{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T14:07:18Z","timestamp":1761919638454},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1490,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Genomic context analysis, also known as phylogenetic profiling, is widely used to infer functional interactions between proteins but rarely applied to non-coding cis-regulatory DNA elements. We were wondering whether this approach could provide insights about utlraconserved non-coding elements (UCNEs). These elements are organized as large clusters, so-called gene regulatory blocks (GRBs) around key developmental genes. Their molecular functions and the reasons for their high degree of conservation remain enigmatic.<\/jats:p>\n               <jats:p>Results: In a special setting of genomic context analysis, we analyzed the fate of GRBs after a whole-genome duplication event in five fish genomes. We found that in most cases all UCNEs were retained together as a single block, whereas the corresponding target genes were often retained in two copies, one completely devoid of UCNEs. This \u2018winner-takes-all\u2019 pattern suggests that UCNEs of a GRB function in a highly cooperative manner. We propose that the multitude of interactions between UCNEs is the reason for their extreme sequence conservation.<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online and at http:\/\/ccg.vital-it.ch\/ucne\/<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts400","type":"journal-article","created":{"date-parts":[[2012,9,7]],"date-time":"2012-09-07T20:35:22Z","timestamp":1347050122000},"page":"i395-i401","source":"Crossref","is-referenced-by-count":22,"title":["Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements"],"prefix":"10.1093","volume":"28","author":[{"given":"Slavica","family":"Dimitrieva","sequence":"first","affiliation":[{"name":"1 Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL)"},{"name":"2 Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland"}]},{"given":"Philipp","family":"Bucher","sequence":"additional","affiliation":[{"name":"1 Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL)"},{"name":"2 Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2012,9,3]]},"reference":[{"key":"2023012513020138200_B1","doi-asserted-by":"crossref","first-page":"e234","DOI":"10.1371\/journal.pbio.0050234","article-title":"Deletion of ultraconserved elements yields viable mice","volume":"5","author":"Ahituv","year":"2007","journal-title":"PLoS Biol."},{"key":"2023012513020138200_B2","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1126\/science.1098119","article-title":"Ultraconserved elements in the human 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