scholarly journals RAD51 Inhibition Induces R-Loop Formation in Early G1 Phase of the Cell Cycle

2021 ◽  
Vol 22 (7) ◽  
pp. 3740
Author(s):  
Zuzana Nascakova ◽  
Barbora Boleslavska ◽  
Vaclav Urban ◽  
Anna Oravetzova ◽  
Edita Vlachova ◽  
...  

R-loops are three-stranded structures generated by annealing of nascent transcripts to the template DNA strand, leaving the non-template DNA strand exposed as a single-stranded loop. Although R-loops play important roles in physiological processes such as regulation of gene expression, mitochondrial DNA replication, or immunoglobulin class switch recombination, dysregulation of the R-loop metabolism poses a threat to the stability of the genome. A previous study in yeast has shown that the homologous recombination machinery contributes to the formation of R-loops and associated chromosome instability. On the contrary, here, we demonstrate that depletion of the key homologous recombination factor, RAD51, as well as RAD51 inhibition by the B02 inhibitor did not prevent R-loop formation induced by the inhibition of spliceosome assembly in human cells. However, we noticed that treatment of cells with B02 resulted in RAD51-dependent accumulation of R-loops in an early G1 phase of the cell cycle accompanied by a decrease in the levels of chromatin-bound ORC2 protein, a component of the pre-replication complex, and an increase in DNA synthesis. Our results suggest that B02-induced R-loops might cause a premature origin firing.

2021 ◽  
Author(s):  
João C. Sabino ◽  
Madalena R. de Almeida ◽  
Patricia L. Abreu ◽  
Ana M. Ferreira ◽  
Marco M. Domingues ◽  
...  

AbstractDNA oxidation by ten-eleven translocation (TET) family enzymes is essential for epigenetic reprogramming. The conversion of 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) initiates developmental and cell-type-specific transcriptional programs through mechanisms that include changes in the chromatin structure. Here, we show that the presence of 5hmC in the transcribed DNA promotes the annealing of the nascent RNA to its template DNA strand, leading to the formation of an R-loop. The genome-wide distribution of 5hmC and R-loops show a positive correlation in mouse and human embryonic stem cells and overlap in half of all active genes. Moreover, R-loop resolution leads to differential expression of a subset of genes that are involved in crucial events during stem cell proliferation. Altogether, our data reveal that epigenetic reprogramming via TET activity promotes co-transcriptional R-loop formation, and disclose novel links between R-loops and the regulation of gene expression programs in stem cells.


Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 2512-2512
Author(s):  
Suchismita Mohanty ◽  
Atish Mohanty ◽  
Natalie Sandoval ◽  
Victoria Bedell ◽  
Joyce Murata-Collins ◽  
...  

Abstract Mantle cell lymphoma (MCL) is rarely curable and therapy resistance often leaves few viable treatment options for patients. Previous studies have identified the importance of cyclin D1 (CCND1) translocation and overexpression in MCL pathogenesis, which leads to increased cyclin-dependent kinase 4 (CDK4) activity and accelerated cell cycle progression. However, targeting this abnormal cell cycle control, mainly through CDK4 inhibition causes only G1-phase growth arrest without significant cell death (Marzec et al. 2006). In contrast, prolonged inhibition of CCND1 with RNA interference induces apoptosis in MCL cell lines (Weinstein et al. 2012), suggesting an essential function of CCND1 independent of CDK4 activity. The mechanism of this non-catalytic role of CCND1 in maintaining MCL cell survival is largely unknown. To clarify the cell cycle role of CCND1 in addition to its CDK4-dependent function, we compared the effects of CCND1 and CDK4 silencing on MCL cell survival. MCL cell lines co-expressing GFP and doxycycline-inducible shRNA targeting CCND1 or CDK4 were generated. Cells with similar GFP expression levels were FACS sorted to normalize for shRNA expression. Both CCND1 and CDK4 silencing resulted in G1-phase arrest, but only CCND1-silenced cells demonstrated a marked increase in apoptosis. Investigation of the potential cause of apoptosis revealed significant accumulation of DNA double-strand breaks following CCND1 ablation, as measured by nuclear gamma-H2AX focus formation. Interestingly, CCND1-silenced cells exhibited a significant increase in 53BP1+ nuclear bodies in G1-phase, reminiscent of 53BP1 foci observed by Lukas and colleagues in cells undergoing aphidicolin-induced replication stress (Lukas et al. 2011). Analysis of replication fork movement in CCND1-depleted cells showed substantially reduced fork speed and increased frequency of origin firing, both of which are indicative of replication stress. In contrast, knockdown of CDK4 did not result in slower forks or increase in the frequency of origin firing. Genomic instability associated with replication stress was also apparent in CCND1-silenced cells, including increased micronucleus formation and recurrent chromatid gaps or breaks detected by cytokinesis-block assay and karyotyping, respectively. Analysis of DNA replicative and damage checkpoints revealed that both ATR-CHEK1 and ATM-CHEK2 pathways were activated by phosphorylation following CCND1 silencing in MCL cell lines, a xenograft animal model, and primary tumor samples, but not in non-MCL tumors. Interestingly, this activation (with the exception of ATM phosphorylation) was unsustainable over time and did not cause down-regulation of the downstream targets CDC25 and CDK1/2 but, instead, we observed an increase in CDC25A/B protein levels and CDK1/2 activity, indicating defective cell cycle checkpoints. Exposing CCND1-silenced cells to replication stress-inducing or DNA-damaging agents such hydroxyurea, aphidicolin, etoposide or ionizing radiation further amplified the checkpoint defects seen in unperturbed cells. We did not observe any significant difference in this checkpoint signaling in control and CDK4 knockdown cells under these conditions. Furthermore, CCND1-deficient cells were more sensitive to pharmacological inhibition of ATR and CHEK1 but not ATM, confirming a constitutive role of CCND1 in the ATR-CHEK1 pathway. In conclusion, these studies revealed an unexpected CDK4-independent role of CCND1 in maintaining DNA replicative checkpoints to prevent replication stress and genome instability in MCL cells. As most cancer treatments rely on agents that create DNA replication stress, targeting this function of CCND1 could provide a rational approach to overcome resistance to conventional therapies in MCL. Disclosures: No relevant conflicts of interest to declare.


eLife ◽  
2013 ◽  
Vol 2 ◽  
Author(s):  
Lamia Wahba ◽  
Steven K Gore ◽  
Douglas Koshland

Genome instability in yeast and mammals is caused by RNA–DNA hybrids that form as a result of defects in different aspects of RNA biogenesis. We report that in yeast mutants defective for transcription repression and RNA degradation, hybrid formation requires Rad51p and Rad52p. These proteins normally promote DNA–DNA strand exchange in homologous recombination. We suggest they also directly promote the DNA–RNA strand exchange necessary for hybrid formation since we observed accumulation of Rad51p at a model hybrid-forming locus. Furthermore, we provide evidence that Rad51p mediates hybridization of transcripts to homologous chromosomal loci distinct from their site of synthesis. This hybrid formation in trans amplifies the genome-destabilizing potential of RNA and broadens the exclusive co-transcriptional models that pervade the field. The deleterious hybrid-forming activity of Rad51p is counteracted by Srs2p, a known Rad51p antagonist. Thus Srs2p serves as a novel anti-hybrid mechanism in vivo.


2013 ◽  
Vol 24 (7) ◽  
pp. 923-932 ◽  
Author(s):  
Dani L. Bodor ◽  
Luis P. Valente ◽  
João F. Mata ◽  
Ben E. Black ◽  
Lars E. T. Jansen

Centromeres are the site of kinetochore formation during mitosis. Centromere protein A (CENP-A), the centromere-specific histone H3 variant, is essential for the epigenetic maintenance of centromere position. Previously we showed that newly synthesized CENP-A is targeted to centromeres exclusively during early G1 phase and is subsequently maintained across mitotic divisions. Using SNAP-based fluorescent pulse labeling, we now demonstrate that cell cycle–restricted chromatin assembly at centromeres is unique to CENP-A nucleosomes and does not involve assembly of other H3 variants. Strikingly, stable retention is restricted to the CENP-A/H4 core of the nucleosome, which we find to outlast general chromatin across several cell divisions. We further show that cell cycle timing of CENP-A assembly is independent of centromeric DNA sequences and instead is mediated by the CENP-A targeting domain. Unexpectedly, this domain also induces stable transmission of centromeric nucleosomes, independent of the CENP-A deposition factor HJURP. This demonstrates that intrinsic properties of the CENP-A protein direct its cell cycle–restricted assembly and induces quantitative mitotic transmission of the CENP-A/H4 nucleosome core, ensuring long-term stability and epigenetic maintenance of centromere position.


2002 ◽  
Vol 1 (2) ◽  
pp. 200-212 ◽  
Author(s):  
Keiichi Watanabe ◽  
Jun Morishita ◽  
Keiko Umezu ◽  
Katsuhiko Shirahige ◽  
Hisaji Maki

ABSTRACT Perturbation of origin firing in chromosome replication is a possible cause of spontaneous chromosome instability in multireplicon organisms. Here, we show that chromosomal abnormalities, including aneuploidy and chromosome rearrangement, were significantly increased in yeast diploid cells with defects in the origin recognition complex. The cell cycle of orc1-4/orc1-4 temperature-sensitive mutant was arrested at the G2/M boundary, after several rounds of cell division at the restrictive temperature. However, prolonged incubation of the mutant cells at 37°C led to abrogation of G2 arrest, and simultaneously the cells started to lose viability. A sharp increase in chromosome instability followed the abrogation of G2 arrest. In orc1-4/orc1-4 rad9Δ/rad9Δ diploid cells grown at 37°C, G2 arrest and induction of cell death were suppressed, while chromosome instability was synergistically augmented. These findings indicated that DNA lesions caused by a defect in Orc1p function trigger the RAD9-dependent checkpoint control, which ensures genomic integrity either by stopping the cell cycle progress until lesion repair, or by inducing cell death when the lesion is not properly repaired. At semirestrictive temperatures, orc2-1/orc2-1 diploid cells demonstrated G2 arrest and loss of cell viability, both of which require RAD9-dependent checkpoint control. However, chromosome instability was not induced in orc2-1/orc2-1 cells, even in the absence of the checkpoint control. These data suggest that once cells lose the damage checkpoint control, perturbation of origin firing can be tolerated by the cells. Furthermore, although a reduction in origin-firing capacity does not necessarily initiate chromosome instability, the Orc1p possesses a unique function, the loss of which induces instability in the chromosome.


2009 ◽  
Vol 30 (1) ◽  
pp. 146-159 ◽  
Author(s):  
Deepankar Roy ◽  
Zheng Zhang ◽  
Zhengfei Lu ◽  
Chih-Lin Hsieh ◽  
Michael R. Lieber

ABSTRACT Upon transcription of some sequences by RNA polymerases in vitro or in vivo, the RNA transcript can thread back onto the template DNA strand, resulting in an R loop. Previously, we showed that initiation of R-loop formation at an R-loop initiation zone (RIZ) is favored by G clusters. Here, using a purified in vitro system with T7 RNA polymerase, we show that increased distance between the promoter and the R-loop-supporting G-rich region reduces R-loop formation. When the G-rich portion of the RNA transcript is downstream from the 5′ end of the transcript, the ability of this portion of the transcript to anneal to the template DNA strand is reduced. When we nucleolytically resect the beginning of the transcript, R-loop formation increases because the G-rich portion of the RNA is now closer to the 5′ end of the transcript. Short G-clustered regions can act as RIZs and reduce the distance-induced suppression of R-loop formation. Supercoiled DNA is known to favor transient separation of the two DNA strands, and we find that this favors R-loop formation even in non-G-rich regions. Most strikingly, a nick can serve as a strong RIZ, even in regions with no G richness. This has important implications for class switch recombination and somatic hypermutation and possibly for other biological processes in transcribed regions.


2019 ◽  
Author(s):  
Maika Malig ◽  
Stella R. Hartono ◽  
Jenna M. Giafaglione ◽  
Lionel A. Sanz ◽  
Frederic Chedin

ABSTRACTR-loops are a prevalent class of non-B DNA structures that form during transcription upon reannealing of the nascent RNA to the template DNA strand. R-loops have been profiled using the S9.6 antibody to immunoprecipitate DNA:RNA hybrids. S9.6-based DNA:RNA immunoprecipitation (DRIP) techniques revealed that R-loops form dynamically over conserved genic hotspots. We developed an orthogonal profiling methodology that queries R-loops via the presence of long stretches of single-stranded DNA on the looped-out strand. Non-denaturing sodium bisulfite treatment catalyzes the conversion of unpaired cytosines to uracils, creating permanent genetic tags for the position of an R-loop. Long read, single-molecule PacBio sequencing allows the identification of R-loop ‘footprints’ at near nucleotide resolution in a strand-specific manner on single DNA molecules and at ultra-deep coverage. Single-molecule R-loop footprinting (SMRF-seq) revealed a strong agreement between S9.6-and bisulfite-based R-loop mapping and confirmed that R-loops form from unspliced transcripts over genic hotspots. Using the largest single-molecule R-loop dataset to date, we show that individual R-loops generate overlapping sets of molecular clusters that pile-up through larger R-loop-prone zones. SMRF-seq further established that R-loop distribution patterns are driven by both intrinsic DNA sequence features and DNA topological constraints, revealing the principles of R-loop formation.


Sign in / Sign up

Export Citation Format

Share Document