Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate

BMC Genomics
Gemma B DanksEric M Thompson

Abstract

Development is largely driven by transitions between transcriptional programs. The initiation of transcription at appropriate sites in the genome is a key component of this and yet few rules governing selection are known. Here, we used cap analysis of gene expression (CAGE) to generate bp-resolution maps of transcription start sites (TSSs) across the genome of Oikopleura dioica, a member of the closest living relatives to vertebrates. Our TSS maps revealed promoter features in common with vertebrates, as well as striking differences, and uncovered key roles for core promoter elements in the regulation of development. During spermatogenesis there is a genome-wide shift in mode of transcription initiation characterized by a novel core promoter element. This element was associated with > 70% of male-specific transcription, including the use of cryptic internal promoters within operons. In many cases this led to the exclusion of trans-splice sites, revealing a novel mechanism for regulating which mRNAs receive the spliced leader. Binding of the cell cycle regulator, E2F1, is enriched at the TSS of maternal genes in endocycling nurse nuclei. In addition, maternal promoters lack the TATA-like element found in zebrafish and have broad...Continue Reading

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Methods Mentioned

BETA
ChIP-chip
immunoprecipitation
Illumina sequencing

Software Mentioned

CAGEscan
Bioconductor R package Ringo
Ensembl
MEME
Bowtie
CAGEr
TOMTOM
Biostrings ” R package
R package “ CAGEr ”
Bioconductor GOstats

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