Return to search results Title: Nucleotide composition-linked divergence of vertebrate core promoter architecture

Summary

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.

Contributors: Gert Jan Veenstra, Simon van Heeringen, Waseem Akhtar, Ulrike Jacobi, Robert Akkers, Yutaka Suzuki, Gert Veenstra

Experiment Type: ChIP-seq profiles of TBP in Xenopus tropicalis stage 12 embryos and TSS-seq profiles of Xenopus oocytes and stage 12 embryos

Article: XB-ART-42761, PubMed

Source: NCBI GEO, Xenbase Download

Sample	View		GSMs	Assay Type
TBP WE - NF12 GSM537039  ChIP-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 12 Tbp Ab2 WE - NF10-12 GSM632116  RNA-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 10 to NF stage 12   WE - unfertilized egg GSM632117  RNA-Seq Xtr   [-] [+] Background: Xtr.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo unfertilized egg stage

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