An essential role for the Ino80 chromatin remodeling complex in regulation of gene expression during cellular quiescence

Abstract

Cellular quiescence is an important physiological state both in unicellular and multicellular eukaryotes. Quiescent cells are halted for proliferation and stop the cell cycle at the G0 stage. Using fission yeast as a model organism, we have previously found that several subunits of a conserved chromatin remodeling complex, Ino80C (INOsitol requiring nucleosome remodeling factor), are required for survival in quiescence. Here, we demonstrate that Ino80C has a key function in the regulation of gene expression in G0 cells. We show that null mutants for two Ino80C subunits, Iec1 and Ies2, a putative subunit Arp42, a null mutant for the histone variant H2A.Z, and a null mutant for the Inositol kinase Asp1 have very similar phenotypes in quiescence. These mutants show reduced transcription genome-wide and specifically fail to activate 149 quiescence genes, of which many are localized to the subtelomeric regions. Using spike in normalized ChIP-seq experiments, we show that there is a global reduction of H2A.Z levels in quiescent wild-type cells but not in iec1∆ cells and that a subtelomeric chromosome boundary element is strongly affected by Ino80C. Based on these observations, we propose a model in which Ino80C is evicting H2A.Z from chromatin in quiescent cells, thereby inactivating the subtelomeric boundary element, leading to a reorganization of the chromosome structure and activation of genes required to survive in quiescence.

Engineering heterothallic strains in fission yeast

“…1A). This strain has been widely used to investigate various processes, including the mechanisms underlying MTS (Heim, 1990; Klar et al, 1991; Yamada-Inagawa et al, 2007; Bähler et al, 1993; Osman et al, 2003; Villahermosa et al, 2017; Zahedi et al, 2023). In these cells, the sequence required to induce the imprint is deleted, abolishing their capacity to undergo MTS.…”

Engineering heterothallic strains in fission yeast

“…One of the heterothallic mutants previously isolated, referred to as the h− Msmt-0 strain, harbors a 263 bp deletion that removes part of the H1 recombination sequence of the mat1 locus as well as a downstream fragment (Styrkársdóttir et al, 1993) (Figure 1a). This strain has been widely used to investigate various processes, including the mechanisms underlying MTS (Bähler et al, 1993;Heim, 1990;Klar et al, 1991;Osman et al, 2003;Villahermosa et al, 2017;Yamada-Inagawa et al, 2007;Zahedi et al, 2023). In these cells, the sequence required for the formation of the imprint is deleted, abolishing their capacity to undergo productive MTS (i.e., a recombination event that results in a change in mating type).…”