Influence of rotational nucleosome positioning on transcription start site selection in animals promoters

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 mechanismof TSS selection in animals.\n\nAuthor SummaryGene transcription is a complex process that starts with the recruitment and positioning of Pol-II enzyme at the transcription start site (TSS). Specific promoter sequences, known as core promoter elements (CPEs) facilitate this process. Surprisingly, only a fraction of promoters contain them. It is still unknown how Pol-II choses the start site in their absence. Arecently proposed alternative mechanism implicates positioned nucleosomes in the TSS selection. Here, we provide new evidence of the existence of such mechanism with a comparative analysis of promoters features across the animal kingdom. We analysed the promoters DNA sequence composition in 5 organisms and found conserved and unique consensus sequencesused to organize chromatin in the region of the first nucleosome downstream the TSS (N+1). Moreover, we found that all organisms show a strong correlation between the spread of Pol-II initiation and the strength of the DNA-encoded signal in the N+1 region. A detailed analysis of Pol-II initiation sites reveals also the presence of a 10 bp periodicity that is correlated with the intensity of the DNA signal in the N+1 region. Importantly, we report that genetic variants that alter the DNA-nucleosome affinity in that region alter Pol-II initiation spread as well.