Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1219134 | 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:Fine-tuning DNA replication and transcription co-occurrence is vital to avoid collisions between their machineries. This is especially relevant near promoters, where RNAPII initiates transcription and often arrests, forming R-loops. Arrested RNAPII poses a roadblock for DNA replication, which evolutionarily initiates near promoters. The mechanisms that salvage arrested RNAPII during elongation to avoid conflicts with incoming replisomes remain unaddressed. In this study, employing genome-wide and proteomic approaches, we identify and characterize CFAP20 as part of a protective pathway that rescues arrested RNAPII in promoter-proximal regions, diverting it from the path of co-directional replisomes. CFAP20-deficient cells accumulate R-loops specifically near promoters, displaying defects in replication origin firing and fork progression. Co-depletion of the Mediator coactivator complex or removal of RNAPII engaged with R-loops rescues these replication phenotypes. Therefore, we propose that CFAP20 salvages arrested RNAPII under conditions of high Mediator-driven transcription to promote RNAPII elongation, thereby preventing collisions with co-directional replisomes.
2025-05-20 | GSE266571 | GEO
Project description:Fine-tuning DNA replication and transcription co-occurrence is vital to avoid collisions between their machineries. This is especially relevant near promoters, where RNAPII initiates transcription and often arrests, forming R-loops. Arrested RNAPII poses a roadblock for DNA replication, which evolutionarily initiates near promoters. The mechanisms that salvage arrested RNAPII during elongation to avoid conflicts with incoming replisomes remain unaddressed. In this study, employing genome-wide and proteomic approaches, we identify and characterize CFAP20 as part of a protective pathway that rescues arrested RNAPII in promoter-proximal regions, diverting it from the path of co-directional replisomes. CFAP20-deficient cells accumulate R-loops specifically near promoters, displaying defects in replication origin firing and fork progression. Co-depletion of the Mediator coactivator complex or removal of RNAPII engaged with R-loops rescues these replication phenotypes. Therefore, we propose that CFAP20 salvages arrested RNAPII under conditions of high Mediator-driven transcription to promote RNAPII elongation, thereby preventing collisions with co-directional replisomes.
2025-05-28 | GSE297966 | GEO
Project description:Yeast Sen1Senataxin is a RNA/DNA helicase that preserves replication forks across RNA Polymerase II-transcribed genes by counteracting RNA:DNA hybrids accumulation. We show that in Sen1-depleted cells early forks clashing head-on with transcription halt, and impair progression of sister forks within the same replicon. Unsolved replication-transcription collisions trigger the local firing of dormant origins that rescue arrested forks. In sen1 mutants the MRX and Mrc1/Ctf4-complexes protect those forks clashing with transcription by preventing genotoxic fork-resection events mediated by the Exo1 nuclease. Hence, sister forks within the same replicon remain coupled when one of the two forks halts. This is different when forks encounter double strand breaks. Moreover, the local firing of dormant origins is not prevented by checkpoint activation but depends on delayed adjacent forks. Furthermore, a productive head-on clash between replication and transcription requires the tuning of origin firing and coordination between Sen1, the MRX and Mrc1/Ctf4-complexes and Exo1.
2017-10-11 | GSE97046 | GEO
Project description:Head-on collisions between the DNA replication machinery and RNA polymerase are potent genotoxic events leading to replication fork stalling, R-loop formation, and DNA breaks. Current models suggest that head-on collisions are avoided through replication initiation site (RIS) placement upstream of active genes, thus ensuring co-orientation of replication fork movement and genic transcription. However, this model does not account for pervasive transcription units, or intragenic replication initiation events. Through mining phased GRO-seq data, and developing a rigorous informatic strategy to identify RIS, we demonstrate that head-on transcription occurs frequently in a breast cancer cell line, and that this transcription is significantly downregulated during S-phase, particularly in regions susceptible to R-loop formation. Collectively, our analysis suggests the existence of a temporally tuned transcriptional regulation mechanism that functions to maintain genome stability.
2022-04-30 | GSE201746 | GEO
Project description:Fine-tuning DNA replication and transcription is crucial to prevent collisions between their machineries, especially at promoters where RNA polymerase II (RNAPII) initiates transcription and forms R-loops. Arrested RNAPII can obstruct DNA replication, which often starts near promoters. The mechanisms that salvage arrested RNAPII during elongation to avoid conflicts with incoming replisomes are unknown. Here, we identify CFAP20 as a key player in rescuing arrested RNAPII in promoter-proximal regions, preventing conflicts with co-directional replisomes. CFAP20-deficient cells accumulate R-loops near promoters and exhibit defects in replication origin firing and fork progression. Co-depleting the Mediator coactivator complex or removing RNAPII engaged with R-loops rescues these defects. Thus, CFAP20 salvages arrested RNAPII under conditions of high Mediator-driven transcription to promote RNAPII elongation, thereby preventing collisions with co-directional replisomes.
2025-11-04 | GSE276603 | GEO
Project description:RTEL1 regulates G4/R-loops to avert replication-transcription collisions
| PRJNA678867 | ENA
Project description:Methylated H3K4 (H3K4me) is highly conserved and has been widely considered to be involved in transcriptional control. However, this once popular model was recently challenged by multiple groups, because blocking this modification does not appreciably affect transcription. Thus, the function of the H3K4me remains unclear. To investigate how H3K4 methylation influences the processes of transcription and replication under HU-stress, we used chromatin immunoprecipitation-sequencing (ChIP-seq) to identify genomic sites of active transcription marked by Rpb3, a subunit of RNA Polymerase II, and sites of replication pausing marked by DNA Pol2, a subunit of DNA Polymerase e. Our data lead us to the surprising conclusion that H3K4me pauses the progression of replication forks, and we propose that high levels of H3K4me deposited by high transcriptional activity result in a large cushioning effect on fork progression to protect against transcription-replication collisions (TRCs), which cause genome instability.
2019-08-31 | GSE133222 | GEO
Project description:Fine-tuning DNA replication and transcription co-occurrence is vital to avoid collisions between their machineries. This is especially relevant near promoters, where RNAPII initiates transcription and often arrests, forming R-loops. Arrested RNAPII poses a roadblock for DNA replication, which evolutionarily initiates near promoters. The mechanisms that salvage arrested RNAPII during elongation to avoid conflicts with incoming replisomes remain unaddressed. In this study, employing genome-wide and proteomic approaches, we identify and characterize CFAP20 as part of a protective pathway that rescues arrested RNAPII in promoter-proximal regions, diverting it from the path of co-directional replisomes. CFAP20-deficient cells accumulate R-loops specifically near promoters, displaying defects in replication origin firing and fork progression. Co-depletion of the Mediator coactivator complex or removal of RNAPII engaged with R-loops rescues these replication phenotypes. Therefore, we propose that CFAP20 salvages arrested RNAPII under conditions of high Mediator-driven transcription to promote RNAPII elongation, thereby preventing collisions with co-directional replisomes.
2025-05-20 | GSE266573 | GEO