The yeast SR-like protein Npl3 links chromatin modification to mRNA processing

PLoS Genet. 2012;8(11):e1003101. doi: 10.1371/journal.pgen.1003101. Epub 2012 Nov 29.

Abstract

Eukaryotic gene expression involves tight coordination between transcription and pre-mRNA splicing; however, factors responsible for this coordination remain incompletely defined. Here, we explored the genetic, functional, and biochemical interactions of a likely coordinator, Npl3, an SR-like protein in Saccharomyces cerevisiae that we recently showed is required for efficient co-transcriptional recruitment of the splicing machinery. We surveyed the NPL3 genetic interaction space and observed a significant enrichment for genes involved in histone modification and chromatin remodeling. Specifically, we found that Npl3 genetically interacts with both Bre1, which mono-ubiquitinates histone H2B as part of the RAD6 Complex, and Ubp8, the de-ubiquitinase of the SAGA Complex. In support of these genetic data, we show that Bre1 physically interacts with Npl3 in an RNA-independent manner. Furthermore, using a genome-wide splicing microarray, we found that the known splicing defect of a strain lacking Npl3 is exacerbated by deletion of BRE1 or UBP8, a phenomenon phenocopied by a point mutation in H2B that abrogates ubiquitination. Intriguingly, even in the presence of wild-type NPL3, deletion of BRE1 exhibits a mild splicing defect and elicits a growth defect in combination with deletions of early and late splicing factors. Taken together, our data reveal a connection between Npl3 and an extensive array of chromatin factors and describe an unanticipated functional link between histone H2B ubiquitination and pre-mRNA splicing.

Publication types

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

MeSH terms

  • Chromatin Assembly and Disassembly / genetics*
  • Endopeptidases / genetics
  • Endopeptidases / metabolism
  • Histones / genetics
  • Histones / metabolism
  • Nuclear Proteins* / genetics
  • Nuclear Proteins* / metabolism
  • RNA Precursors / genetics
  • RNA Precursors / metabolism
  • RNA Processing, Post-Transcriptional / genetics
  • RNA Splicing*
  • RNA-Binding Proteins* / genetics
  • RNA-Binding Proteins* / metabolism
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae Proteins* / genetics
  • Saccharomyces cerevisiae Proteins* / metabolism
  • Trans-Activators / genetics
  • Trans-Activators / metabolism
  • Transcription, Genetic*
  • Ubiquitin-Conjugating Enzymes / genetics
  • Ubiquitin-Conjugating Enzymes / metabolism
  • Ubiquitination / genetics

Substances

  • Bre1 protein, S cerevisiae
  • Histones
  • NPL3 protein, S cerevisiae
  • Nuclear Proteins
  • RNA Precursors
  • RNA-Binding Proteins
  • SAGA complex, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • Trans-Activators
  • RAD6 protein, S cerevisiae
  • Ubiquitin-Conjugating Enzymes
  • Endopeptidases
  • UBP8 protein, S cerevisiae