title: Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes.
abstract: BACKGROUND
  Recent advances in genome sequencing suggest a remarkable conservation in gene content of mammalian organisms. The similarity in gene repertoire present in different organisms has increased interest in studying regulatory mechanisms of gene expression aimed at elucidating the differences in phenotypes. In particular, a proximal promoter region contains a large number of regulatory elements that control the expression of its downstream gene. Although many studies have focused on identification of these elements, a broader picture on the complexity of transcriptional regulation of different biological processes has not been addressed in mammals. The regulatory complexity may strongly correlate with gene function, as different evolutionary forces must act on the regulatory systems under different biological conditions. We investigate this hypothesis by comparing the conservation of promoters upstream of genes classified in different functional categories.
  
  
  RESULTS
  By conducting a rank correlation analysis between functional annotation and upstream sequence alignment scores obtained by human-mouse and human-dog comparison, we found a significantly greater conservation of the upstream sequence of genes involved in development, cell communication, neural functions and signaling processes than those involved in more basic processes shared with unicellular organisms such as metabolism and ribosomal function. This observation persists after controlling for G+C content. Considering conservation as a functional signature, we hypothesize a higher density of cis-regulatory elements upstream of genes participating in complex and adaptive processes.
  
  
  CONCLUSIONS
  We identified a class of functions that are associated with either high or low promoter conservation in mammals. We detected a significant tendency that points to complex and adaptive processes were associated with higher promoter conservation, despite the fact that they have emerged relatively recently during evolution. We described and contrasted several hypotheses that provide a deeper insight into how transcriptional complexity might have been emerged during evolution.
authors.affiliation: Bioinformatics Program, Boston University, Boston, MA 02215, USA. duplexa@bu.edu
authors.forename: Soohyun
authors.initials: S
authors.lastname: Lee
authors.forename: Isaac
authors.initials: I
authors.lastname: Kohane
authors.forename: Simon
authors.initials: S
authors.lastname: Kasif
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence; D018899:CpG Islands; D004285:Dogs; D019143:Evolution, Molecular; D005786:Gene Expression Regulation; D016678:Genome; D015894:Genome, Human; D006801:Humans; D051379:Mice; D008957:Models, Genetic; D010641:Phenotype; D011401:Promoter Regions, Genetic; D012270:Ribosomes / Q000378:metabolism; D013045:Species Specificity; D014158:Transcription, Genetic