title: The evolution of transcription-associated biases of mutations across vertebrates.
abstract: BACKGROUND
  The interplay between transcription and mutational processes can lead to particular mutation patterns in transcribed regions of the genome. Transcription introduces several biases in mutational patterns; in particular it invokes strand specific mutations. In order to understand the forces that have shaped transcripts during evolution, one has to study mutation patterns associated with transcription across animals.
  
  
  RESULTS
  Using multiple alignments of related species we estimated the regional single-nucleotide substitution patterns along genes in four vertebrate taxa: primates, rodents, laurasiatheria and bony fishes. Our analysis is focused on intronic and intergenic regions and reveals differences in the patterns of substitution asymmetries between mammals and fishes. In mammals, the levels of asymmetries are stronger for genes starting within CpG islands than in genes lacking this property. In contrast to all other species analyzed, we found a mutational pressure in dog and stickleback, promoting an increase of GC-contents in the proximity to transcriptional start sites.
  
  
  CONCLUSIONS
  We propose that the asymmetric patterns in transcribed regions are results of transcription associated mutagenic processes and transcription coupled repair, which both seem to evolve in a taxon related manner. We also discuss alternative mechanisms that can generate strand biases and involves error prone DNA polymerases and reverse transcription. A localized increase of the GC content near the transcription start site is a signature of biased gene conversion (BGC) that occurs during recombination and heteroduplex formation. Since dog and stickleback are known to be subject to rapid adaptations due to population bottlenecks and breeding, we further hypothesize that an increase in recombination rates near gene starts has been part of an adaptive process.
authors.affiliation: Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany. polak@molgen.mpg.de
authors.forename: Paz
authors.initials: P
authors.lastname: Polak
authors.forename: Robert
authors.initials: R
authors.lastname: Querfurth
authors.forename: Peter F
authors.initials: PF
authors.lastname: Arndt
mesh_terms: D000818:Animals; D001482:Base Composition; D018899:CpG Islands; D019175:DNA Methylation; D004252:DNA Mutational Analysis; D021901:DNA, Intergenic; D004285:Dogs / Q000235:genetics; D019143:Evolution, Molecular; D005399:Fishes / Q000235:genetics; D007438:Introns; D016013:Likelihood Functions; D008322:Mammals / Q000235:genetics; D009154:Mutation; D011323:Primates / Q000235:genetics; D012377:Rodentia / Q000235:genetics; D016415:Sequence Alignment; D023701:Smegmamorpha / Q000235:genetics; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D021901:DNA, Intergenic