{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T12:58:21Z","timestamp":1773665901804,"version":"3.50.1"},"reference-count":45,"publisher":"World Scientific Pub Co Pte Ltd","issue":"02","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2014,4]]},"abstract":"<jats:p>Biological development depends on the coordinated expression of genes in time and space. Developmental genes have extensive cis-regulatory regions which control their expression. These regions are organized in a modular manner, with different modules controlling expression at different times and locations. Both how modularity evolved and what function it serves are open questions. We present a computational model for the cis-regulation of the hunchback (hb) gene in the fruit fly (Drosophila). We simulate evolution (using an evolutionary computation approach from computer science) to find the optimal cis-regulatory arrangements for fitting experimental hb expression patterns. We find that the cis-regulatory region tends to readily evolve modularity. These cis-regulatory modules (CRMs) do not tend to control single spatial domains, but show a multi-CRM\/multi-domain correspondence. We find that the CRM-domain correspondence seen in Drosophila evolves with a high probability in our model, supporting the biological relevance of the approach. The partial redundancy resulting from multi-CRM control may confer some biological robustness against corruption of regulatory sequences. The technique developed on hb could readily be applied to other multi-CRM developmental genes.<\/jats:p>","DOI":"10.1142\/s0219720014410091","type":"journal-article","created":{"date-parts":[[2014,3,6]],"date-time":"2014-03-06T11:54:44Z","timestamp":1394106884000},"page":"1441009","source":"Crossref","is-referenced-by-count":6,"title":["<i>In silico<\/i>evolution of the<i>hunchback<\/i>gene indicates redundancy in cis-regulatory organization and spatial gene expression"],"prefix":"10.1142","volume":"12","author":[{"given":"Elizaveta A.","family":"Zagrijchuk","sequence":"first","affiliation":[{"name":"Lab Modeling of Evolution, I.M. Sechenov Institute of Evolutionary Physiology &amp; Biochemistry, Russian Academy of Sciences, Thorez Pr. 44, St.-Petersburg, 2194223, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marat A.","family":"Sabirov","sequence":"additional","affiliation":[{"name":"Lab Modeling of Evolution, I.M. Sechenov Institute of Evolutionary Physiology &amp; Biochemistry, Russian Academy of Sciences, Thorez Pr. 44, St.-Petersburg, 2194223, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David M.","family":"Holloway","sequence":"additional","affiliation":[{"name":"Mathematics Department, British Columbia Institute of Technology, 3700 Willingdon Ave. Burnaby, B.C. V5G 3H2, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander V.","family":"Spirov","sequence":"additional","affiliation":[{"name":"Lab Modeling of Evolution, I.M. Sechenov Institute of Evolutionary Physiology &amp; Biochemistry, Russian Academy of Sciences, Thorez Pr. 44, St.-Petersburg, 2194223, Russia"},{"name":"Computer Science and CEWIT, SUNY Stony Brook, Stony Brook, 1500 Stony Brook Road, Stony Brook, 11794 NY, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"219","published-online":{"date-parts":[[2014,4,9]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0408031102"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1038\/nrg2499"},{"key":"rf3","doi-asserted-by":"publisher","DOI":"10.1038\/nature09645"},{"key":"rf4","doi-asserted-by":"publisher","DOI":"10.1016\/j.gep.2008.10.005"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1016\/j.ydbio.2011.12.001"},{"key":"rf6","doi-asserted-by":"publisher","DOI":"10.1016\/j.gep.2012.05.004"},{"key":"rf7","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth0705-535"},{"key":"rf8","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0060137"},{"key":"rf9","doi-asserted-by":"publisher","DOI":"10.1126\/science.1160631"},{"key":"rf10","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm727"},{"key":"rf11","doi-asserted-by":"publisher","DOI":"10.1101\/gad.1509607"},{"key":"rf12","doi-asserted-by":"publisher","DOI":"10.1242\/dev.02239"},{"key":"rf13","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3207"},{"key":"rf14","doi-asserted-by":"publisher","DOI":"10.1038\/nature09158"},{"key":"rf15","doi-asserted-by":"publisher","DOI":"10.1101\/gad.1620408"},{"key":"rf16","doi-asserted-by":"publisher","DOI":"10.1002\/bies.201100121"},{"key":"rf17","doi-asserted-by":"publisher","DOI":"10.1038\/nature09158"},{"key":"rf18","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2010.07.043"},{"key":"rf19","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1109873108"},{"key":"rf20","doi-asserted-by":"publisher","DOI":"10.1242\/dev.081497"},{"key":"rf21","doi-asserted-by":"publisher","DOI":"10.1242\/dev.015826"},{"key":"rf22","doi-asserted-by":"publisher","DOI":"10.1016\/j.ydbio.2010.04.026"},{"key":"rf23","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2008.01.014"},{"key":"rf24","first-page":"1","volume":"22","author":"Perry M. 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