The Active Mechanism of Nucleosome Depletion by Poly(dA:dT) Tracts In Vivo

Abstract

Poly(dA:dT) tracts cause nucleosome depletion in many species, e.g., at promoters and replication origins. Their intrinsic biophysical sequence properties make them stiff and unfavorable for nucleosome assembly, as probed by in vitro nucleosome reconstitution. The mere correlation between nucleosome depletion over poly(dA:dT) tracts in in vitro reconstituted and in in vivo chromatin inspired an intrinsic nucleosome exclusion mechanism in vivo that is based only on DNA and histone properties. However, we compile here published and new evidence that this correlation does not reflect mechanistic causation. (1) Nucleosome depletion over poly(dA:dT) in vivo is not universal, e.g., very weak in S. pombe. (2) The energy penalty for incorporating poly(dA:dT) tracts into nucleosomes is modest (<10%) relative to ATP hydrolysis energy abundantly invested by chromatin remodelers. (3) Nucleosome depletion over poly(dA:dT) is much stronger in vivo than in vitro if monitored without MNase and (4) actively maintained in vivo. (5) S. cerevisiae promoters evolved a strand-biased poly(dA) versus poly(dT) distribution. (6) Nucleosome depletion over poly(dA) is directional in vivo. (7) The ATP dependent chromatin remodeler RSC preferentially and directionally displaces nucleosomes towards 5’ of poly(dA). Especially distribution strand bias and displacement directionality would not be expected for an intrinsic mechanism. Together, this argues for an in vivo mechanism where active and species-specific read out of intrinsic sequence properties, e.g., by remodelers, shapes nucleosome organization.

Chromatin accessibility: methods, mechanisms, and biological insights

“…However, ORC is required for coordinating the spacing of nearby nucleosomes that play key roles in origin firing [ 344 , 348 , 349 ]. A recent review has challenged the inherent ability of dA:dT tracts to establish nucleosome-depleted regions [ 350 ], suggesting that trans-factors may play important roles in helping to establish these nucleosome-depleted regions and regulating origin loading. To this end, the binding of the pioneer Forkhead family TF (Fhk1) was also found to be an important correlate of ORC loading at ~25% of origins [ 351 , 352 ].…”

Nucleosome patterns in four plant pathogenic fungi with contrasted genome structures

“…Nucleosome landscapes can thus be viewed as the final result of active positioning forces (the action of chromatin remodelers) combined with destabilizing nucleotide content, including poly(A+T) tracts (see above). Recently, this scenario was proposed to be species-specific (Barnes and Korber, 2021; Oberbeckmann, Krietenstein, et al ., 2021), supporting that several combinatorial nucleosome arraying rules can form during the course of evolution. Indeed, when we restricted our analysis to conserved single-copy orthologous fungal genes, the overall profiles and the intensities of “+1 nucleosome” and NDRs were more homogenous between fungi.…”

Nucleosome patterns in four plant pathogenic fungi with contrasted genome structures

“…Nucleosome landscapes can thus be viewed as the final result of active positioning forces (the action of chromatin remodelers) combined with destabilizing nucleotide content, including poly(A+T) tracts (see above). Recently, this scenario was proposed to be species-specific (Barnes and Korber, 2021;Oberbeckmann, Krietenstein, et al, 2021), supporting that several combinatorial nucleosome arraying rules can form during the course of evolution. Indeed, when we restricted our analysis to conserved single-copy orthologous fungal genes, the overall profiles and the intensities of "+1 nucleosome" and NDRs were more homogenous between fungi.…”