Chromatin Remodeling Factors Isw2 and Ino80 Regulate Chromatin, Replication, and Copy Number of the Saccharomyces cerevisiae Ribosomal DNA Locus

Abstract

In the budding yeast Saccharomyces cerevisiae, ribosomal RNA genes are encoded in a highly repetitive tandem array referred to as the ribosomal DNA (rDNA) locus. The yeast rDNA is the site of a diverse set of DNA-dependent processes, including transcription of ribosomal RNAs by RNA polymerases I and III, transcription of noncoding RNAs by RNA polymerase II, DNA replication initiation, replication fork blocking, and recombination-mediated regulation of rDNA repeat copy number. All of this takes place in the context of chromatin, but little is known about the roles played by ATP-dependent chromatin remodeling factors at the yeast rDNA. In this work, we report that the Isw2 and Ino80 chromatin remodeling factors are targeted to this highly repetitive locus. We characterize for the first time their function in modifying local chromatin structure, finding that loss of these factors decreases the fraction of actively transcribed 35S ribosomal RNA genes and the positioning of nucleosomes flanking the ribosomal origin of replication. In addition, we report that Isw2 and Ino80 promote efficient firing of the ribosomal origin of replication and facilitate the regulated increase of rDNA repeat copy number. This work significantly expands our understanding of the importance of ATP-dependent chromatin remodeling for rDNA biology.

Mec1 Is Activated at the Onset of Normal S Phase by Low-dNTP Pools Impeding DNA Replication

“…3C). This result was further confirmed by plotting Ddc2 and -H2A enrichment at origins relative to RNAPIII (Rpo31) levels (Cutler et al, 2018) (Fig. S3B).…”

The biogenesis and function of nucleosome arrays

“…Comparable effects were observed after NHP10 deletion in transcribing WT and TKO cells (Supplementary Fig. 5e, g, k) 40 and after deletion of the 300 N-terminal amino acid residues of the Ino80 ATPase subunit (Supplementary Fig. 5f, h, k ).…”

Regulation of Gene Expression and Replication Initiation by Non‐Coding Transcription: A Model Based on Reshaping Nucleosome‐Depleted Regions

“…In this model we propose that nucleosome repositioning probably occurs through nucleosome sliding, and we hypothesize that chromatin remodelers can regulate this process. In agreement with this idea, a recent publication indicates that loss of Ino80 and Isw2 chromatin remodelers leads to closure of the ARSs associated with ribosomal DNA and defects in ribosomal DNA replication . Moreover, the SWI/SNF remodeling complex has already been proposed to be important for replication initiation .…”