RNA Repair

RNA repair involves three sequential actvities:

  1. Spontaneous or enzyme-catalyzed RNA cleavage (“damage”).
  2. Remodeling of new RNA termini by RNA end modifying enzymes (“healing”).
  3. Rejoining of the broken ends by an RNA ligase (“sealing”).

RNA repair catalyzes rejoining of RNA fragments generated during tRNA splicing and a unique mRNA processing event that regulates the unfolded protein response. There are hints that RNA repair may play a bigger role in gene expression. For example, many proteins of unknown function tend to co-evolve with RNA repair genes. And there are suggestions that damaged ribosomes can be repaired, presumably to mitigate the cost of building a new ribosome.

We are broadly interested in understanding how cells use RNA repair to remodel the transcriptome.

tRNA splicing

We exploited a previously developed strategy to bypass the essential function of RNA repair enzymes in budding yeast. Cells that express “pre-spliced” tRNAs are viable in the absence of the tRNA ligase and 2´-phosphotransferase. We are using these cells to understand tRNA processing and translational fidelity.

Unfolded protein response

The unfolded protein reponse (UPR) is a conserved pathway that increases the protein folding capacity of the endoplasmic reticulum during periods of protein folding stress. In budding yeast, the UPR is activated by the transmembrane kinase/endoribonucuelase Ire1, which liberates an intron from the HAC1 pre-mRNA. Ligation of the exons leads to translation of the Hac1 transcription factor, which moves to the nucleus and upregulates hundreds of stress-reponse genes.

Using the RNA repair mutants, we uncovered new regulatory points during HAC1 splicing in the unfolded protein response.

New substrates of RNA repair

We are conducting targeted and genome-wide searches for other targets of RNA repair. Such studies could provide new insights into the role of RNA repair in cellular physiology.

RNA-seq methods to study RNA repair

We previously developed methods to capture the 2´,3´-cyclic phosphate and 5´-OH products of RNA decay and have used these broadly to study spontaneous and enzyme-catalyzed RNA cleavage.

Funding

This work is funded by an NIH MIRA grant (R35 GM119550).