Genetic interaction mapping reveals a role for the SWI/SNF nucleosome remodeler in spliceosome activation in fission yeast.

Kristin L Patrick,Jesse J Lipp,Michael Shales,Assen Roguev,Kelly E Nissen,Christine Guthrie,Nevan J Krogan,Jiewei Xu,Colm J Ryan,David Bentley

doi:10.1371/journal.pgen.1005074

Abstract

Although numerous regulatory connections between pre-mRNA splicing and chromatin have been demonstrated, the precise mechanisms by which chromatin factors influence spliceosome assembly and/or catalysis remain unclear. To probe the genetic network of pre-mRNA splicing in the fission yeast Schizosaccharomyces pombe, we constructed an epistatic mini-array profile (E-MAP) and discovered many new connections between chromatin and splicing. Notably, the nucleosome remodeler SWI/SNF had strong genetic interactions with components of the U2 snRNP SF3 complex. Overexpression of SF3 components in ΔSWI/SNF cells led to inefficient splicing of many fission yeast introns, predominantly those with non-consensus splice sites. Deletion of SWI/SNF decreased recruitment of the splicing ATPase Prp2, suggesting that SWI/SNF promotes co-transcriptional spliceosome assembly prior to first step catalysis. Importantly, defects in SWI/SNF as well as SF3 overexpression each altered nucleosome occupancy along intron-containing genes, illustrating that the chromatin landscape both affects—and is affected by—co-transcriptional splicing.

Highlights

Recent work has uncovered extensive crosstalk amongst chromatin, transcription and RNA processing machineries
It has recently become apparent that most introns are removed from pre-mRNA while the transcript is still engaged with RNA polymerase II (RNAPII)
The SWI/SNF remodeling complex is typically thought to activate gene expression by relieving barriers to polymerase elongation imposed by nucleosomes

Summary

Introduction

Recent work has uncovered extensive crosstalk amongst chromatin, transcription and RNA processing machineries. Nucleosomal contacts with DNA are constantly modulated by ATP-dependent chromatin remodeling complexes (e.g. SWI/SNF, Ino, and RSC), that function to deposit, remove, and/or slide nucleosomes [4]. Primarily studied in the context of regulation of transcription, nucleosome remodeling is likely to influence splicing in numerous ways: altering RNA polymerase II elongation rates, promoting RNAPII pauses, and/or recruiting the spliceosome to chromatin via protein-protein interactions (Reviewed in [5]). Most of what we know about co-transcriptional splicing regulation comes from studies of alternative splicing in mammals, in which histone modifications (e.g. H3K36me3 [6]) and chromatin remodelers (e.g. SWI/SNF [7,8]) have been shown to modulate exon skipping (reviewed in [9,10]). While there is good evidence that splicing can direct histone H3K36 tri-methylation [11,12] and H3K4 tri-methylation [13], we still know very little about how splicing may more broadly influence chromatin states

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Conclusion