title: Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online and at http://ccg.vital-it.ch/ucne/
authors.affiliation: Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
authors.forename: Slavica
authors.initials: S
authors.lastname: Dimitrieva
authors.forename: Philipp
authors.initials: P
authors.lastname: Bucher
mesh_terms: D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence; D019143:Evolution, Molecular; D005399:Fishes / Q000235:genetics; D050437:Genes, Developmental; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D007438:Introns; D010802:Phylogeny; D012045:Regulatory Sequences, Nucleic Acid; D014714:Vertebrates / Q000235:genetics