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

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:

• Synthetic genetic array analysis
• spliceosome assembly
• co-transcriptional splicing
• chromatin modifiers
• H2A.Z

Abbreviations

GO	=	gene ontology
NGI	=	negative genetic interaction
RPG	=	ribosomal protein gene
Subset_45	=	down regulated differentially scored transreads

Acknowledgments

We are grateful to the Boone Lab for the SGA data analyses. We thank members of the Sunnerhagen Lab for stimulating discussions. We thank Eva Krellerová for expert technical assistance and Dr. Marian Novotný for the molecular visualizations in Figure 1.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The authors confirm that the data supporting the findings of this study are available within the article and its supplementary materials.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/15476286.2024.2348896

Additional information

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).