Abstract
Nucleosomes regulate many DNA-dependent processes by controlling the accessibility of DNA, and DNA sequences such as the poly-dA:dT element are known to affect nucleosome binding. We demonstrate that poly-dA:dT tracts form an asymmetric barrier to nucleosome movement in vivo, mediated by ATP-dependent chromatin remodelers. We theorize that nucleosome transit over poly-A elements is more energetically favourable in one direction, leading to an asymmetric arrangement of nucleosomes around these sequences. We demonstrate that different arrangements of poly-A and poly-T tracts result in very different outcomes for nucleosome occupancy in yeast, mouse, and human, and show that yeast takes advantage of this phenomenon in its promoter architecture.
Highlights
Promoters are characterized by a nucleosome free region (NFR) that is followed by a periodic phasing of wellpositioned nucleosomes continuing into the gene body
Upon addition of ATP, which activates chromatin remodelers (CRs) present in the whole cell extract (WCE), the sequence becomes further depleted, but in an asymmetric fashion; a nucleosome becomes well-positioned 59 to the poly-A sequence, but not 39, and the NFR is offset 59 to the poly-A sequence, similar to the trend observed in vivo (Figure 2)
The poly-T/poly-A combination results in the most robust NFR (Figure 3C), which could explain why this arrangement is preferred in yeast promoters
Summary
Promoters are characterized by a nucleosome free region (NFR) that is followed by a periodic phasing of wellpositioned nucleosomes continuing into the gene body. Hypothesizing that the asymmetric arrangement of these elements in promoters may have evolved to maintain promoter NFRs through some effect on nucleosome occupancy, we identified all non-overlapping poly-A sequences of exactly length five (AAAAA) in the yeast genome and analyzed the nucleosome occupancy [1] surrounding these elements (Figure 2).
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