Chromatin-associated MRN complex protects highly transcribing genes from genomic instability

Salifou, Kader; Burnard, Callum; Basavarajaiah, Poornima; Grasso, Giuseppa; Helsmoortel, Marion; Mac, Victor; Depierre, David; Franckhauser, Celine; Beyne, Emmanuelle; Contreras, Xavier; Déjardin, Jérôme; Rouquier, Sylvie; Cuvier, Olivier; Kiernan, Rosemary

doi:10.1126/sciadv.abb2947

Cited by 19 publications

(24 citation statements)

References 46 publications

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“…To summarize our finding so far, chromatin binding sites of O -GlcNAc and MRE11 overlap, and genes marked by the two resist CDK9 inhibitor effects at the mRNA level. MRE11 has been previously shown to be enriched on the highly transcribing genes [ 40 ]. However, it is not known if OGT activity affects MRE11 function.…”

Section: Resultsmentioning

confidence: 99%

O-GlcNAc transferase couples MRE11 to transcriptionally active chromatin to suppress DNA damage

et al. 2022

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Background Transcription, metabolism and DNA damage response are tightly regulated to preserve the genomic integrity, and O-GlcNAc transferase (OGT) is positioned to connect the three. Prostate cancer is the most common cancer in men, and androgen-ablation therapy halts disease progression. However, a significant number of prostate cancer patients develop resistance against anti-androgens, and this incurable disease is termed castration-resistant prostate cancer (CRPC). We have shown that combined inhibition of OGT and the transcription elongation kinase CDK9 induce CRPC-selective anti-proliferative effects. Here, we explain the functional basis for these combinatorial effects. Methods We used comprehensive mass spectrometry profiling of short-term CDK9 inhibitor effects on O-GlcNAcylated proteins in an isogenic cell line system that models transition from PC to CRPC. In addition, we used both ChIP-seq and RNA-seq profiling, and pulldown experiments in multiple CRPC models. Finally, we validated our findings in prostate cancer patient samples. Results Inhibition of CDK9 results in an OGT-dependent remodeling of the proteome in prostate cancer cells. More specifically, the activity of the DNA damage repair protein MRE11 is regulated in response to CDK9 inhibition in an OGT-dependent manner. MRE11 is enriched at the O-GlcNAc-marked loci. CDK9 inhibition does not decrease the expression of mRNAs whose genes are bound by both O-GlcNAc and MRE11. Combined inhibition of CDK9 and OGT or MRE11 further decreases RNA polymerase II activity, induces DNA damage signaling, and blocks the survival of prostate cancer cells. These effects are seen in CRPC cells but not in normal prostate cells. Mechanistically, OGT activity is required for MRE11 chromatin-loading in cells treated with CDK9 inhibitor. Finally, we show that MRE11 and O-GlcNAc are enriched at the prostate cancer-specific small nucleotide polymorphic sites, and the loss of MRE11 activity results in a hyper-mutator phenotype in patient tumors. Conclusions Both OGT and MRE11 are essential for the repair of CDK9 inhibitor-induced DNA damage. Our study raises the possibility of targeting CDK9 to elicit DNA damage in CRPC setting as an adjuvant to other treatments. Graphical Abstract

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Section: Resultsmentioning

confidence: 99%

O-GlcNAc transferase couples MRE11 to transcriptionally active chromatin to suppress DNA damage

et al. 2022

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“…The remainder of the DNA-PKcs genomic binding sites show RNAPII but are devoid of other DSB factors. Recent work also shows that MRN occupancy in the genome is strongly correlated with RNAPII abundance 51 .…”

Section: Discussionmentioning

confidence: 96%

Genome-wide analysis of DNA-PK-bound MRN cleavage products supports a sequential model of DSB repair pathway choice

Deshpande

Marín-González

et al. 2022

Preprint

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SummaryThe Mre11-Rad50-Nbs1 (MRN) complex recognizes and processes DNA double-strand breaks for homologous recombination by performing short-range removal of 5ʹ strands. Endonucleolytic processing by MRN requires a stably bound protein at the break site—a role we postulate is played by DNA-dependent protein kinase (DNA-PK) in mammals. Here we interrogate the sites of MRN-dependent processing by isolating and sequencing DNA-PK-bound DNA fragments that are products of MRN cleavage. These intermediates are generated with highest efficiency when DNA-PK is catalytically blocked, yielding products within 200 bp of the break site, whereas DNA-PK products in the absence of kinase inhibition show much greater dispersal. Use of light-activated Cas9 to induce breaks facilitates temporal resolution of DNA-PK and Mre11 binding, showing that Mre11 and DNA-PK both bind to DNA ends before release of DNA-PK-bound products. These results support a sequential model of double-strand break repair involving collaborative interactions between homologous and non-homologous repair complexes.

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“…11c–h ). Although MRE11 was significantly reduced, it was not completely abolished, which suggests that MRE11 may have additional targeting mechanisms, such as direct interaction with free DSB ends or association with transcriptional machinery 33 , 36 . If NPAS4–NuA4 stimulates repair, the depletion of NPAS4–NuA4 subunits should result in increased DSBs in neurons.…”

Section: Npas4–nua4 Disruption Impairs Dsb Repairmentioning

confidence: 95%

A NPAS4–NuA4 complex couples synaptic activity to DNA repair

Pollina

Gilliam

Landau

et al. 2023

Nature

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Neuronal activity is crucial for adaptive circuit remodelling but poses an inherent risk to the stability of the genome across the long lifespan of postmitotic neurons1–5. Whether neurons have acquired specialized genome protection mechanisms that enable them to withstand decades of potentially damaging stimuli during periods of heightened activity is unknown. Here we identify an activity-dependent DNA repair mechanism in which a new form of the NuA4–TIP60 chromatin modifier assembles in activated neurons around the inducible, neuronal-specific transcription factor NPAS4. We purify this complex from the brain and demonstrate its functions in eliciting activity-dependent changes to neuronal transcriptomes and circuitry. By characterizing the landscape of activity-induced DNA double-strand breaks in the brain, we show that NPAS4–NuA4 binds to recurrently damaged regulatory elements and recruits additional DNA repair machinery to stimulate their repair. Gene regulatory elements bound by NPAS4–NuA4 are partially protected against age-dependent accumulation of somatic mutations. Impaired NPAS4–NuA4 signalling leads to a cascade of cellular defects, including dysregulated activity-dependent transcriptional responses, loss of control over neuronal inhibition and genome instability, which all culminate to reduce organismal lifespan. In addition, mutations in several components of the NuA4 complex are reported to lead to neurodevelopmental and autism spectrum disorders. Together, these findings identify a neuronal-specific complex that couples neuronal activity directly to genome preservation, the disruption of which may contribute to developmental disorders, neurodegeneration and ageing.

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Chromatin-associated MRN complex protects highly transcribing genes from genomic instability

Cited by 19 publications

References 46 publications

O-GlcNAc transferase couples MRE11 to transcriptionally active chromatin to suppress DNA damage

O-GlcNAc transferase couples MRE11 to transcriptionally active chromatin to suppress DNA damage

Genome-wide analysis of DNA-PK-bound MRN cleavage products supports a sequential model of DSB repair pathway choice

A NPAS4–NuA4 complex couples synaptic activity to DNA repair

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