Truncating the spliceosomal ‘rope protein’ Prp45 results in Htz1 dependent phenotypes

Spliceosome assembly contributes an important but incompletely understood aspect of splicing regulation. Prp45 is a yeast splicing factor which runs as an extended fold through the spliceosome, and which may be important for bringing its components together. We performed a whole genome analysis of the genetic interaction network of the truncated allele of <i>PRP45</i> (<i>prp45</i>(1–169)) using synthetic genetic array technology and found chromatin remodellers and modifiers as an enriched category. In agreement with related studies, H2A.Z-encoding <i>HTZ1</i>, and the components of SWR1, INO80, and SAGA complexes represented prominent interactors, with <i>htz1</i> conferring the strongest growth defect. Because the truncation of Prp45 disproportionately affected low copy number transcripts of intron-containing genes, we prepared strains carrying intronless versions of <i>SRB2</i>, <i>VPS75</i>, or <i>HRB1</i>, the most affected cases with transcription-related function. Intron removal from <i>SRB2</i>, but not from the other genes, partly repaired some but not all the growth phenotypes identified in the genetic screen. The interaction of <i>prp45</i>(1–169) and <i>htz1</i>Δ was detectable even in cells with <i>SRB2</i> intron deleted (<i>srb2</i>Δi). The less truncated variant, <i>prp45</i>(1–330), had a synthetic growth defect with <i>htz1</i>Δ at 16°C, which also persisted in the <i>srb2</i>Δi background. Moreover, <i>htz1</i>Δ enhanced <i>prp45</i>(1–330) dependent pre-mRNA hyper-accumulation of both high and low efficiency splicers, genes <i>ECM33</i> and <i>COF1</i>, respectively. We conclude that while the expression defects of low expression intron-containing genes contribute to the genetic interactome of <i>prp45</i>(1–169), the genetic interactions between <i>prp45</i> and <i>htz1</i> alleles demonstrate the sensitivity of spliceosome assembly, delayed in <i>prp45</i>(1–169), to the chromatin environment.