Truncating the spliceosomal 'rope protein' Prp45 results in Htz1 dependent phenotypes

RNA Biol. 2024 Jan;21(1):1-17. doi: 10.1080/15476286.2024.2348896. Epub 2024 May 6.

Abstract

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 PRP45 (prp45(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 HTZ1, and the components of SWR1, INO80, and SAGA complexes represented prominent interactors, with htz1 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 SRB2, VPS75, or HRB1, the most affected cases with transcription-related function. Intron removal from SRB2, but not from the other genes, partly repaired some but not all the growth phenotypes identified in the genetic screen. The interaction of prp45(1-169) and htz1Δ was detectable even in cells with SRB2 intron deleted (srb2Δi). The less truncated variant, prp45(1-330), had a synthetic growth defect with htz1Δ at 16°C, which also persisted in the srb2Δi background. Moreover, htz1Δ enhanced prp45(1-330) dependent pre-mRNA hyper-accumulation of both high and low efficiency splicers, genes ECM33 and COF1, respectively. We conclude that while the expression defects of low expression intron-containing genes contribute to the genetic interactome of prp45(1-169), the genetic interactions between prp45 and htz1 alleles demonstrate the sensitivity of spliceosome assembly, delayed in prp45(1-169), to the chromatin environment.

Keywords: H2A.Z; Synthetic genetic array analysis; chromatin modifiers; co-transcriptional splicing; spliceosome assembly.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Gene Expression Regulation, Fungal
  • Histones / genetics
  • Histones / metabolism
  • Introns*
  • Phenotype*
  • RNA Splicing Factors / genetics
  • RNA Splicing Factors / metabolism
  • RNA Splicing*
  • Saccharomyces cerevisiae Proteins* / genetics
  • Saccharomyces cerevisiae Proteins* / metabolism
  • Saccharomyces cerevisiae* / genetics
  • Saccharomyces cerevisiae* / metabolism
  • Spliceosomes* / genetics
  • Spliceosomes* / metabolism

Substances

  • Saccharomyces cerevisiae Proteins
  • RNA Splicing Factors
  • Histones

Grants and funding

The work of K.A. was funded by The Education for Competitiveness Operational Program (ECOP) and co-financed by the European Social Fund and the state budget of the Czech Republic (CZ.1.07/2.3.00/30.0022). We acknowledge the support of K.A. through the Marie Curie Host fellowship (QLK-CT2000-60036) and the EMBO Short Term Fellowship (ASTF 226-2005) during her stays in P. Sunnerhagen’s Laboratory. The research was further supported by Charles University grants SVV260083, GAUK119710, GAUK441711, and GAUK8214, and the Swedish Cancer Fund (22-2014).