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Gene expression profile in mouse tumor RIF-1 cell line after knockdown of Bre1a (Rnf20) or Bre1b (Rnf40).

ABSTRACT: Mammalian Bre1 complexes (BRE1A/B (RNF20/40) in humans and Bre1a/b (Rnf20/40) in mice) function similarly to their yeast homolog Bre1 as ubiquitin ligases in monoubiquitination of histone H2B. This ubiquitination facilitates methylation of histone H3 at K4 and K79, and accounts for the roles of Bre1 and its homologs in transcriptional regulation. Recent studies by others suggested that Bre1 acts as a tumor suppressor, augmenting expression of select tumor suppressor genes and suppressing select oncogenes. In this study we present an additional mechanism of tumor suppression by Bre1 through maintenance of genomic stability. We track the evolution of genomic instability in Bre1-deficient cells from replication-associated double-strand breaks (DSBs) to specific genomic rearrangements that explain a rapid increase in DNA content and trigger breakage-fusion-bridge cycles. We show that aberrant RNA-DNA structures (R-loops) constitute a significant source of DSBs in Bre1-deficient cells. Combined with a previously reported defect in homologous recombination, generation of R-loops is a likely initiator of replication stress and genomic instability in Bre1-deficient cells. We propose that genomic instability triggered by Bre1 deficiency may be an important early step that precedes acquisition of an invasive phenotype, as we find decreased levels of BRE1A/B and dimethylated H3K79 in testicular seminoma and in the premalignant lesion in situ carcinoma. A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. Knock down by RNA interference: gene knocked down in RIF-1 cell line

ORGANISM(S): Mus musculus

PROVIDER: GSE34977 | GEO | 2013/01/09

SECONDARY ACCESSION(S): PRJNA151109

REPOSITORIES: GEO

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Gene expression profile in mouse tumor RIF-1 cell line after knockdown of Bre1a (Rnf20) or Bre1b (Rnf40).

Project description:Mammalian Bre1 complexes (BRE1A/B (RNF20/40) in humans and Bre1a/b (Rnf20/40) in mice) function similarly to their yeast homolog Bre1 as ubiquitin ligases in monoubiquitination of histone H2B. This ubiquitination facilitates methylation of histone H3 at K4 and K79, and accounts for the roles of Bre1 and its homologs in transcriptional regulation. Recent studies by others suggested that Bre1 acts as a tumor suppressor, augmenting expression of select tumor suppressor genes and suppressing select oncogenes. In this study we present an additional mechanism of tumor suppression by Bre1 through maintenance of genomic stability. We track the evolution of genomic instability in Bre1-deficient cells from replication-associated double-strand breaks (DSBs) to specific genomic rearrangements that explain a rapid increase in DNA content and trigger breakage-fusion-bridge cycles. We show that aberrant RNA-DNA structures (R-loops) constitute a significant source of DSBs in Bre1-deficient cells. Combined with a previously reported defect in homologous recombination, generation of R-loops is a likely initiator of replication stress and genomic instability in Bre1-deficient cells. We propose that genomic instability triggered by Bre1 deficiency may be an important early step that precedes acquisition of an invasive phenotype, as we find decreased levels of BRE1A/B and dimethylated H3K79 in testicular seminoma and in the premalignant lesion in situ carcinoma. A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. Knock down by RNA interference: gene knocked down in RIF-1 cell line cellular_modification_design

2013-01-09 | E-GEOD-34977 | biostudies-arrayexpress

Mapping of TOP1cc and R-loops im MCF-7 after TOP1 KD and/or RNase H OE [CHiP_DRIP_Seq]

Project description:DNA double-stranded breaks (DSBs) pose a significant threat to genomic integrity, and their generation during essential cellular processes like transcription remains poorly understood. In this study, we employed DRIP-seq and ChIP-seq to map the change in TOP1cc and R-loops after the depletion of TOP1 and R-loops, to comprehensively investigate the interplay between transcription, DSBs, Topoisomerase 1 (TOP1), and R-loops. Our findings revealed the presence of DSBs at highly expressed genes enriched with TOP1 and R-loops, indicating their crucial involvement in transcription-associated genomic instability. Depletion of R-loops and TOP1 specifically reduced DSBs at highly expressed genes, uncovering their pivotal roles in transcriptional DSB formation. By elucidating the intricate interplay between TOP1cc trapping, R-loops, and DSBs, our study provides novel insights into the mechanisms underlying transcription-associated genomic instability. Moreover, we establish a link between transcriptional DSBs and early molecular changes driving cancer development. Notably, our study highlights the distinct etiology and molecular characteristics of driver mutations compared to passenger mutations, shedding light on the potential for targeted therapeutic strategies. Overall, these findings deepen our understanding of the regulatory mechanisms governing DSBs in hypertranscribed genes associated with carcinogenesis, opening avenues for future research and therapeutic interventions.

2024-05-22 | GSE241307 | GEO

Mapping of physiological DNA double stranded breaks in normal breast cells and breast cancer cells [BLISS]

Project description:DNA double-stranded breaks (DSBs) pose a significant threat to genomic integrity, and their generation during essential cellular processes like transcription remains poorly understood. In this study, we employed the advanced BLISS techniques to map DSBs, with different genetic manipulations to comprehensively investigate the interplay between transcription, DSBs, Topoisomerase 1 (TOP1), and R-loops. Our findings revealed the presence of DSBs at highly expressed genes enriched with TOP1 and R-loops, indicating their crucial involvement in transcription-associated genomic instability. Depletion of R-loops and TOP1 specifically reduced DSBs at highly expressed genes, uncovering their pivotal roles in transcriptional DSB formation. By elucidating the intricate interplay between TOP1cc trapping, R-loops, and DSBs, our study provides novel insights into the mechanisms underlying transcription-associated genomic instability. Moreover, we establish a link between transcriptional DSBs and early molecular changes driving cancer development. Notably, our study highlights the distinct etiology and molecular characteristics of driver mutations compared to passenger mutations, shedding light on the potential for targeted therapeutic strategies. Overall, these findings deepen our understanding of the regulatory mechanisms governing DSBs in hypertranscribed genes associated with carcinogenesis, opening avenues for future research and therapeutic interventions.

2024-05-22 | GSE241305 | GEO

R-loops and Topoisomerase 1 facilitate formation of transcriptional DSBs at gene bodies of hypertranscribed cancer genes

Project description:DNA double-stranded breaks (DSBs) pose a significant threat to genomic integrity, and their generation during essential cellular processes like transcription remains poorly understood. In this study, we employed advanced techniques to map DSBs, R-loops, and Topoisomerase 1 cleavage complex (TOP1cc) and re-analyzed ChIP-seq and DRIP-seq data to comprehensively investigate the interplay between transcription, DSBs, Topoisomerase 1 (TOP1), and R-loops. Our findings revealed the presence of DSBs at highly expressed genes enriched with TOP1 and R-loops, indicating their crucial involvement in transcription-associated genomic instability. Depletion of R-loops and TOP1 specifically reduced DSBs at highly expressed genes, uncovering their pivotal roles in transcriptional DSB formation. By elucidating the intricate interplay between TOP1cc trapping, R-loops, and DSBs, our study provides novel insights into the mechanisms underlying transcription-associated genomic instability. Moreover, we establish a link between transcriptional DSBs and early molecular changes driving cancer development. Notably, our study highlights the distinct etiology and molecular characteristics of driver mutations compared to passenger mutations, shedding light on the potential for targeted therapeutic strategies. Overall, these findings deepen our understanding of the regulatory mechanisms governing DSBs in hypertranscribed genes associated with carcinogenesis, opening avenues for future research and therapeutic interventions. This SuperSeries is composed of the SubSeries listed below.

2024-05-22 | GSE241309 | GEO

Effect of TOP1 knockdown and/or RNase H OE on the transcriptional profile of MCF-7 cells [CEL_Seq]

Project description:DNA double-stranded breaks (DSBs) pose a significant threat to genomic integrity, and their generation during essential cellular processes like transcription remains poorly understood. In this study, we employed CEL-seq technique to investigate the effect of TOP1 KD and RNase H OE on transcriptional profile, with the different genetic manipulations. Our findings revealed the presence of DSBs at highly expressed genes enriched with TOP1 and R-loops, indicating their crucial involvement in transcription-associated genomic instability. Depletion of R-loops and TOP1 specifically reduced DSBs at highly expressed genes, uncovering their pivotal roles in transcriptional DSB formation. By elucidating the intricate interplay between TOP1cc trapping, R-loops, and DSBs, our study provides novel insights into the mechanisms underlying transcription-associated genomic instability. Moreover, we establish a link between transcriptional DSBs and early molecular changes driving cancer development. Notably, our study highlights the distinct etiology and molecular characteristics of driver mutations compared to passenger mutations, shedding light on the potential for targeted therapeutic strategies. Overall, these findings deepen our understanding of the regulatory mechanisms governing DSBs in hypertranscribed genes associated with carcinogenesis, opening avenues for future research and therapeutic interventions.

2024-05-22 | GSE241306 | GEO

Transcription dynamics prevents RNA-mediated genomic instability through SRPK2-dependent DDX23 phosphorylation

Project description:Genomic instability is frequently caused by nucleic acids structures formed during transcription termed R-loops. Despite their harmful potential, mechanisms that sense, signal and suppress these structures remain elusive. Here we report that oscillations in transcription dynamics are a major sensor of R-loops. We show that pausing of RNA polymerase II (RNA Pol II) initiates a signaling cascade whereby the serine/arginine protein kinase 2 (SRPK2) phosphorylates the DDX23 helicase culminating in the suppression of R-loops. We show that in the absence of either SRPK2 or DDX23, accumulation of R-loops leads to massive genomic instability revealed by high levels of DNA double-strand breaks (DSBs). Importantly, we found DDX23 mutations in several cancers and detected homozygous deletions of the entire DDX23 locus in 10 (17%) adenoid cystic carcinoma samples. Our results unravel molecular details of a novel link between transcription dynamics and RNA-mediated genomic instability that may play important roles in cancer development.

2016-12-22 | GSE76777 | GEO

Phosphorylation of SMURF2 by ATM exerts a negative feedback control of DNA damage response

Project description:Timely repair of DNA double-strand breaks (DSBs) is essential to maintaining genomic integrity and preventing illnesses induced by genetic abnormalities. We previously demonstrated that the E3 ubiquitin ligase Smad ubiquitin regulatory factor 2 (SMURF2) plays a critical tumor suppressing role via its interaction with ring finger protein 20 (RNF20) in shaping chromatin landscape and preserving genomic stability. Here, we show that upon the onset of the DNA-damage response, Smurf2 becomes phosphorylated at S384 by ataxia telangiectasia mutated (ATM) and this phosphorylation is required for its interaction with RNF20. We demonstrate that Smurf2 mutant with an S384A substitution has reduced capacity to ubiquitinate RNF20 while promoting Smad3 ubiquitination unabatedly. More importantly, mouse embryonic fibroblasts (MEFs) expressing the SMURF2 S384A mutant show a weakened ability to sustain the DSB response compared to those expressing wild type SMURF2 following etoposide treatment. These data indicate that SMURF2-mediated RNF20 ubiquitination and degradation controlled by ATM-induced phosphorylation at S384 constitutes a negative feedback loop that regulates DSB repair.

2020-10-26 | PXD021420 | Pride

Topoisomerase I poisoning induces R-loop changes and DNA damage in human cancer cells [END-seq]

Project description:DNA topoisomerase I is an essential enzyme in higher eukaryotes that regulates DNA torsional tension during fundamental processes, such as replication and transcription. During its catalytic activity, a transient Topoisomerase I-DNA cleavage complex, called Top1cc, forms to allow strand rotation and duplex relaxation. However, the stabilization of Top1cc can lead to increased DNA:RNA hybrid duplexes, DNA double-strand cuts (DSBs) and genome instability as shown by formation of micronuclei, extranuclear chromatin enveloped by a nuclear membrane. To better comprehend the underlying mechanisms, we have established genomic maps of Top1cc-mediated R-loop changes and DSBs at short times upon Top1cc induction. Our findings show that Top1ccs dynamically changed the genomic distribution of R-loops, with regions of stable hybrid gains. DSBs were at specific gene loci, strongly associated with stable anterior R-loops at highly-transcribed genes and close to backtracked RNA polymerase II. Moreover, DSBs and stable anterior R-loops were highly enriched at early replication origins, thus revealing the location of replication conflicts with backtracked RNA polymerases.

2024-06-05 | GSE239327 | GEO

Topoisomerase I poisoning induces R-loop changes and DNA damage in human cancer cells [DRIP-seq]

2024-06-05 | GSE239326 | GEO

HELZ promotes R loop resolution to facilitate DNA double-strand break repair by homologous recombination

Project description:Successful R-loop homeostasis consists of its timely biogenesis and removal throughout the genome to regulate diverse cellular processes. Yet, they are considered hazardous source to our genome when their turnover goes awry. Here, we report HELZ, a novel player in R-loop homeostasis and DNA repair pathway. HELZ mediates resistance to several DNA damaging agents, and localizes to DSBs and its depletion increases R-loops fostering genomic instability. Loss of HELZ results in impaired homologous recombination (HR) due to R-loops accumulation, with an increase in classical-non-homologous end joining (c-NHEJ), suggesting a role for HELZ in regulating DSB repair pathway choice. Rad51 retention at DSBs is governed by HELZ mediated R-loop accumulation. Mechanistically, our data show that HELZ complexes with BRCA1 and facilitates its recruitment to DSBs in an R-loop dependent manner. Collectively, our data support a model in which HELZ recruits BRCA1 and facilitates R loop resolution at DSBs to promote HR and therefore maintains genome stability.

2023-11-01 | GSE242527 | GEO

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