Genome-wide rules of nucleosome phasing

Abstract

Regular successions of positioned nucleosomes -phased nucleosome arrays (PNAs) -are predominantly known from transcriptional start sites (TSS). It is unclear whether PNAs occur elsewhere in the genome. To generate a comprehensive inventory of PNAs for Drosophila, we applied spectral analysis to nucleosome maps and identified thousands of PNAs throughout the genome. About half of them are not near TSS and strongly enriched for a novel sequence motif. Through genome-wide reconstitution of physiological chromatin in Drosophila embryo extracts we uncovered the molecular basis of PNA formation. We identified Phaser, an unstudied zinc finger protein that positions nucleosomes flanking the new motif. It also revealed how the global activity of the chromatin remodeler CHRAC/ACF, together with local barrier elements, generates islands of regular phasing throughout the genome. Our work demonstrates the potential of chromatin assembly by embryo extracts as a powerful tool to reconstitute chromatin features on a global scale in vitro.

DNA Double Strand Break Repair and Its Control by Nucleosome Remodeling

“…Importantly, these remodelers also sense the presence of barrier-factors bound at specific sites in the genome to which the array is aligned to or "phased" (Eaton et al, 2010;Li et al, 2015;Krietenstein et al, 2016;Kubik et al, 2018;Rossi et al, 2018). Typical barrier factors are DNA-binding factors, like the abundant general regulatory factors Abf1, Rap1 or Reb1 in budding yeast or genome organizing factors like CTCF in mammals or Phaser in flies (Fu et al, 2008;Wiechens et al, 2016;Baldi et al, 2018). Importantly, recent in vitro work suggests that also DSBs are sensed as a barrier-factor by nucleosome remodelers and guide the formation of nucleosome arrays (Oberbeckmann et al, 2021a).…”

“…The precise mechanism by which these remodelers promote resection and HR is however uncertain. Moreover, even if these remodelers established nucleosome arrays around DSBs, it is at this point entirely unclear whether such arrays will have a positive function in DSB repair or whether they are simply a consequence of the enzymatic mechanism of positioning remodelers (Baldi et al, 2018). Therefore, despite first hints that nucleosome arrays could form in the proximity of DSBs, the role of positioning remodelers in DSB repair still needs to be determined.…”