Peter F Arndt1, Terence Hwa. 1. Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany. peter.arndt@molgen.mpg.de
Abstract
MOTIVATION: Substantial regional variations of substitutional processes have recently been reported from human/mouse comparisons. However, several features including the C + G dependence and the CpG-based transition effect remain obscure. RESULTS: Utilizing the vast amount of transposable elements in the human genome, we performed detailed analysis of the substitutional and insertion/deletion patterns along the human lineage in a regional and time-resolved fashion. We observed a drastic increase in the CpG-based transition frequency at about the time of the mammalian radiation. We also observed clear regional biases of substitution patterns, most notably a bias to enrich the C+G content toward the telomeres. AVAILABILITY: The programs used are available upon request from the authors.
MOTIVATION: Substantial regional variations of substitutional processes have recently been reported from human/mouse comparisons. However, several features including the C + G dependence and the CpG-based transition effect remain obscure. RESULTS: Utilizing the vast amount of transposable elements in the human genome, we performed detailed analysis of the substitutional and insertion/deletion patterns along the human lineage in a regional and time-resolved fashion. We observed a drastic increase in the CpG-based transition frequency at about the time of the mammalian radiation. We also observed clear regional biases of substitution patterns, most notably a bias to enrich the C+G content toward the telomeres. AVAILABILITY: The programs used are available upon request from the authors.
Authors: Valerie M Schaibley; Matthew Zawistowski; Daniel Wegmann; Margaret G Ehm; Matthew R Nelson; Pamela L St Jean; Gonçalo R Abecasis; John Novembre; Sebastian Zöllner; Jun Z Li Journal: Genome Res Date: 2013-08-29 Impact factor: 9.043