Fission Yeast Iec1-Ino80-Mediated Nucleosome Eviction Regulates Nucleotide and Phosphate Metabolism

Abstract

Ino80 is an ATP-dependent nucleosome-remodeling enzyme involved in transcription, replication, and the DNA damage response. Here, we characterize the fission yeast Ino80 and find that it is essential for cell viability. We show that the Ino80 complex from fission yeast mediates ATP-dependent nucleosome remodeling in vitro. The purification of the Ino80-associated complex identified a highly conserved complex and the presence of a novel zinc finger protein with similarities to the mammalian transcriptional regulator Yin Yang 1 (YY1) and other members of the GLI-Krüppel family of proteins. Deletion of this Iec1 protein or the Ino80 complex subunit arp8, ies6, or ies2 causes defects in DNA damage repair, the response to replication stress, and nucleotide metabolism. We show that Iec1 is important for the correct expression of genes involved in nucleotide metabolism, including the ribonucleotide reductase subunit cdc22 and phosphate-and adenineresponsive genes. We find that Ino80 is recruited to a large number of promoter regions on phosphate starvation, including those of phosphate-and adenine-responsive genes that depend on Iec1 for correct expression. Iec1 is required for the binding of Ino80 to target genes and subsequent histone loss at the promoter and throughout the body of these genes on phosphate starvation. This suggests that the Iec1-Ino80 complex promotes transcription through nucleosome eviction.The structure of chromatin is modulated by chromatin-remodeling factors, such as histone-modifying enzymes and ATP-dependent chromatin-remodeling complexes (7,35,45,54). The latter are usually multisubunit protein complexes containing an ATPase from the SWI2/SNF2 superfamily, which uses the energy derived from ATP hydrolysis to disrupt histone-DNA interactions (6,13,26).Ino80 is a member of this SWI2/SNF superfamily and is the catalytic subunit of the Ino80 chromatin-remodeling complex (65). Initially characterized in budding yeast (Saccharomyces cerevisiae), the Ino80 complex plays a central role in DNA-mediated processes, such as DNA doublestrand break repair, homologous recombination, and the regulation of the DNA damage cell cycle checkpoint response, chromosomal-DNA replication, and transcription (5,10,18,23,24,38,39,52,56,57,65,69,74,76,80,82; reviewed in reference 4). Ino80 complexes purified from budding yeast and mammalian cells contain core subunits, which are conserved across species, as well as species-specific proteins (36,65). In budding yeast, the core Ino80 complex is composed of INO80, ARP5, ARP8, ARP4, RVB1, RVB2, IES2, and IES6 (63,65). The actin-like proteins ARP5 and ARP8 are unique to the Ino80 complex and are required for an active complex in budding yeast (38,63). ARP4 plays a role in the response to DNA damage in budding yeast and is also a member of the chromatin-remodeling complex SWR1 and the histone acetyltransferase complex NuA4 (16,42,52,76). The Rvb1 and Rvb2 proteins (also called Pontin/Tip49 and Reptin/Tip48, respectively, in mammalian cells) are AAA ϩ ATPases related to the Hol...

Multiple modes of regulation of the human Ino80 SNF2 ATPase by subunits of the INO80 chromatin-remodeling complex

“…Our findings identify the Ies2 protein as a potent activator of Ino80 catalytic activity and bring to light an important role for the Ies6 and Arp5 proteins in nucleosome recognition and binding. These observations may provide a mechanistic basis for previous evidence that Ies2, Arp5, and Ies6 contribute to various Ino80-dependent nuclear transactions in fungi and in higher eukaryotes (4,10,(22)(23)(24)(25).…”

“…T he evolutionarily conserved Ino80 SNF2 family ATPase is the catalytic subunit of the multisubunit INO80 chromatin-remodeling complex (INO80) with functions in transcription, DNA replication, and DNA repair (1)(2)(3)(4)(5)(6)(7)(8). Although it is well established that SNF2 family ATPases have evolved to play critical roles as ATPdependent motors that drive many types of chromatin transactions, in most cases how their intrinsic catalytic activities are regulated by their diverse array of associated proteins is poorly understood.…”

Structure of Yin Yang 1 Oligomers That Cooperate with RuvBL1-RuvBL2 ATPases

“…1A). Putative structural and functional homologs in Schizosaccharomyces pombe (Iec1) (9) and Drosophila melanogaster (PHO (pleiohomeotic) and PHOL (pleiohomeotic-like)) (10) have been studied. YY1 hallmark is four C 2 H 2 -type zinc finger motifs located at its C terminus (residues 298 -397), responsible for the sequence-specific recognition of a consensus DNA sequence (5Ј-(C/g/a)(G/t)(C/t/a)CATN(T/a)(T/g/c)-3Ј, where the uppercase letters indicate the preferred base for each position) being the most frequent ACAT and CCAT.…”

Subunit Organization of the Human INO80 Chromatin Remodeling Complex

“…Both human and Drosophila INO80 complexes were found to include the GLI-Kruppel family zinc finger transcription factor YY1 (referred to as Pleiohomeotic (PHO) in flies) (6,8,12). Although YY1 and PHO were initially thought to be metazoanspecific subunits of the INO80 complex, the recently characterized Schizosaccharomyces pombe INO80 complex contains a GLIKruppel family zinc finger protein referred to as Iec1 (13), which may be orthologous to YY1 and PHO.…”