Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion Lumos
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Fibroblast
DISEASE(S): Cockayne Syndrome
SUBMITTER: 
Jeroen Demmers
LAB HEAD: Jeroen Demmers
PROVIDER: PXD025304 | Pride | 2021-04-20
REPOSITORIES: Pride
Similar Datasets
Project description:Correct transcription is crucial for life. However, DNA damage severely impedes elongating RNA Polymerase II (Pol II), causing transcription inhibition and transcription-replication conflicts. Cells have evolved intricate mechanisms to counteract the severe consequence of these transcription-blocking lesions, however the exact mechanism and factors involved remain largely unknown. Here, using a genome-wide CRISPR/cas9 screen, we identified elongation factor ELOF1 as an important new factor in the damage-induced transcription stress response. ELOF1 has an evolutionary-conserved role in TC-NER where it promotes the recruitment of the TC-NER factors UVSSA and TFIIH and facilitates Pol II ubiquitylation to efficiently repair TBLs. Importantly, ELOF1 has an additional role in protecting cells from transcription-mediated replication hindrance, thereby preserving genome stability. Thus, ELOF1 protects the transcription machinery from DNA damage by two distinct mechanisms.
2020-04-18 | GSE148844 | GEO
Project description:DNA-protein crosslinks (DPCs), arise from enzymatic intermediates, endogenous metabolism or exogenous chemicals like chemotherapeutics. DPCs are highly cytotoxic as they will impede DNA transacting processes such as replication, which is counteracted by proteolysis-mediated DPC removal by the protease SPRTN or the proteasome. However, how DPCs affect transcription and how transcription-blocking DPCs are repaired remains largely unknown. Here, we show that DPCs severely inhibit RNA polymerase II (Pol II)-mediated transcription, resulting in the recruitment of the transcription-coupled nucleotide excision repair (TC-NER) factors CSA and CSB. Interestingly, CSA and CSB are indispensable for transcription-coupled DPC (TC-DPC) repair, while the downstream TC-NER factors UVSSA and XPA are not, indicative of a non-canonical TC-NER mechanism. TC-DPC repair functions independent of SPRTN, but is mediated by the activities of the ubiquitin ligase CRL4CSA and the proteasome. Thus, DPCs are preferentially repaired in genes by a dedicated transcription-coupled repair mechanism, which is crucial to warrant correct transcription.
2024-02-09 | PXD041679 | Pride
Project description:Transcription-blocking DNA lesions are specifically targeted by transcription-coupled nucleotide excision repair (TC-NER), which removes a broad spectrum of DNA lesions to preserve transcriptional output and thereby cellular homeostasis to counteract aging. TC-NER is initiated by the stalling of RNA polymerase II at DNA lesions, which triggers the assembly of the TC-NER-specific proteins CSA, CSB and UVSSA. CSA, a WD40-repeat containing protein, is the substrate receptor subunit of a cullin-RING ubiquitin ligase complex composed of DDB1, CUL4A/B and RBX1 (CRL4CSA). Although ubiquitination of several TC-NER proteins by CRL4CSA has been reported, it is still unknown how this complex is regulated. To unravel the dynamic molecular interactions and the regulation of this complex, we applied a single-step protein-complex isolation coupled to mass spectrometry analysis and identified DDA1 as a CSA interacting protein. Cryo-EM analysis showed that DDA1 is an integral component of the CRL4CSA complex. Functional analysis revealed that DDA1 coordinates ubiquitination dynamics during TC-NER and is required for efficient turnover and progression of this process.
2024-05-02 | PXD051638 | Pride
Project description:Transcription-blocking DNA lesions are removed by transcription-coupled nucleotide excision repair (TC-NER) to preserve cell viability. TC-NER is triggered by the stalling of RNA polymerase II at DNA lesions, leading to the recruitment of TC-NER-specific factors such as the CSA-DDB1-CUL4A-RBX1 cullin-RING ubiquitin ligase complex (CRLCSA). Despite its vital role in TC-NER, little is known about the regulation of the CRLCSA complex during TC-NER. Using conventional and cross-linking immunoprecipitations coupled to mass spectrometry, we uncover a stable interaction between CSA and the TRiC chaperonin. TRiC’s binding to CSA ensures its stability and DDB1-dependent assembly into the CRLCSA complex. Consequently, loss of TRiC leads to mislocalization and depletion of CSA, as well as impaired transcription recovery following UV damage, suggesting defects in TC-NER. Furthermore, Cockayne syndrome (CS)-causing mutations in CSA lead to increased TRiC binding and a failure to compose the CRLCSA complex. Thus, we uncover CSA as a novel TRiC substrate and reveal a role for TRiC in regulating CSA-dependent TC-NER and the development of CS.
2018-05-02 | PXD008868 | Pride
Project description:Transcription-coupled nucleotide excision repair (TC-NER) is promptly triggered by 'local' elongating RNAP II molecules encountering DNA adducts such as cyclobutane pyrimidine dimers (CPD) induced by ultraviolet light and speeds up removing and repair in transcribed loci. Genome-wide measurements have revealed a dramatic shutdown of global transcription with a few exceptions of individual genes that are consequently highly upregulated by DNA damage. Deciphering the underlying mechanisms of the multifaceted transcriptional response always comprises one of the most fascinating frontiers in DNA repair research. Recent reports have revealed that persistent RNAP II initiation at the transcription start site of active regulatory regions with the continuous synthesis of start-RNAs guarantee sufficient scanning and repair of the whole transcribed genome, although transcription elongation drastically slows down shortly after genotoxic stress. Furthermore, a recent study found that RNA is extremely rapidly m6A methylated by METTL3 in response to UV irradiation which is crucial for recruitment of Pol k to DNA damage sites and subsequently mediates TC-NER. Together, these findings substantiate the molecular processes underlying the transcription-coordinated cellular response upon genotoxic stress might be more complex than previously believed. Unfortunately, all these findings merely focused on the early phase of recovery (within 4 hr after DNA damage). It remains to be determined how accessible chromatin reconfigures and regulates transcriptional programs in UV-induced DNA damage repair. It is also unclear whether the dynamics of gene expression are associated with other epigenomic reconstruction events such as global DNA methylation and demethylation. Moreover, the roles of internal messenger RNA modifications like N6-methyladenosine in TC-NER are poorly understood. Our integrative analyses provide a comprehensive view of the spatio-temporal chromatin configuration and epigenetic characterizations that accompanies TC-NER.
2020-11-20 | GSE161789 | GEO
Project description:Transcription-coupled nucleotide excision repair (TC-NER) is promptly triggered by 'local' elongating RNAP II molecules encountering DNA adducts such as cyclobutane pyrimidine dimers (CPD) induced by ultraviolet light and speeds up removing and repair in transcribed loci. Genome-wide measurements have revealed a dramatic shutdown of global transcription with a few exceptions of individual genes that are consequently highly upregulated by DNA damage. Deciphering the underlying mechanisms of the multifaceted transcriptional response always comprises one of the most fascinating frontiers in DNA repair research. Recent reports have revealed that persistent RNAP II initiation at the transcription start site of active regulatory regions with the continuous synthesis of start-RNAs guarantee sufficient scanning and repair of the whole transcribed genome, although transcription elongation drastically slows down shortly after genotoxic stress. Furthermore, a recent study found that RNA is extremely rapidly m6A methylated by METTL3 in response to UV irradiation which is crucial for recruitment of Pol k to DNA damage sites and subsequently mediates TC-NER. Together, these findings substantiate the molecular processes underlying the transcription-coordinated cellular response upon genotoxic stress might be more complex than previously believed. Unfortunately, all these findings merely focused on the early phase of recovery (within 4 hr after DNA damage). It remains to be determined how accessible chromatin reconfigures and regulates transcriptional programs in UV-induced DNA damage repair. It is also unclear whether the dynamics of gene expression are associated with other epigenomic reconstruction events such as global DNA methylation and demethylation. Moreover, the roles of internal messenger RNA modifications like N6-methyladenosine in TC-NER are poorly understood. Our integrative analyses provide a comprehensive view of the spatio-temporal chromatin configuration and epigenetic characterizations that accompanies TC-NER.
2020-11-20 | GSE161791 | GEO
Project description:Transcription-coupled nucleotide excision repair (TC-NER) is promptly triggered by 'local' elongating RNAP II molecules encountering DNA adducts such as cyclobutane pyrimidine dimers (CPD) induced by ultraviolet light and speeds up removing and repair in transcribed loci. Genome-wide measurements have revealed a dramatic shutdown of global transcription with a few exceptions of individual genes that are consequently highly upregulated by DNA damage. Deciphering the underlying mechanisms of the multifaceted transcriptional response always comprises one of the most fascinating frontiers in DNA repair research. Recent reports have revealed that persistent RNAP II initiation at the transcription start site of active regulatory regions with the continuous synthesis of start-RNAs guarantee sufficient scanning and repair of the whole transcribed genome, although transcription elongation drastically slows down shortly after genotoxic stress. Furthermore, a recent study found that RNA is extremely rapidly m6A methylated by METTL3 in response to UV irradiation which is crucial for recruitment of Pol k to DNA damage sites and subsequently mediates TC-NER. Together, these findings substantiate the molecular processes underlying the transcription-coordinated cellular response upon genotoxic stress might be more complex than previously believed. Unfortunately, all these findings merely focused on the early phase of recovery (within 4 hr after DNA damage). It remains to be determined how accessible chromatin reconfigures and regulates transcriptional programs in UV-induced DNA damage repair. It is also unclear whether the dynamics of gene expression are associated with other epigenomic reconstruction events such as global DNA methylation and demethylation. Moreover, the roles of internal messenger RNA modifications like N6-methyladenosine in TC-NER are poorly understood. Our integrative analyses provide a comprehensive view of the spatio-temporal chromatin configuration and epigenetic characterizations that accompanies TC-NER.
2020-11-20 | GSE161790 | GEO
Project description:Transcription-coupled nucleotide excision repair (TC-NER) is promptly triggered by 'local' elongating RNAP II molecules encountering DNA adducts such as cyclobutane pyrimidine dimers (CPD) induced by ultraviolet light and speeds up removing and repair in transcribed loci. Genome-wide measurements have revealed a dramatic shutdown of global transcription with a few exceptions of individual genes that are consequently highly upregulated by DNA damage. Deciphering the underlying mechanisms of the multifaceted transcriptional response always comprises one of the most fascinating frontiers in DNA repair research. Recent reports have revealed that persistent RNAP II initiation at the transcription start site of active regulatory regions with the continuous synthesis of start-RNAs guarantee sufficient scanning and repair of the whole transcribed genome, although transcription elongation drastically slows down shortly after genotoxic stress. Furthermore, a recent study found that RNA is extremely rapidly m6A methylated by METTL3 in response to UV irradiation which is crucial for recruitment of Pol k to DNA damage sites and subsequently mediates TC-NER. Together, these findings substantiate the molecular processes underlying the transcription-coordinated cellular response upon genotoxic stress might be more complex than previously believed. Unfortunately, all these findings merely focused on the early phase of recovery (within 4 hr after DNA damage). It remains to be determined how accessible chromatin reconfigures and regulates transcriptional programs in UV-induced DNA damage repair. It is also unclear whether the dynamics of gene expression are associated with other epigenomic reconstruction events such as global DNA methylation and demethylation. Moreover, the roles of internal messenger RNA modifications like N6-methyladenosine in TC-NER are poorly understood. Our integrative analyses provide a comprehensive view of the spatio-temporal chromatin configuration and epigenetic characterizations that accompanies TC-NER.
2020-11-20 | GSE161792 | GEO
Project description:Repair of UV damage from the transcribed strand (TS) of yeast genes is rapid due to the transcription coupled nucleotide excision repair (TC-NER) pathway. TC-NER is triggered when RNA polymerase stalls at UV damage, such as a UV-induced cyclobutane pyrimidine dimer (CPD). During transcription, the histone methyltransferase Set2 methylates histone H3K36, but it is not known if Set2 regulates TC-NER. Here, we report genome-wide repair maps of UV-induced cyclobutane pyrimidine dimers (CPDs) in yeast cells lacking Set2.
2022-02-21 | GSE179794 | GEO
Project description:Transcription-coupled nucleotide excision repair (TC-NER) is an important DNA repair mechanism that responds to RNA polymerase (RNAP) stalling and removes DNA lesions from transcribed genes. Activation of TC-NER requires specific factors, such as human Cockayne syndrome group B (CSB) protein or its yeast homolog Rad26. Mutations in CSB are associated with the severe neurological disorder Cockayne syndrome. However, the genome-wide role of CSB/Rad26 in TC-NER, particularly in the context of chromatin organization, is not fully understood. Here we used single-nucleotide resolution UV damage mapping data to investigate the genome-wide function of Rad26 in TC-NER. Our data shows that Rad26 is critical for TC-NER in transcribed regions downstream of the first (+1) nucleosome; however, Rad26 is largely dispensable for TC-NER in the +1 nucleosome. We further show that the Rad26-independent TC-NER in the +1 nucleosome is correlated with high occupancy of the transcription initiation/repair factor TFIIH. Downstream of the +1 nucleosome, the combination of low TFIIH occupancy and high occupancy of the transcription elongation factor Spt4/Spt5 suppresses TC-NER when Rad26 is dysfunctional. Deletion of SPT4 significantly restores TC-NER in the downstream nucleosomes in a rad26∆ mutant. Collectively, these data indicate that the requirement for Rad26 in TC-NER is modulated by the distribution of TFIIH and Spt4/Spt5, and Rad26 mainly functions in the downstream nucleosomes to remove TC-NER suppression by Spt4/Spt5.
2020-06-30 | GSE145911 | GEO