CRE combine to affect gene expression. These insights can be synthesized into a global, biophysically realistic, and quantitative genotype-phenotype (GP) map for gene regulation, a ‘holy grail’ for the application of evolutionary theory. A global map provides a rare opportunity to simulate the long-term evolution of regulatory sequences and pose several fundamental questions: How long does it take to evolve CREs de novo? How many non-trivial regulatory functions exist in sequence space? How connected are they? For which regulatory architecture is CRE evolution most rapid and evolvable? In this article, the second of a two-part series, we review the application of evolutionary concepts — epistasis, robustness, evolvability, tunability, plasticity, and bet-hedging — to the evolution of gene regulatory sequences. We then evaluate the potential for a unifying theory for the evolution of regulatory sequences and identify key open challenges."}],"article_number":"102472","volume":98,"quality_controlled":"1","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"date_created":"2026-04-26T22:01:46Z","corr_author":"1","language":[{"iso":"eng"}],"publication_status":"epub_ahead","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.gde.2026.102472"}],"acknowledgement":"We thank Calin Guet and Santiago Herrera-Álvarez for essential contributions to this manuscript.\r\nE.M. acknowledges support from the APART-USA fellowship, jointly funded by the Austrian Academy of Sciences (ÖAW) and the Institute of Science and Technology Austria (ISTA). N.B. acknowledges funding from the ERC Advanced Grant 101055327 “HaplotypeStructure”.\r\nThis study was also supported by the European Molecular Biology Laboratory (N.O.B., J.C.).","publication_identifier":{"eissn":["1879-0380"],"issn":["0959-437X"]},"oa":1,"author":[{"id":"776a6ed0-a053-11f0-8635-80b95e0e0d53","first_name":"Elia","full_name":"Mascolo, Elia","last_name":"Mascolo","orcid":"0000-0003-2977-7844"},{"id":"50FDE43E-AA30-11E9-A72B-8A12E6697425","first_name":"Reka E","full_name":"Körei, Reka E","last_name":"Körei"},{"first_name":"Noa O.","full_name":"Borst, Noa O.","last_name":"Borst"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"full_name":"Crocker, Justin","last_name":"Crocker","first_name":"Justin"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"publication":"Current Opinion in Genetics and Development","scopus_import":"1","intvolume":"        98","article_processing_charge":"Yes (via OA deal)","citation":{"ama":"Mascolo E, Körei RE, Borst NO, Barton NH, Crocker J, Tkačik G. Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges. <i>Current Opinion in Genetics and Development</i>. 2026;98. doi:<a href=\"https://doi.org/10.1016/j.gde.2026.102472\">10.1016/j.gde.2026.102472</a>","apa":"Mascolo, E., Körei, R. E., Borst, N. O., Barton, N. H., Crocker, J., &#38; Tkačik, G. (2026). Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges. <i>Current Opinion in Genetics and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2026.102472\">https://doi.org/10.1016/j.gde.2026.102472</a>","chicago":"Mascolo, Elia, Reka E Körei, Noa O. Borst, Nicholas H Barton, Justin Crocker, and Gašper Tkačik. “Long-Term Evolution of Regulatory DNA Sequences. Part 2: Theory and Future Challenges.” <i>Current Opinion in Genetics and Development</i>. Elsevier, 2026. <a href=\"https://doi.org/10.1016/j.gde.2026.102472\">https://doi.org/10.1016/j.gde.2026.102472</a>.","ista":"Mascolo E, Körei RE, Borst NO, Barton NH, Crocker J, Tkačik G. 2026. Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges. Current Opinion in Genetics and Development. 98, 102472.","short":"E. Mascolo, R.E. Körei, N.O. Borst, N.H. Barton, J. Crocker, G. Tkačik, Current Opinion in Genetics and Development 98 (2026).","mla":"Mascolo, Elia, et al. “Long-Term Evolution of Regulatory DNA Sequences. Part 2: Theory and Future Challenges.” <i>Current Opinion in Genetics and Development</i>, vol. 98, 102472, Elsevier, 2026, doi:<a href=\"https://doi.org/10.1016/j.gde.2026.102472\">10.1016/j.gde.2026.102472</a>.","ieee":"E. Mascolo, R. E. Körei, N. O. Borst, N. H. Barton, J. Crocker, and G. Tkačik, “Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges,” <i>Current Opinion in Genetics and Development</i>, vol. 98. Elsevier, 2026."},"_id":"21759","title":"Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges","month":"04","OA_place":"publisher","doi":"10.1016/j.gde.2026.102472","OA_type":"hybrid","article_type":"review","day":"15","type":"journal_article","publisher":"Elsevier","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2026-04-15T00:00:00Z","project":[{"name":"Understanding the evolution of continuous genomes","grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00"}],"year":"2026","oa_version":"Published Version","date_updated":"2026-04-28T12:41:00Z"}]