# CRISPR-based editing of RNA and cellular mechanisms that govern RNA repair

> **NIH NIH R00** · UNIVERSITY OF FLORIDA · 2024 · $249,000

## Abstract

PROJECT SUMMARY
 CRISPR-based technologies have transformed science by enabling targeted DNA modification. DNA
editing technologies have enriched our mechanistic understanding of DNA repair, and new insights in repair
are frequently used to improve methods for gene editing. However, despite the remarkable achievements in
targeted DNA modifications, RNA repair is understudied, and RNA editing tools are limited. The long-term goal
of this proposal is to understand the molecular mechanisms that govern RNA repair and to develop disruptive
new RNA editing tools for applications in science and medicine. The research proposed here integrates
synergistic efforts to develop CRISPR-based tools for dissecting viral mechanisms of host cell take over and
identify viral RNA repair mechanisms that support acute respiratory syndrome coronavirus (SARS-CoV-2)
replication. In Aim 1, I will repurpose RNA-targeting CRISPR systems for deleting, inserting, and substituting
sequences in viral RNAs. I have designed CRISPR-Cas systems to delete regions of ORF7a in the SARS-
CoV-2 genome and recreate naturally occurring mutations. Based on my previous work, I anticipate that
targeted deletions in ORF7a limit viral suppression of the host interferon response and lead to a replication
defect. Further, tools developed in this application will be used to test emerging viral variants for new
phenotypes. Aim 2 investigates the antagonistic activities of host antiviral nucleases and host RNA ligases in
the replication and evolution of SARS-CoV-2. Aim 3 develops a CRISPR-based RNA capture system to enrich
sequence-specific RNAs from a complex mixture. I will use CRISPR-based enrichment to map RNA
modifications in SARS-CoV-2 viral RNAs and identify molecular signatures associated with interspecies
transitions. Successful completion of the K99 phase of this application will require training in the Biosafety
Level 3 facility, bioinformatics training to identify and annotate CRISPR systems, as well as new competencies
in RNA biochemistry. Collectively, the research and training objectives outlined here establish a solid scientific
foundation that will facilitate my transition to independence.

## Key facts

- **NIH application ID:** 11080122
- **Project number:** 4R00AI171893-03
- **Recipient organization:** UNIVERSITY OF FLORIDA
- **Principal Investigator:** Artem Aleksandrovich Nemudryi
- **Activity code:** R00 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $249,000
- **Award type:** 4N
- **Project period:** 2022-08-17 → 2026-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/11080122

## Citation

> US National Institutes of Health, RePORTER application 11080122, CRISPR-based editing of RNA and cellular mechanisms that govern RNA repair (4R00AI171893-03). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/11080122. Licensed CC0.

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