000181680 001__ 181680
000181680 005__ 20190617200657.0
000181680 0247_ $$2doi$$a10.1093/bioinformatics/bts400
000181680 02470 $$2ISI$$a000308532300014
000181680 037__ $$aARTICLE
000181680 245__ $$aGenomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements
000181680 269__ $$a2012
000181680 260__ $$bOxford University Press$$c2012$$aOxford
000181680 300__ $$a7
000181680 336__ $$aJournal Articles
000181680 520__ $$aMotivation: Genomic context analysis, also known as phylogenetic profiling, is widely used to infer functional interactions between proteins but rarely applied to non-coding cis-regulatory DNA elements. We were wondering whether this approach could provide insights about utlraconserved non-coding elements (UCNEs). These elements are organized as large clusters, so-called gene regulatory blocks (GRBs) around key developmental genes. Their molecular functions and the reasons for their high degree of conservation remain enigmatic. Results: In a special setting of genomic context analysis, we analyzed the fate of GRBs after a whole-genome duplication event in five fish genomes. We found that in most cases all UCNEs were retained together as a single block, whereas the corresponding target genes were often retained in two copies, one completely devoid of UCNEs. This ‘winner-takes-all’ pattern suggests that UCNEs of a GRB function in a highly cooperative manner. We propose that the multitude of interactions between UCNEs is the reason for their extreme sequence conservation. Supplementary information: Supplementary data are available at Bioinformatics online and at http://ccg.vital-it.ch/ucne/
000181680 6531_ $$aEVOLUTION
000181680 6531_ $$aPHYLOGENY AND COMPARATIVE GENOMICS
000181680 700__ $$0243606$$g190564$$aDimitrieva, Slavica
000181680 700__ $$aBucher, Philipp$$0244404$$g113607
000181680 773__ $$j28$$tBioinformatics$$k18$$qI395-I401
000181680 8564_ $$uhttps://infoscience.epfl.ch/record/181680/files/Bioinformatics-2012-Dimitrieva-i395-401-1.pdf$$zn/a$$s401220$$yn/a
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000181680 937__ $$aEPFL-ARTICLE-181680
000181680 973__ $$rREVIEWED$$sPUBLISHED$$aEPFL
000181680 980__ $$aARTICLE