# Ribothrypsis: mechanisms and implications for gene expression regulation

> **NIH NIH R01** · UNIVERSITY OF PENNSYLVANIA · 2022 · $325,000

## Abstract

Ribothrypsis: mechanisms and implications for gene expression regulation
PROJECT SUMMARY / ABSTRACT
 Messenger RNAs transmit the genetic information that dictates protein production and are a
nexus for numerous pathways that regulate gene expression. The prevailing view of canonical mRNA
decay is that it is mediated by deadenylation and decapping followed by exonucleolysis from the 3'
and 5' ends. We recently described ribothrypsis, an endonucleolytic pathway of cotranslational mRNA
decay, mediated by ribosome-phased cleavages of the mRNA as it exits the ribosome channel. We posit
that ribothrypsis is a unifying and evolutionary conserved mechanism that underlies cotranslational
decay of all mRNAs: canonical and aberrant mRNAs that degrade via surveillance mechanisms, such
as No-Go Decay (NGD) or Non-Stop Decay (NSD). In that sense, ribothrypsis may be viewed as
“NGD/NSD on steroids”; or conversely NGD/NSD may be viewed as a subset of ribothrypsis. The
central integrator of mRNA decay in ribothrypsis is the translating ribosome that under certain
conditions activates or recruits an unknown endonuclease (ribothrypsin) to cleave the mRNA as it exits
the ribosome. In this proposal, we will investigate the impact of ribothrypsis in gene expression
analysis; and mechanisms and impact of ribothrypsis in gene expression regulation. We discovered
that endogenously generated mRNA fragments represent a sizable fraction of the total mRNA pool.
This finding complicates interpretation of results obtained with all current methods that assay mRNAs,
which do not take ribothrypsis into account, and necessitates the development of new experimental
and computational tools for RNA sequencing, which we will develop in Aim1. In Aim2, we will
investigate ribothrypsis triggers and unexpected roles of ribothrypsis in gene expression regulation via
upstream Open Reading Frames (uORFs), and in the decay of long noncoding RNAs (lncRNAs). We
will also study molecular mechanisms of ribothrypsis in vitro and in vivo and identify ribothrypsin.

## Key facts

- **NIH application ID:** 10413119
- **Project number:** 5R01GM133154-04
- **Recipient organization:** UNIVERSITY OF PENNSYLVANIA
- **Principal Investigator:** ZISSIMOS MOURELATOS
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $325,000
- **Award type:** 5
- **Project period:** 2019-09-15 → 2024-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10413119

## Citation

> US National Institutes of Health, RePORTER application 10413119, Ribothrypsis: mechanisms and implications for gene expression regulation (5R01GM133154-04). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10413119. Licensed CC0.

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