Genome-wide mapping of yeast histone chaperone anti-silencing function 1 reveals its role in condensin binding with chromatin

PLoS One. 2014 Sep 29;9(9):e108652. doi: 10.1371/journal.pone.0108652. eCollection 2014.

Abstract

Genome-wide participation and importance of the histone chaperone Asf1 (Anti-Silencing Function 1) in diverse DNA transactions like replication, repair, heterochromatic silencing and transcription are well documented. Yet its genome-wide targets have not been reported. Using ChIP-seq method, we found that yeast Asf1 associates with 590 unique targets including centromeres, telomeres and condensin-binding sites. It is found selectively on highly transcribed regions, which include replication fork pause sites. Asf1 preferentially associates with the genes transcribed by RNA polymerase (pol) III where its presence affects RNA production and replication-independent histone exchange. On pol II-transcribed genes, a negative correlation is found between Asf1 and nucleosome occupancy. It is not enriched on most of the reported sites of histone exchange or on the genes, which are misregulated in the asf1Δ cells. Interestingly, chromosome-wide distributions of Asf1 and one of the condensin subunits, Brn1 show a nearly identical pattern. Moreover, Brn1 shows reduced occupancy at various condensin-binding sites in asf1Δ cells. These results along with high association of Asf1 with heterochromatic centromeres and telomeres ascribe novel roles to Asf1 in condensin loading and chromatin dynamics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphatases / metabolism*
  • Binding Sites
  • Cell Cycle Proteins / genetics*
  • Centromere / metabolism
  • Chromatin / metabolism*
  • Chromatin Assembly and Disassembly / genetics
  • Chromosome Mapping
  • DNA-Binding Proteins / metabolism*
  • Histone Chaperones / genetics
  • Histones / metabolism
  • Molecular Chaperones / genetics*
  • Multiprotein Complexes / metabolism*
  • Nucleosomes / genetics
  • Protein Binding
  • RNA Polymerase III / genetics
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae Proteins / genetics*
  • Telomere / metabolism
  • Transcription, Genetic / genetics

Substances

  • ASF1 protein, S cerevisiae
  • Cell Cycle Proteins
  • Chromatin
  • DNA-Binding Proteins
  • Histone Chaperones
  • Histones
  • Molecular Chaperones
  • Multiprotein Complexes
  • Nucleosomes
  • Saccharomyces cerevisiae Proteins
  • condensin complexes
  • RNA Polymerase III
  • Adenosine Triphosphatases

Associated data

  • GEO/GSE40717

Grant support

This work was partially supported by the in-house Institutional funding and partially by a research grant (BT/PR8568/BRB/10/524/2006, www.dbtindia.nic.in) to PB from the Department of Biotechnology, Govt. of India. The grant term is over now. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.