DRIP-seq reveals REXO4 and RNaseH1 work together to process R-loops in the same genomic region across the genome.
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE253653 | GEO | 2026/01/08
REPOSITORIES: GEO
Similar Datasets
Project description:Excessive accumulation of R-loops is thought to be one of the major causes of genome instability. Endonuclease RNaseH1 acts as a classic, common R-loop resolvase to prevent R-loop accumulation genome-widely, whether there is any exonuclease complementing and teaming up with RNaseH1 to more efficiently resolve genome-wide R-loops is worth investigation. Here we identify an exonuclease REXO4, which collaborates with RNaseH1 endonuclease to more efficiently degrade R-loops in an “endo- and exo-cleavage coupling” manner. Specifically, among many members of DEDDh exonuclease family, REXO4 has the most significant effect on R-loop suppression. REXO4 directly degrades RNA strand in R-loop from the end or internal nick through its 3’-5’ exonuclease activity, and also stimulates RNaseH1 endonuclease activity. The genome-wide R-loop regions regulated by REXO4 highly overlap with those regulated by RNaseH1, and REXO4 overexpression counteracts genome-wide R-loop accumulation caused by RNaseH1 deficiency. Furthermore, REXO4-deficient tumors display elevated R-loop mutation burden, and tumor patient-derived mutations in REXO4 enzymatic region all impair R-loop cleavage activity. Interfering with REXO4 increases the sensitivity of tumor cells to alkylating and G4 stabilizing drugs. Therefore, our study proposes a model for highly efficient processing of genome-wide R-loops by endo- and exo-cleavage, which provides additional insights into understanding the link between R-loop associated genome instability and tumors.
2026-01-08 | GSE269749 | GEO
Project description:R-loops represent three-stranded nucleic acid structures comprising an RNA-DNA hybrid and a displaced single-stranded DNA. Deregulation of R-loop dynamics can obstruct DNA transcription and replication processes, compromising genome integrity and contributing to human diseases. Here, we identify EXD2(exonuclease 3′–5′ domain-containing 2) as a crucial R-Loop resolvase. We demonstrate that EXD2, through direct interaction with PARP1 via poly(ADP-ribose) (PAR) polymers, is recruited proximally to R-loops, where it undergoes acetylation by the acetyl-transferase CBP at Lys416. This modification increases EXD2’s binding affinity towards R-loop structures, enabling its transition to and retention on R-loops, despite the rapid turnover of PAR polymers. Once localized, EXD2 acts as an exonuclease, preferentially degrading RNA strands within R-loops to promote their resolution. Consequently, loss of EXD2 results in the intracellular accumulation of R-loops, exacerbating transcription-replication conflicts, and ultimately leading to genomic instability. These findings support a model in which R-loop-triggered PARP1 activation orchestrates EXD2-mediated resolution of R-loops, thereby preserving genome stability.
2025-06-12 | GSE276077 | GEO
Project description:Zika virus (ZIKV) infection in human neural progenitors triggers DNA damage and activates DNA damage response, leading to cell cycle arrest that can retard brain development. Here we link the ZIKV- induced S phase arrest to replication fork stalling and R-loop induction. DRIP-seq reveals that ZIKV infection induces R-loops at specific loci strongly enriched in the interferon-stimulated genes (ISGs). Bru-seq results further indicate that nascent ISGs transcripts are prone to R-loop induction upon infection. Knockout of interferon receptor eliminated the R-loops on ISGs and partially rescued S phase arrest in infected cells. And overexpression of RNaseH1 reduced ZIKV-mediated DNA damage and cell cycle arrest. We conclude that unscheduled expression of ISGs induced by ZIKV alters R-loop homeostasis and perturbs replication fork progression, leading to fork stalling and eventually DNA damage. IFN- dependent R-loop induction represents a previously unknown, nucleic acid-based mechanism for cell cycle arrest.
2025-05-29 | GSE274207 | GEO
Project description:DRIP-seq reveals REXO4 and RNaseH1 work together to process R-loops in the same genomic region across the genome.
| PRJNA1066715 | ENA
Project description:R-loop induces genome instability and regulates gene expression. However, regulatory mechanism of R-loop in stem cell biology remains unclear. Here, we mapped the profiling of R-loops during reprogramming process and revealed that R-loops change prior to gene expression and are mainly accumulated and enriched at terminator of genes. Disrupting homeostasis of R-loops via RNaseH1 loss-of-function blocks reprogramming in a medium independent manner. Interestingly, Sox2 but not other Yamanaka factors overcomes the inhibitory effects of RNaseH1 loss on reprogramming. Sox2 forms a complex with Ddx5 and R-loop in cells and common targets for Sox2 and Ddx5 at R-loops are mainly associated with pluripotent genes. Furthermore, Sox2 inhibits the resolving activity of RNA helicase Ddx5 at R-loops to facilitate reprogramming. Together, these results indicate that the importance of R-loops balance for reprogramming and shed light on the regulation Sox2/Ddx5 on R-loops during reprogramming.
2020-06-12 | GSE125644 | GEO
Project description:R-loops are dynamic three-stranded nucleic acid structures that regulate genome function but can threaten genome stability if not properly resolved. BRCA2, a key player in homologous recombination (HR), also regulates R-loops, though the mechanisms remain unclear. To uncover novel R-loop regulators, we employed a BioID-DSS1 proximity labeling system, leveraging DSS1’s stable interaction with BRCA2 to map its protein interaction network under DNA damage conditions. This approach identified HELZ, a putative RNA helicase, as a new BRCA2-DSS1 interactor. We found that HELZ functions as an RNA-specific R-loop resolvase, revealing a previously unrecognized BRCA2-HELZ axis in R-loop resolution. This work provides new insights into how BRCA2 safeguards genome integrity beyond its canonical role in HR.
2025-12-30 | PXD066766 | Pride
Project description:Numerous chromatin-remodelling factors are regulated by interactions with RNA. However, the contexts in which chromatin-remodelling factors encounter various RNA species, as well as the molecular functions of RNA binding, are poorly understood. Here we show that R-loops, RNA:DNA hybrids consisting of nascent transcripts hybridized to template DNA strands, facilitate embryonic stem cell (ESC) differentiation by modulating the binding of two key chromatin-remodelling enzymes near gene promoters. As previously shown for polycomb repressive complex 2 (PRC2)1-5, we find that the Tip60-p400 histone acetyltransferase and nucleosome-remodelling complex binds in cis to nascent transcripts. However, whereas chromatin binding by PRC2 is broadly inhibited by transcription6, transcription is necessary for maximal Tip60-p400 binding at most target loci. Given that nascent transcripts expressed from GC-rich promoters frequently form R-loops7, we mapped the genomic locations of R-loops in mouse ESCs, observing higher average Tip60-p400 levels and lower average PRC2 levels at genes with R-loops near their transcription start sites (TSSs). Disruption of R-loops by overexpression of RNaseH1 broadly reduced Tip60-p400 and increased PRC2 enrichment, demonstrating R-loops exert both positive and negative effects on chromatin association by regulatory factors. Consistent with these findings, RNaseH1 overexpression results in widespread changes in gene expression and inhibits ESC differentiation, allowing undifferentiated cells to persist for at least two weeks after differentiation is induced. These results define a novel mechanism by which promoter-proximal R-loops modulate chromatin structure to facilitate changes in cellular identity.
2015-09-30 | GSE67581 | GEO
Project description:Transcription can pose a threat to genomic stability through the formation of R-loops that obstruct the progression of replication forks. R-loops are three-stranded nucleic acid structures formed by an RNA-DNA hybrid with a displaced non-template DNA strand. We developed RDProx to identify proteins that regulate R-loops in human cells. RDProx relies on the expression of the hybrid-binding domain (HBD) of Ribonuclease H1 (RNaseH1) fused to the ascorbate peroxidase (APEX2), which permits mapping of the R-loop proximal proteome using quantitative mass spectrometry. We associated R-loop regulation with different cellular proteins and identified a role of the tumor suppressor DEAD box protein 41 (DDX41) in opposing R-loop-dependent genomic instability. Depletion of DDX41 resulted in replication stress, double strand breaks and increased inflammatory signaling. Furthermore, DDX41 opposes accumulation of R-loops at gene promoters and its loss leads to upregulated expression of TGFβ and NOTCH signaling genes. Germline loss-of-function mutations in DDX41 lead to predisposition to acute myeloid leukemia (AML) in adulthood. We propose that accumulation of co-transcriptional R-loops, associated gene expression changes and inflammatory response contribute to the development of familial AML with mutated DDX41.
2021-11-25 | PXD024517 | Pride
Project description:R loops induce transcription-replication (T-R) conflicts, but recent reports have suggested that R-loops are caused by T-R conflicts. Identifying how R loops are generated is crucial to know how transcription compromise genome integrity. Genome-wide analyses of conditional yeast mutants reveal that transcription factors, such as the THO complex. prevents R loop formation in G1 and S-phase, whereas the Sen1 DNA-RNA helicase prevents them only in S-phase. Interestingly, damage accumulates asymmetrically downstream of the RF in sen1 cells but symmetrically in the hpr1 THO mutant. Our results unambiguously indicate that: R loops forms co-transcriptionally independently of DNA replication; THO is a general and cell-cycle independent safeguard against R loops, and Sen1, in contrast to previously believed, is an S-phase-specific R loop resolvase. These conclusions have important implications for the mechanism of R loop formation and the role of other factors reported to impact on R loop homeostasis
2021-07-22 | GSE159870 | GEO
Project description:We report the correlation we found between R-loops and antisense trasncription initiation. Our in vitro data suggests that RNA pol II can initiate transcription off the displaced single stranded DNA from within the R-loop. Therefore we generated Chromatin associated RNA-seq with and without over-expressing RNaseH1 and RDIP-seq (the directional RNA-seq of the RNA moeity from within the S9.6 pull down R-loop) as well as RR-ChIP-seq (the directional RNA-seq of the RNA moeity from within the catalytically dead RNaseH1-GFP GFP pull down R-loop) and confirm the correlation in vivo. We also aligned our findings with ChrCAP-seq (which is is a library enriched for RNA polymerase II capped RNA using chromatin associated RNA as the initial source) and found that capped antisense RNA were sensitive to RNase H1 overexpression.
2019-10-22 | GSE87607 | GEO