Suppressors that make the essential transcription factor Spn1/Iws1 dispensable

Abstract

The conserved process of eukaryotic transcription is regulated by many transcription factors, some of which are essential for viability. Spn1/Iws1 is a conserved protein that is essential for viability and associated with disease. Multiple in vivo studies propose that Spn1 is a transcription factor, while an in vitro study suggests that it also a histone chaperone that binds histones H3 and H4 and regulates nucleosome assembly. Our goal was to determine why Spn1 is essential for viability and what its functions are in vivo. We performed a genetic selection and screen to identify suppressors in Saccharomyces cerevisiae that bypass the inviability caused by a spn1 null mutation (spn1Δ). After mutant isolation, whole-genome sequencing, and genetic analysis, we identified mutations that suppress spn1Δ inviability in eight genes with chromatin-associated functions: SET2, RCO1, RTT109, CHD1, POB3, SPT16, EAF3, and SGF73. We performed genetic analyses to determine how alteration of the first five genes, which regulate histone acetylation, suppress spn1Δ. We discovered that spn1Δ suppression can be achieved by at least two different mechanisms: suppression by loss of Set2 and Rco1 requires the presence of Gcn5-dependent histone H3 acetylation, while suppression by alteration of Rtt109, Chd1 or Pob3 does not. We further studied these two distinct suppression mechanisms by investigating spn1Δ suppression by loss of Set2 and Rtt109. By studying spn1Δ suppression by loss of Set2, we discovered that, surprisingly, Spn1 modestly represses the level of H4 acetylation genome-wide and maintains the occupancy of histones H3 and H4 at the 5’ region of a small subset of highly-transcribed genes. By studying spn1Δ suppression by loss of Rtt109, we found that loss of the acetyltransferase activity of Rtt109 suppresses spn1Δ, while a mutation in the H3K56 target of Rtt109 or loss of the Vps75 histone chaperone, necessary for Rtt109’s activity, only very weakly suppress spn1Δ. Additional studies are required to better understand how loss of Set2 and Rtt109 suppresses spn1Δ. Although further investigation is necessary to understand the cause of Spn1 essentiality, our studies reveal that Spn1 can be bypassed by disrupting multiple chromatin-associated processes and that Spn1 is a regulator of histone acetylation.