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.
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/