Back
Full-text
Journal article

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

  • Dreos R Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
  • Ambrosini G Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
  • Bucher P Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
  • 2016-10-08
Published in:
  • PLoS computational biology. - 2016
Base Sequence
Binding Sites
Computer Simulation
DNA
Models, Genetic
Molecular Sequence Data
Nucleosomes
Promoter Regions, Genetic
RNA Polymerase II
Transcription Initiation Site
Transcription, Genetic
Transcriptional Activation
English 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.
Language
  • English
Open access status
gold
Identifiers
Persistent URL
https://sonar.ch/global/documents/278908
Statistics
Document views: 18 File downloads:
  • Full-text: 0