# R-loop-induced DNA damage during immunoglobulin class switch recombination

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA AT DAVIS · 2021 · $32,250

## Abstract

Project Abstract/Summary for the parent grant
Class switch recombination (CSR) is a genetic process where a B cell switches antibody isotype production
through site-specific intra-chromosomal DNA rearrangement stimulated by the formation of DNA double-strand
breaks (DSBs) at the immunoglobulin heavy chain (IgH) locus. Recurrent oncogenic translocations involving
IgH distinguish many human lymphoid malignancies; these translocations originate from mis-repaired DNA
DSBs generated during normal lymphocyte development. DSBs are normally repaired by the non-homologous
end-joining (NHEJ) and alternative-end joining (alt-EJ) DNA repair pathways. During CSR, DSB formation is
highly regulated involving a complex interplay of transcriptional activation, protein recruitment and chromatin
reorganization. Understanding the factors regulating DSB formation and repair has a high impact on
lymphomagenesis. R loops are three stranded RNA:DNA hybrid structures formed at IgH during CSR. While R
loops are implicated in promoting DSB formation at IgH, their role in class switch recombination remains
undefined. To determine how persistent R loops impede DNA repair during CSR, and the role R loop
metabolism plays in suppressing genome instability at IgH. we bred mice lacking two proteins involved in R
loop removal: the helicase Senataxin (Setx-/-) which unwinds R loops; and Rnaseh2b is defective for the
RNase H2 nuclease that specifically digests the RNA component of R loops (Rrnaseh2bf/fCD19cre).
We find that B cells from Setx-/-Rnaseh2bf/f mice are proficient at class switch recombination, and contain high
levels of unrepaired breaks and chromosome fusions at IgH. We hypothesize that persistent R loops block
efficient DNA repair by non-homologous end joining at the immunoglobulin heavy chain locus during
class switch recombination, leading to persistent, unrepaired breaks. We will functionally dissect the
consequences of aberrant R loop formation on DNA repair and chromosome fusions arising during CSR in
Setx-/-, Rnaseh2bf/f, and Setx-/- Rnaseh2bf/f cells (Aim 1). To define the impact persistent R loops have on
NHEJ, we will characterize DNA repair protein recruitment in Setx-/-, Rrnaseh2bf/f, and Setx-/- Rrnaseh2bf/f cells
(Aim 2). We will also identify genomic loci involved in IgH translocations using high-throughput genome-wide
translocation sequencing (HTGTS-Seq). Finally, we will define the molecular pathways driving the frequent
chromosome fusions observed in Setx-/- Rnaseh2bf/f cells (Aim 3). Our work will define how persistent R loops
interfere with class switch recombination, leading to unrepaired breaks, and will uncover the molecular
mechanisms promoting chromosome fusions at IgH. We are in the second year of this award which will run
until 7/31/2024.

## Key facts

- **NIH application ID:** 10294876
- **Project number:** 3R01GM134537-02S1
- **Recipient organization:** UNIVERSITY OF CALIFORNIA AT DAVIS
- **Principal Investigator:** Jacqueline Barlow
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $32,250
- **Award type:** 3
- **Project period:** 2019-08-05 → 2024-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10294876

## Citation

> US National Institutes of Health, RePORTER application 10294876, R-loop-induced DNA damage during immunoglobulin class switch recombination (3R01GM134537-02S1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10294876. Licensed CC0.

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