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

Pooran Singh Dewari,Purnima Bhargava

doi:10.1371/journal.pone.0108652

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.

Highlights

Organization of the eukaryotic genome into chromatin enables its compaction inside the cell nucleus and concomitant regulation of DNA-related processes [1]
The number of assigned AntiSilencing Function 1 (Asf1) peaks on a chromosome shows a linear relationship with the chromosome length (Figure 1A), indicating that Asf1 is uniformly distributed on all chromosomes
Using MIPS Functional Catalogue annotation to find whether these ORFs represent genes of a special functional category, we found that the genes for ribogenesis contribute the major fraction of the ORFs targeted by Asf1 (Table S4)

Summary

Introduction

Organization of the eukaryotic genome into chromatin enables its compaction inside the cell nucleus and concomitant regulation of DNA-related processes [1]. Several mechanisms including histone modifications and ATP-dependent chromatin-remodeling, culminate into an altered chromatin structure [2,3], which renders the cis-acting sites on the DNA accessible to the trans-acting factors They often involve localized chromatin assembly/disassembly via eviction/deposition of the histones by specific histone chaperones, which bind dimers of canonical or variant histones H2A/H2B or H3/H4 [4,5]. AntiSilencing Function 1 (Asf1) is a highly conserved histone chaperone, which assists essentially all aspects of chromatin biology, including genome silencing by evicting/depositing H3/ H4 dimers [8] It participates in regulating histone synthesis [9], maintains supply of histones, interacts with DNA replication machinery at active replication forks, helps progression of replication fork and maintains replisome integrity [10,11,12]. It cooperates with other chaperones like CAF1, HIR, FACT and several other histone-binding factors in replication-coupled or replication-independent chromatin assembly [13,14,15,16]

Methods

Results

Conclusion