Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters

René Dreos,Philipp Bucher,Giovanna Ambrosini

doi:10.1371/journal.pcbi.1005144

Abstract

The recruitment of RNA-Pol-II to the transcription start site (TSS) is an important step in gene regulation in all organisms. Core promoter elements (CPE) are conserved sequence motifs that guide Pol-II to the TSS by interacting with specific transcription factors (TFs). However, only a minority of animal promoters contains CPEs. It is still unknown how Pol-II selects the TSS in their absence. Here we present a comparative analysis of promoters’ sequence composition and chromatin architecture in five eukaryotic model organisms, which shows the presence of common and unique DNA-encoded features used to organize chromatin. Analysis of Pol-II initiation patterns uncovers that, in the absence of certain CPEs, there is a strong correlation between the spread of initiation and the intensity of the 10 bp periodic signal in the nearest downstream nucleosome. Moreover, promoters’ primary and secondary initiation sites show a characteristic 10 bp periodicity in the absence of CPEs. We also show that DNA natural variants in the region immediately downstream the TSS are able to affect both the nucleosome-DNA affinity and Pol-II initiation pattern. These findings support the notion that, in addition to CPEs mediated selection, sequence–induced nucleosome positioning could be a common and conserved mechanism of TSS selection in animals.

Highlights

An essential step in gene regulation is the recruitment of RNA-Pol-II (Pol-II) to the transcription start sites (TSS) at gene promoters [1,2,3]
Gene transcription is a complex process that starts with the recruitment and positioning of Pol-II enzyme at the transcription start site (TSS)
We investigate the molecular mechanisms of TSS selection by jointly analyzing experimentally determined chromatin architectures, DNA-encoded nucleosome signals, Pol-II initiation site patterns and natural genetic variation in promoters stratified by the presence or absence of specific core promoter elements (CPEs) and/or the breadth of the initiation patterns

Summary

Introduction

An essential step in gene regulation is the recruitment of RNA-Pol-II (Pol-II) to the transcription start sites (TSS) at gene promoters [1,2,3] This is often facilitated by the presence of conserved sequence motifs known as core promoter elements (CPEs), which are found at a fixed or nearly fixed distance from the TSS [4,5]. Promoters have a remarkably conserved chromatin architecture consisting of a nucleosome free region that spans 100–150 bp upstream the TSS followed by a well-positioned nucleosome (+1 nucleosome) [15,16]. This general conformation can be altered by diverse factors. CGI-promoters resemble the broad promoters described in other species and may not be considered a separate class

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