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RNA metabolism in response to cellular stress

Principal Supervisor: Dr Pawel Grzechnik, School of Biosciences

Co-supervisor: Dr Saverio Brogna, School of Biosciences

PhD project title: RNA metabolism in response to cellular stress

University of Registration: University of Birmingham

Project outline:

The aim of the project is to understand roles for mRNA processing during the stress response in eukaryotic cells.

Exposure to acute stress reduces cell viability or fitness and therefore immediate adaption is crucial for cell survival. Such rapid change of cell physiology requires coordinate and precise alteration of gene expression. One of the most dramatic transformations happens at the transcriptional level. Transcription of large number of genes is shut down while stress responders are activated and robustly transcribed. Synthesized stress-induced mRNAs are not subjected to quality control [1] and are exported to the cytoplasm via specific, promoter-dependent mechanisms [2]. Such unusual mRNA biology of stress-induced genes enables cells to immediately tailor protein production and allows them to survive extreme conditions.

In eukaryotic cells mRNA 3' end processing, which involves endonucleolytic cleavage followed by the addition of the poly(A) tail, is one of the most important steps in gene expression regulation [3]. For example, the 3’ end maturation complex responds to cellular stimuli and decides about the nuclear and cytoplasmic fate of mRNA through the generation of distinct 3’ end termini. Furthermore, a poly(A) tail protects mRNA from degradation and promotes translation. The function of the cleavage and polyadenylation machinery extends far beyond simple maturation of mRNA ends.

Recent studies reveal that cellular stress such as osmotic shock, viral infections or carcinogenesis can all affect mRNA 3’ end formation [4-6]. Thus, the goal of this project is to employ a wide range of high-throughput and classic RNA analysis in a model organism Saccharomyces cerevisiae, to investigate how the mRNA 3’ processing regulates expression of stress-induced genes and contributes to the cellular stress response.


  • Zander, G., et al., mRNA quality control is bypassed for immediate export of stress-responsive transcripts. Nature, 2016.
  • Zid, B.M. and E.K. O'Shea, Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast. Nature, 2014. 514(7520): p. 117-21.
  • Proudfoot, N.J., Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut. Science, 2016. 352(6291): p. aad9926.
  • Vilborg, A., et al., Widespread Inducible Transcription Downstream of Human Genes. Mol Cell, 2015. 59(3): p. 449-61.
  • Rutkowski, A.J., et al., Widespread disruption of host transcription termination in HSV-1 infection. Nat Commun, 2015. 6: p. 7126.
  • Grosso, A.R., et al., Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma. Elife, 2015. 4.

BBSRC Strategic Research Priority: Molecules, Cells and Systems

Techniques that will be undertaken during the project:

  • High-throughput RNA analyses:
  • Total and nuclear RNA sequencing (RNA-seq)
  • Transient transcriptome sequencing (TT-seq)
  • Classic RNA analyses:
  • Northern blotting
  • Reverse transcription followed by quantitative PCR (RT-qPCR; real-time PCR)
  • Chromatin immunoprecipitation (ChIP and ChIP-seq)
  • Western blotting
  • Cell sorting
  • Protein depletion approaches: Anchor Away and Degron-tag techniques
  • Fluorescent microscopy
  • Cloning, yeast strain constructions: tagging, gene deletions
  • Survival assays

Contact: Dr Pawel Grzechnik, School of Biosciences