RNA-Seq analysis of INO80 complex deletion mutants

ATP-dependent chromatin remodeling complexes are essential for transcription regulation, and yet it is unclear how these multisubunit complexes coordinate their activities to facilitate diverse transcriptional responses. In this study, we found that the conserved Arp5 and Ies6 subunits of the Saccharomyces cerevisiae INO80 chromatin-remodeler form an abundant and distinct subcomplex in vivo and stimulate INO80-mediated activity in vitro. Moreover, our genomic studies reveal that the relative occupancy of Arp5-Ies6 correlates with nucleosome positioning at transcriptional start sites and expression levels of >1,000 INO80- regulated genes. Notably, these genes are significantly enriched in energy metabolism pathways. Specifically, arp5d, ies6d, and ino80d mutants demonstrate decreased expression of genes involved in glycolysis and increased expression of genes in the oxidative phosphorylation pathway. Deregulation of these metabolic pathways results in constitutively elevated mitochondrial potential and oxygen consumption. Our results illustrate the dynamic nature of the INO80 complex assembly and demonstrate for the first time that a chromatin remodeler regulates glycolytic and respiratory capacity, thereby maintaining metabolic stability. Overall design: RNA-Seq was performed on two biological replicates of each of the following yeast strains: WT (BY4741), ino80del, arp8del, arp5del, and ies6del.

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Yao W, King DA, Beckwith SL, Gowans GJ, Yen K, Zhou C, Morrison AJ