# Mechanisms of R-loop-Associated Genome Instability

> **NIH NIH R01** · STANFORD UNIVERSITY · 2023 · $10,871

## Abstract

PROJECT SUMMARY (from parent application)
Replication and transcription are fundamental physiological processes, yet paradoxically they both threaten
genome stability. Replication forks encounter various types of endogenous and exogenous obstacles that keep
them from accurately completing DNA replication. Recent studies suggest that the deleterious effects of
transcription could be a consequence of R-loops, three-stranded nucleic acid structures containing an RNA-DNA
hybrid and a region of single-stranded DNA. R-loops occur throughout the genome of mammalian cells and
regulate various aspects of gene expression, but their accumulation leads to DNA damage, particularly when
cells are undergoing DNA replication. Increasing evidence suggests that conflicts between transcription-
associated R-loops and replication protein complexes are important factors underlying genome instability, but
the specific mechanisms driving this instability are currently unknown. The long-term goal of this research
program is to understand how cells distinguish and resolve regulatory and deleterious R-loops, and how this is
perturbed in human disease. It is hypothesized that R-loops are dynamic structures that become susceptible to
processing when they accumulate, leading to the formation of DNA breaks and ultimately resulting in genome
instability. The object of this application is to define how R-loops are recognized and processed in the cells
throughout the cell cycle, to determine where in the genome processing occurs, and to determine how conflicts
with the replication machinery contribute to R-loop processing. In the first aim, the processing of R-loops by
cellular endonucleases involved in DNA repair will be explored in cells using molecular and cell biological
approaches. In the second aim, the sites and products of R-loop formation and processing will be identified and
mapped. These studies will take advantage of cutting-edge genomic approaches that have been developed to
map the spatial distribution of R-loops and R-loop processing products throughout the genome. Finally, in the
third aim, the impact of an R-loop on collisions between replication and transcription machineries will be studied
in cells. These studies will take advantage of a novel system recently developed to control such collisions and
R-loop formation in the context of the replication fork and recent break-mapping strategies.

## Key facts

- **NIH application ID:** 10806721
- **Project number:** 3R01GM119334-08S1
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** Karlene A Cimprich
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $10,871
- **Award type:** 3
- **Project period:** 2016-07-01 → 2024-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10806721

## Citation

> US National Institutes of Health, RePORTER application 10806721, Mechanisms of R-loop-Associated Genome Instability (3R01GM119334-08S1). Retrieved via AI Analytics 2026-05-28 from https://api.ai-analytics.org/grant/nih/10806721. Licensed CC0.

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