Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1137835 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Collisions of the transcription and replication machineries on the same DNA strand can pose a significant threat to genomic stability. These collisions occur in part due to the formation of RNA-DNA hybrids termed R-loops, in which a newly transcribed RNA molecule hybridizes with the DNA template strand. This study investigated the role of RAD52, a known DNA repair factor, in preventing collisions by directing R-loop formation and resolution. We show that RAD52 deficiency increases R-loop accumulation, exacerbating collisions and resulting in elevated DNA damage. Furthermore, RAD52's ability to interact with the transcription machinery, coupled with its capacity to facilitate R-loop dissolution, highlights its role in preventing collisions. Lastly, we provide evidence of an increased mutational burden from double-strand breaks at conserved R-loop sites in human tumor samples, which is increased in tumors with low RAD52 expression. In summary, this study underscores the importance of RAD52 in orchestrating the balance between replication and transcription processes to prevent collisions and maintain genome stability.
2024-08-25 | PXD054611 | Pride
Project description:Collisions of transcription and replication machinery on the same DNA strand can pose a significant threat to genomic stability. These collision occur in part due to of RNA-DNA hybrids termed R-loops, in which a newly synthesized RNA molecule hybridizes with the DNA template strand. This study investigated the novel role of RAD52, a known DNA repair factor, in preventing collisions by managing R-loop formation and resolution. We show that RAD52 deficiency increases R-loop accumulation, exacerbating collisions and resulting in elevated DNA damage. Further, RAD52's ability to interact with the transcription machinery, coupled with its capacity to facilitate R-loop dissolution, highlights its role in preventing collisions. Lastly, we provide the first evidence of an increased mutational burden at conserved R-loop sites in human tumor samples. In summary, this study underscores the importance of RAD52 in orchestrating the delicate balance between replication and transcription processes to prevent collisions and maintain genome stability.
2024-07-11 | GSE266483 | GEO
Project description:ATP-dependent chromatin remodelers are commonly mutated in human cancer. Mammalian SWI/SNF complexes comprise three conserved multi-subunit chromatin remodelers (cBAF, ncBAF and PBAF) that share the BRG1 (also known as SMARCA4) subunit responsible for the main ATPase activity. BRG1 is the most frequently mutated Snf2-like ATPase in cancer. Here we have investigated the role of SWI/SNF in genome instability, a hallmark of cancer cells, given its role in transcription, DNA replication and DNA damage repair. We show that depletion of BRG1 increases R-loops and R-loop-dependent DNA breaks, as well as transcription-replication conflicts. BRG1 colocalizes with R-loops and replication fork blocks, as determined by FANCD2 foci, with BRG1 depletion being epistatic to FANCD2 silencing. Our study, extended to other components of SWI/SNF, uncovers a key role of the SWI/SNF complex, in particular cBAF, in helping resolve R-loop-mediated transcription-replication conflicts; thus, unveiling a novel mechanism by which chromatin remodeling protects genome integrity.
2021-05-10 | GSE154631 | GEO
Project description:R-loops are formed when replicative forks collide with the transcriptional machinery and can cause genomic instability. However, it is unclear how R-loops are regulated at transcription-replication conflicts (TRC) sites and how replisome proteins are regulated to prevent R-loop formation or mediate R-loop tolerance. Here, we report that ATAD5, a PCNA unloader, plays dual functions to reduce R-loops both under normal and replication stress conditions. ATAD5 interacts with RNA helicases such as DDX1, DDX5, DDX21 and DHX9 and increases the abundance of these helicases at replication forks to facilitate R-loop resolution. Depletion of ATAD5 or RNA helicases consistently increases R-loops during the S phase and reduces the replication rate, both of which are enhanced by replication stress. In addition to R-loop resolution, ATAD5 prevents the generation of new R-loops behind the replication forks by unloading PCNA which, otherwise, accumulates and persists on DNA, causing a collision with the transcription machinery. Depletion of ATAD5 reduces transcription rates due to PCNA accumulation. Consistent with the role of ATAD5 and RNA helicases in maintaining genomic integrity by regulating R-loops, the corresponding genes were mutated or downregulated in several human tumors.
2021-09-09 | PXD018207 | Pride
Project description:RNA interference (RNAi) plays an important role in the nucleus critical to genome maintenance and heterochromatin silencing. In the fission yeast Schizosaccharomyces pombe, Dicer (Dcr1) also plays a critical role in releasing RNA polymerase II (Pol II) to limit transcription-replication (T-R) stress, but a mechanistic insight is still lacking. Here, we show that Dcr1 resolves T-R conflicts by processing promoter-proximal co-transcriptional R-loops, facilitating replication progression and limiting DNA damage. We found in RNase H-deficient cells, which accumulated pathological R-loops, that further mutating Dcr1 caused hypersensitivity to genotoxic stress. Genetic evidence implicates Dcr1 in regulating nascent transcription, with the helicase domain providing an additional catalytic function in genome stability reminiscent of archaeal helicase homologs involved in replication. In the absence of Dcr1, DNA breaks accumulate around transcription start sites (TSSs), termination sites (TTSs) and pause sites, consistent with replication collision, and DNA replication processivity and speed are impaired in a manner dependent on transcriptional activity and directionality. Argonaute (Ago1) is implicated in dcr1Δ-induced genome instability, as its deletion suppressed the genotoxic stress phenotype of dcr1Δ. Our results demonstrate a novel nuclear function of Dcr1, likely ancestral to the RNAi pathway.
2025-10-30 | GSE278836 | GEO
Project description:RNA interference (RNAi) plays an important role in the nucleus critical to genome maintenance and heterochromatin silencing. In the fission yeast Schizosaccharomyces pombe, Dicer (Dcr1) also plays a critical role in releasing RNA polymerase II (Pol II) to limit transcription-replication (T-R) stress, but a mechanistic insight is still lacking. Here, we show that Dcr1 resolves T-R conflicts by processing promoter-proximal co-transcriptional R-loops, facilitating replication progression and limiting DNA damage. We found in RNase H-deficient cells, which accumulated pathological R-loops, that further mutating Dcr1 caused hypersensitivity to genotoxic stress. Genetic evidence implicates Dcr1 in regulating nascent transcription, with the helicase domain providing an additional catalytic function in genome stability reminiscent of archaeal helicase homologs involved in replication. In the absence of Dcr1, DNA breaks accumulate around transcription start sites (TSSs), termination sites (TTSs) and pause sites, consistent with replication collision, and DNA replication processivity and speed are impaired in a manner dependent on transcriptional activity and directionality. Argonaute (Ago1) is implicated in dcr1Δ-induced genome instability, as its deletion suppressed the genotoxic stress phenotype of dcr1Δ. Our results demonstrate a novel nuclear function of Dcr1, likely ancestral to the RNAi pathway.
2025-10-30 | GSE278849 | GEO
Project description:RNA interference (RNAi) plays an important role in the nucleus critical to genome maintenance and heterochromatin silencing. In the fission yeast Schizosaccharomyces pombe, Dicer (Dcr1) also plays a critical role in releasing RNA polymerase II (Pol II) to limit transcription-replication (T-R) stress, but a mechanistic insight is still lacking. Here, we show that Dcr1 resolves T-R conflicts by processing promoter-proximal co-transcriptional R-loops, facilitating replication progression and limiting DNA damage. We found in RNase H-deficient cells, which accumulated pathological R-loops, that further mutating Dcr1 caused hypersensitivity to genotoxic stress. Genetic evidence implicates Dcr1 in regulating nascent transcription, with the helicase domain providing an additional catalytic function in genome stability reminiscent of archaeal helicase homologs involved in replication. In the absence of Dcr1, DNA breaks accumulate around transcription start sites (TSSs), termination sites (TTSs) and pause sites, consistent with replication collision, and DNA replication processivity and speed are impaired in a manner dependent on transcriptional activity and directionality. Argonaute (Ago1) is implicated in dcr1Δ-induced genome instability, as its deletion suppressed the genotoxic stress phenotype of dcr1Δ. Our results demonstrate a novel nuclear function of Dcr1, likely ancestral to the RNAi pathway.
2025-10-30 | GSE278847 | GEO
Project description:RNA interference (RNAi) plays an important role in the nucleus critical to genome maintenance and heterochromatin silencing. In the fission yeast Schizosaccharomyces pombe, Dicer (Dcr1) also plays a critical role in releasing RNA polymerase II (Pol II) to limit transcription-replication (T-R) stress, but a mechanistic insight is still lacking. Here, we show that Dcr1 resolves T-R conflicts by processing promoter-proximal co-transcriptional R-loops, facilitating replication progression and limiting DNA damage. We found in RNase H-deficient cells, which accumulated pathological R-loops, that further mutating Dcr1 caused hypersensitivity to genotoxic stress. Genetic evidence implicates Dcr1 in regulating nascent transcription, with the helicase domain providing an additional catalytic function in genome stability reminiscent of archaeal helicase homologs involved in replication. In the absence of Dcr1, DNA breaks accumulate around transcription start sites (TSSs), termination sites (TTSs) and pause sites, consistent with replication collision, and DNA replication processivity and speed are impaired in a manner dependent on transcriptional activity and directionality. Argonaute (Ago1) is implicated in dcr1Δ-induced genome instability, as its deletion suppressed the genotoxic stress phenotype of dcr1Δ. Our results demonstrate a novel nuclear function of Dcr1, likely ancestral to the RNAi pathway.
2025-10-30 | GSE278843 | GEO
Project description:RNA interference (RNAi) plays an important role in the nucleus critical to genome maintenance and heterochromatin silencing. In the fission yeast Schizosaccharomyces pombe, Dicer (Dcr1) also plays a critical role in releasing RNA polymerase II (Pol II) to limit transcription-replication (T-R) stress, but a mechanistic insight is still lacking. Here, we show that Dcr1 resolves T-R conflicts by processing promoter-proximal co-transcriptional R-loops, facilitating replication progression and limiting DNA damage. We found in RNase H-deficient cells, which accumulated pathological R-loops, that further mutating Dcr1 caused hypersensitivity to genotoxic stress. Genetic evidence implicates Dcr1 in regulating nascent transcription, with the helicase domain providing an additional catalytic function in genome stability reminiscent of archaeal helicase homologs involved in replication. In the absence of Dcr1, DNA breaks accumulate around transcription start sites (TSSs), termination sites (TTSs) and pause sites, consistent with replication collision, and DNA replication processivity and speed are impaired in a manner dependent on transcriptional activity and directionality. Argonaute (Ago1) is implicated in dcr1Δ-induced genome instability, as its deletion suppressed the genotoxic stress phenotype of dcr1Δ. Our results demonstrate a novel nuclear function of Dcr1, likely ancestral to the RNAi pathway.
2025-10-30 | GSE278840 | GEO