Endogenous aldehyde-induced DNA–protein crosslinks are resolved by transcription-coupled repair

Nature Cell Biology, Год журнала: 2024, Номер 26(5), С. 784 - 796

Опубликована: Апрель 10, 2024

Abstract DNA–protein crosslinks (DPCs) induced by aldehydes interfere with replication and transcription. Hereditary deficiencies in DPC repair aldehyde clearance processes cause progeria, including Ruijs–Aalfs syndrome (RJALS) AMeD (AMeDS) humans. Although the elimination of during has been well established, how cells overcome lesions transcription remains elusive. Here we show that endogenous aldehyde-induced roadblocks are efficiently resolved transcription-coupled (TCR). We develop a high-throughput sequencing technique to measure genome-wide distribution DPCs (DPC-seq). Using proteomics DPC-seq, demonstrate conventional TCR complex as VCP/p97 proteasome required for removal formaldehyde-induced DPCs. TFIIS-dependent cleavage RNAPII transcripts protects against obstacles. Finally, mouse model lacking both confirms accumulation actively transcribed regions. Collectively, our data provide evidence (TC-DPCR) crucial protecting metabolic genotoxin, thus explaining molecular pathogenesis AMeDS other disorders associated defects TCR, such Cockayne syndrome.

Язык: Английский

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Transcription-coupled repair of DNA–protein cross-links depends on CSA and CSB

Nature Cell Biology, Год журнала: 2024, Номер 26(5), С. 797 - 810

Опубликована: Апрель 10, 2024

Abstract Covalent DNA–protein cross-links (DPCs) are toxic DNA lesions that block replication and require repair by multiple pathways. Whether transcription blockage contributes to the toxicity of DPCs how cells respond when RNA polymerases stall at is unknown. Here we find DPC formation arrests induces ubiquitylation degradation polymerase II. Using genetic screens a method for genome-wide mapping adducts, sequencing, discover Cockayne syndrome (CS) proteins CSB CSA provide resistance DPC-inducing agents promoting in actively transcribed genes. Consequently, CSB- or CSA-deficient fail efficiently restart after induction DPCs. In contrast, nucleotide excision factors act downstream ultraviolet light-induced dispensable. Our study describes transcription-coupled pathway suggests defects this may contribute unique neurological features CS.

Язык: Английский

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Decitabine cytotoxicity is promoted by dCMP deaminase DCTD and mitigated by SUMO-dependent E3 ligase TOPORS

The EMBO Journal, Год журнала: 2024, Номер 43(12), С. 2397 - 2423

Опубликована: Май 17, 2024

Язык: Английский

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Transcription-coupled AID deamination damage depends on ELOF1-associated RNA polymerase II

Molecular Cell, Год журнала: 2025, Номер unknown

Опубликована: Март 1, 2025

Язык: Английский

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STK19 facilitates the clearance of lesion-stalled RNAPII during transcription-coupled DNA repair

Cell, Год журнала: 2024, Номер 187(25), С. 7107 - 7125.e25

Опубликована: Ноя. 14, 2024

Transcription-coupled DNA repair (TCR) removes bulky lesions impeding RNA polymerase II (RNAPII) transcription. Recent studies have outlined the stepwise assembly of TCR factors CSB, CSA, UVSSA, and transcription factor IIH (TFIIH) around lesion-stalled RNAPII. However, mechanism required for transition to downstream steps, including RNAPII removal provide proteins access lesion, remain unclear. Here, we identify STK19 as a facilitating this transition. Loss does not impact initial complex or ubiquitylation but delays clearance, thereby interfering with reaction. Cryoelectron microscopy (cryo-EM) mutational analysis reveal that associates complex, positioning itself between RNAPII, CSA. The structural insights molecular modeling suggest positions ATPase subunits TFIIH onto in front Together, these findings new into mechanisms TCR.

Язык: Английский

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Distinct DNA repair mechanisms prevent formaldehyde toxicity during development, reproduction and aging

Nucleic Acids Research, Год журнала: 2024, Номер 52(14), С. 8271 - 8285

Опубликована: Июнь 19, 2024

Abstract Formaldehyde (FA) is a recognized environmental and metabolic toxin implicated in cancer development aging. Inherited mutations the FA-detoxifying enzymes ADH5 ALDH2 genes lead to FA overload severe multisystem AMeD syndrome. accumulation causes genome damage including DNA–protein-, inter- intra-strand crosslinks oxidative lesions. However, influence of distinct DNA repair systems on organismal resistance remains elusive. We have here investigated consequence range mutants model endogenous generated by downregulating orthologs human C. elegans. focused components nucleotide excision (NER) during developmental growth, reproduction Our results reveal three modes FA-induced damage: Transcription-coupled (TCR) operating NER-independently growth or through NER adulthood, and, concert with global-genome (GG-) NER, germline early embryonic development. Additionally, we show that Cockayne syndrome B (CSB) factor involved resolution DNA–protein crosslinks, antioxidant quencher N-acetyl-l-cysteine (NAC) reverses sensitivity detoxification defects development, suggesting therapeutic intervention revert FA-pathogenic consequences.

Язык: Английский

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STK19 drives transcription-coupled repair by stimulating repair complex stability, RNA Pol II ubiquitylation, and TFIIH recruitment

Molecular Cell, Год журнала: 2024, Номер unknown

Опубликована: Ноя. 1, 2024

Transcription-coupled nucleotide excision repair (TC-NER) efficiently eliminates DNA damage that impedes gene transcription by RNA polymerase II (RNA Pol II). TC-NER is initiated the recognition of lesion-stalled CSB, which recruits CRL4

Язык: Английский

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Differential processing of RNA polymerase II at DNA damage correlates with transcription-coupled repair syndrome severity

Nucleic Acids Research, Год журнала: 2024, Номер 52(16), С. 9596 - 9612

Опубликована: Июль 18, 2024

Abstract DNA damage severely impedes gene transcription by RNA polymerase II (Pol II), causing cellular dysfunction. Transcription-Coupled Nucleotide Excision Repair (TC-NER) specifically removes such transcription-blocking damage. TC-NER initiation relies on the CSB, CSA and UVSSA proteins; loss of any results in complete deficiency. Strikingly, deficiency UV-Sensitive Syndrome (UVSS), with mild cutaneous symptoms, while or CSB activity severe Cockayne (CS), characterized neurodegeneration premature aging. Thus far underlying mechanism for these contrasting phenotypes remains unclear. Live-cell imaging approaches reveal that proficient cells, lesion-stalled Pol is swiftly resolved, knockout (KO) elongating damage-bound, likely obstructing other transacting processes shielding from alternative repair pathways. In contrast, KO cleared via VCP-mediated proteasomal degradation which fully dependent CRL4CSA ubiquitin ligase activity. This might provide access mechanisms, as GG-NER, to remove Collectively, our data indicate inability clear chromatin, rather than deficiency, causes observed CS.

Язык: Английский

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Transcription blocking properties and transcription-coupled repair of N2-alkylguanine adducts as a model for aldehyde-induced DNA damage

Journal of Biological Chemistry, Год журнала: 2025, Номер unknown, С. 108459 - 108459

Опубликована: Март 1, 2025

The N2 position of guanine is a preferential reaction site in DNA for numerous dietary and environmental carcinogens or their electrophilic metabolites, aldehydes arising from lipid peroxidation as well reactive by-products normal metabolism. However, repair mechanisms the resulting covalent adducts mammalian cells are not understood, with nucleotide excision (NER), base (BER), dioxygenase-mediated damage reversal being discussed likely pathways. Considering fundamentally different recognition principles between global genome (GG)-NER transcription-coupled (TC)-NER, we here assessed transcription blocking capacities four synthetic deoxyguanosine (dGuo) variable size geometry, using transfection-based reporter assay. Notably, aliphatic N2-ethylguanine (EtG), exocyclic 1,N2-ethenoguanine (εG), bulky polycyclic 3-(deoxyguanosin-N2-yl)-2-acetylaminofluorene (AAFG), displayed robust strand-specific transcription-blocking properties. specific TC-NER components CSA CSB were consistently required removal all N2-dGuo adducts, whereas absence XPC DDB2/XPE (both to GG-NER) did compromise isogenic human cell models. In contrast, no inhibition gene expression was detected constructs carrying N2-methylguanine (MeG) even NER-deficient XP-A line, suggesting that this adduct either bypassed very high efficiency during repaired by mechanism NER. Collectively, results identify bigger than MeG structural subclass lesions whose heavily relies on pathway.

Язык: Английский

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Clearance of DNA damage-arrested RNAPII is selectively impaired in Cockayne syndrome cells

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 18, 2024

Abstract Arrest of elongating RNA polymerase II (RNAPII) at DNA lesions initiates transcription-coupled repair (TCR), involving the concerted action specific TCR factors, followed by downstream nucleotide excision steps. Remarkedly, only congenital defects in CSA or CSB genes cause neurodegenerative disorder Cockayne syndrome, which is not observed with other genes, despite their equal importance TCR. An explanation for this discrepancy has been lacking. In study, we developed an assay to track fate RNAPII sites UV-induced lesions. Employing method on isogenic collection knockout cells reveals a selective clearance defect defective CSB, contrast knockouts genes. Our findings provide evidence that deficiency processing and prolonged transcription arrests response damage, rather than compromised repair, may underlie syndrome-like phenotype.

Язык: Английский

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