Transcriptomics,Genomics

Dataset Information

298

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 human promoters. Whereas the distribution of some core promoter motifs is conserved independent of species-specific nucleotide bias, the frequency of another class of motifs correlates with the single nucleotide frequencies. This class includes the well-known TATA box and SP1 motifs, which are more abundant in Xenopus and human promoters, respectively. While these motifs are enriched above the local nucleotide background in both organisms, their frequency varies in step with this background. These differences are likely adaptive as these motifs can recruit TFIID to either CpG island or sharply initiating promoters. Our results highlight both conserved and diverged aspects of vertebrate transcription, most notably showing co-opted motif usage to recruit the transcriptional machinery to promoters with diverging nucleotide composition. This shows how sweeping changes in nucleotide composition are compatible with highly conserved mechanisms of transcription initiation. ChIP-seq profiles of TBP in Xenopus tropicalis stage 12 embryos and TSS-seq profiles of Xenopus oocytes and stage 12 embryos

SUBMITTER: Waseem Akhtar   Gert Jan Veenstra  Robert C Akkers  Gert J Veenstra  Ulrike G Jacobi  Yutaka Suzuki  Simon J van Heeringen 

PROVIDER: E-GEOD-21482 | ArrayExpress | 2010-12-30

SECONDARY ACCESSION(S): GSE21482SRP002372PRJNA126041

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Nucleotide composition-linked divergence of vertebrate core promoter architecture.

van Heeringen Simon J SJ   Akhtar Waseem W   Jacobi Ulrike G UG   Akkers Robert C RC   Suzuki Yutaka Y   Veenstra Gert Jan C GJ  

Genome research 20110110 3


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  ...[more]

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