Genome-wide analysis of core promoter structures in Schizosaccharomyces pombe with DeepCAGE

RNA Biology
Hua LiZhifeng Shao

Abstract

The core promoter, which immediately flanks the transcription start site (TSS), plays a critical role in transcriptional regulation of eukaryotes. Recent studies on higher eukaryotes have revealed an unprecedented complexity of core promoter structures that underscores diverse regulatory mechanisms of gene expression. For unicellular eukaryotes, however, the structures of core promoters have not been investigated in detail. As an important model organism, Schizosaccharomyces pombe still lacks the precise annotation for TSSs, thus hampering the analysis of core promoter structures and their relationship to higher eukaryotes. Here we used a deep sequencing-based approach (DeepCAGE) to generate 16 million uniquely mapped tags, corresponding to 93,736 positions in the S. pombe genome. The high-resolution TSS landscape enabled identification of over 8,000 core promoters, characterization of 4 promoter classes and observation of widespread alternative promoters. The landscape also allowed precise determination of the representative TSSs within core promoters, thus redefining the 5' UTR for 82.8% of S. pombe genes. We further identified the consensus initiator (Inr) sequence--PyPyPuN(A/C)(C/A), the TATA-enriched region (between positi...Continue Reading

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Citations

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Datasets Mentioned

BETA
E-MTAB-3188

Methods Mentioned

BETA
RNA-Seq
ChIP-Seq
ChIP

Software Mentioned

Bowtie
R
DeepCAGE
WebLogo
Cap Analysis of Gene Expression ( CAGE )
MEME
GOEAST

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