Nucleotide composition-linked divergence of vertebrate core promoter architecture.

ABSTRACT: Transcription initiation involves the recruitment of basal transcription factors to the core promoter. A variety of core promoter elements exists; however for most of these motifs, the distribution across species is unknown. Here we report on the comparison of human and amphibian promoter sequences. We have used oligo-capping in combination with deep sequencing to determine transcription start sites in Xenopus tropicalis. To systematically predict regulatory elements, we have developed a de novo motif finding pipeline using an ensemble of computational tools. A comprehensive comparison of human and amphibian promoter sequences revealed both similarities and differences in core promoter architecture. Some of the differences stem from a highly divergent nucleotide composition of Xenopus and

SUBMITTER: van Heeringen SJ 

PROVIDER: S-EPMC3044855 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature