The ribosome assembly gene network is controlled by the feedback regulation of transcription elongation

Nucleic Acids Res. 2017 Sep 19;45(16):9302-9318. doi: 10.1093/nar/gkx529.

Abstract

Ribosome assembly requires the concerted expression of hundreds of genes, which are transcribed by all three nuclear RNA polymerases. Transcription elongation involves dynamic interactions between RNA polymerases and chromatin. We performed a synthetic lethal screening in Saccharomyces cerevisiae with a conditional allele of SPT6, which encodes one of the factors that facilitates this process. Some of these synthetic mutants corresponded to factors that facilitate pre-rRNA processing and ribosome biogenesis. We found that the in vivo depletion of one of these factors, Arb1, activated transcription elongation in the set of genes involved directly in ribosome assembly. Under these depletion conditions, Spt6 was physically targeted to the up-regulated genes, where it helped maintain their chromatin integrity and the synthesis of properly stable mRNAs. The mRNA profiles of a large set of ribosome biogenesis mutants confirmed the existence of a feedback regulatory network among ribosome assembly genes. The transcriptional response in this network depended on both the specific malfunction and the role of the regulated gene. In accordance with our screening, Spt6 positively contributed to the optimal operation of this global network. On the whole, this work uncovers a feedback control of ribosome biogenesis by fine-tuning transcription elongation in ribosome assembly factor-coding genes.

MeSH terms

  • ATP-Binding Cassette Transporters / genetics
  • Adenosine Triphosphatases / genetics
  • Feedback, Physiological
  • Gene Regulatory Networks*
  • Histone Chaperones / genetics*
  • Histone Chaperones / metabolism
  • Mutation
  • Organelle Biogenesis*
  • RNA Processing, Post-Transcriptional
  • RNA, Ribosomal / metabolism
  • Ribosomal Proteins / genetics
  • Ribosomes / genetics*
  • Ribosomes / metabolism
  • Saccharomyces cerevisiae
  • Saccharomyces cerevisiae Proteins / genetics*
  • Saccharomyces cerevisiae Proteins / metabolism
  • Synthetic Lethal Mutations
  • Transcription Elongation, Genetic*
  • Transcriptional Elongation Factors / genetics*
  • Transcriptional Elongation Factors / metabolism
  • Transcriptome

Substances

  • ATP-Binding Cassette Transporters
  • Histone Chaperones
  • RNA, Ribosomal
  • Ribosomal Proteins
  • SPT6 protein, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • Transcriptional Elongation Factors
  • Adenosine Triphosphatases
  • ARB1 protein, S cerevisiae