scholarly journals A Genome-wide Screen Identifies p97 as an Essential Regulator of DNA Damage-Dependent CDT1 Destruction

2011 ◽  
Vol 44 (1) ◽  
pp. 72-84 ◽  
Author(s):  
Malavika Raman ◽  
Courtney G. Havens ◽  
Johannes C. Walter ◽  
J. Wade Harper
Keyword(s):  
Dna Damage ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-wide screening identifies cell cycle control as a synthetic lethal pathway with SRSF2P95H mutation

2021 ◽  
Author(s):  
Jane Jialu Xu ◽  
Alistair M Chalk ◽  
Iva Nikolic ◽  
Kaylene Simpson ◽  
Monique F Smeets ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Dna Damage ◽  
Cell Lines ◽  
Dna Damage Response ◽  
Functional Screening ◽  
Wild Type ◽  
Synthetic Lethal ◽  
Genome Wide ◽  
A Genome ◽  
Damage Response

Current strategies to target RNA splicing mutant myeloid cancers proposes targeting the remaining splicing apparatus. This approach has only been modestly sensitizing and is also toxic to non-mutant bearing wild-type cells. To explore potentially exploitable genetic interactions with spliceosome mutations, we combined data mining and functional screening for synthetic lethal interactions with an Srsf2P95H/+ mutation. Analysis of mis-splicing events in a series of both human and murine SRSF2P95H mutant samples across multiple myeloid diseases (AML, MDS, CMML) was performed to identify conserved mis-splicing events. From this analysis, we identified that the cell cycle and DNA repair pathways were overrepresented within the conserved mis-spliced transcript sets. In parallel, to functionally define pathways essential for survival and proliferation of Srsf2P95H/+ cells, we performed a genome-wide CRISPR loss of function screen using Hoxb8 immortalized R26-CreERki/+ Srsf2P95H/+ and R26-CreERki/+ Srsf2+/+ cell lines. We assessed loss of sgRNA representation at three timepoints: immediately after Srsf2P95H/+ activation, and at one week and two weeks post Srsf2P95H/+ mutation. Pathway analysis demonstrated that the cell cycle and DNA damage response pathways were amongst the top synthetic lethal pathways with Srsf2P95H/+ mutation. Based on the loss of guide RNAs targeting Cdk6, we identified that Palbociclib, a CDK6 inhibitor, showed preferential sensitivity in Srsf2P95H/+ cell lines and in primary non-immortalized lin-cKIT+Sca-1+ cells compared to wild type controls. Our data strongly suggest that the cell cycle and DNA damage response pathways are required for Srsf2P95H/+ cell survival, and that Palbociclib could be an alternative therapeutic option for targeting SRSF2 mutant cancers.

scholarly journals A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response

2012 ◽  
Vol 14 (3) ◽  
pp. 318-328 ◽  
Author(s):  
Britt Adamson ◽  
Agata Smogorzewska ◽  
Frederic D. Sigoillot ◽  
Randall W. King ◽  
Stephen J. Elledge
Keyword(s):  
Dna Damage ◽  
Homologous Recombination ◽  
Dna Damage Response ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Genome Wide ◽  
A Genome ◽  
Damage Response

scholarly journals RADAR-seq: A RAre DAmage and Repair sequencing method for detecting DNA damage on a genome-wide scale

DNA Repair ◽  
2019 ◽  
Vol 80 ◽  
pp. 36-44 ◽  
Author(s):  
Kelly M. Zatopek ◽  
Vladimir Potapov ◽  
Lisa L. Maduzia ◽  
Ece Alpaslan ◽  
Lixin Chen ◽  
...  
Keyword(s):  
Dna Damage ◽  
Genome Wide ◽  
Sequencing Method ◽  
A Genome ◽  
Wide Scale

scholarly journals MTBP phosphorylation controls DNA replication origin firing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pedro Ferreira ◽  
Verena Höfer ◽  
Nora Kronshage ◽  
Anika Marko ◽  
Karl-Uwe Reusswig ◽  
...  
Keyword(s):  
Dna Damage ◽  
Replication Origin ◽  
Genome Duplication ◽  
Origin Firing ◽  
Cyclin Dependent Kinases ◽  
Genome Wide ◽  
A Genome ◽  
Cyclin C ◽  
Dna Replication Origin ◽  
Eukaryotic Origin

AbstractFaithful genome duplication requires regulation of origin firing to determine loci, timing and efficiency of replisome generation. Established kinase targets for eukaryotic origin firing regulation are the Mcm2-7 helicase, Sld3/Treslin/TICRR and Sld2/RecQL4. We report that metazoan Sld7, MTBP (Mdm2 binding protein), is targeted by at least three kinase pathways. MTBP was phosphorylated at CDK consensus sites by cell cycle cyclin-dependent kinases (CDK) and Cdk8/19-cyclin C. Phospho-mimetic MTBP CDK site mutants, but not non-phosphorylatable mutants, promoted origin firing in human cells. MTBP was also phosphorylated at DNA damage checkpoint kinase consensus sites. Phospho-mimetic mutations at these sites inhibited MTBP’s origin firing capability. Whilst expressing a non-phospho MTBP mutant was insufficient to relieve the suppression of origin firing upon DNA damage, the mutant induced a genome-wide increase of origin firing in unperturbed cells. Our work establishes MTBP as a regulation platform of metazoan origin firing.

scholarly journals Genome-Wide Adductomics Analysis Reveals Heterogeneity in the Induction and Loss of Cyclobutane Thymine Dimers across Both the Nuclear and Mitochondrial Genomes

2019 ◽  
Vol 20 (20) ◽  
pp. 5112 ◽  
Author(s):  
Alaa S. Alhegaili ◽  
Yunhee Ji ◽  
Nicolas Sylvius ◽  
Matthew J. Blades ◽  
Mahsa Karbaschi ◽  
...  
Keyword(s):  
Dna Damage ◽  
Nuclear Dna ◽  
Mitochondrial Genomes ◽  
Differential Distribution ◽  
Dna Damage And Repair ◽  
Specific Level ◽  
Genome Wide ◽  
A Genome ◽  
High Resolution Map ◽  
Cellular Dna

The distribution of DNA damage and repair is considered to occur heterogeneously across the genome. However, commonly available techniques, such as the alkaline comet assay or HPLC-MS/MS, measure global genome levels of DNA damage, and do not reflect potentially significant events occurring at the gene/sequence-specific level, in the nuclear or mitochondrial genomes. We developed a method, which comprises a combination of Damaged DNA Immunoprecipitation and next generation sequencing (DDIP-seq), to assess the induction and repair of DNA damage induced by 0.1 J/cm2 solar-simulated radiation at the sequence-specific level, across both the entire nuclear and mitochondrial genomes. DDIP-seq generated a genome-wide, high-resolution map of cyclobutane thymine dimer (T<>T) location and intensity. In addition to being a straightforward approach, our results demonstrated a clear differential distribution of T<>T induction and loss, across both the nuclear and mitochondrial genomes. For nuclear DNA, this differential distribution existed at both the sequence and chromosome level. Levels of T<>T were much higher in the mitochondrial DNA, compared to nuclear DNA, and decreased with time, confirmed by qPCR, despite no reported mechanisms for their repair in this organelle. These data indicate the existence of regions of sensitivity and resistance to damage formation, together with regions that are fully repaired, and those for which > 90% of damage remains, after 24 h. This approach offers a simple, yet more detailed approach to studying cellular DNA damage and repair, which will aid our understanding of the link between DNA damage and disease.

scholarly journals A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Diana van den Heuvel ◽  
Cornelia G. Spruijt ◽  
Román González-Prieto ◽  
Angela Kragten ◽  
Michelle T. Paulsen ◽  
...  
Keyword(s):  
Dna Damage ◽  
Rna Polymerase Ii ◽  
Transcription Elongation ◽  
Genotoxic Stress ◽  
Dna Lesions ◽  
Damage Repair ◽  
Genome Wide ◽  
A Genome ◽  
Processivity Factor ◽  
Dependent Pathway

AbstractBulky DNA lesions in transcribed strands block RNA polymerase II (RNAPII) elongation and induce a genome-wide transcriptional arrest. The transcription-coupled repair (TCR) pathway efficiently removes transcription-blocking DNA lesions, but how transcription is restored in the genome following DNA repair remains unresolved. Here, we find that the TCR-specific CSB protein loads the PAF1 complex (PAF1C) onto RNAPII in promoter-proximal regions in response to DNA damage. Although dispensable for TCR-mediated repair, PAF1C is essential for transcription recovery after UV irradiation. We find that PAF1C promotes RNAPII pause release in promoter-proximal regions and subsequently acts as a processivity factor that stimulates transcription elongation throughout genes. Our findings expose the molecular basis for a non-canonical PAF1C-dependent pathway that restores transcription throughout the human genome after genotoxic stress.

scholarly journals The NuRD chromatin–remodeling complex regulates signaling and repair of DNA damage

2010 ◽  
Vol 190 (5) ◽  
pp. 741-749 ◽  
Author(s):  
Godelieve Smeenk ◽  
Wouter W. Wiegant ◽  
Hans Vrolijk ◽  
Aldo P. Solari ◽  
Albert Pastink ◽  
...  
Keyword(s):  
Dna Damage ◽  
Chromatin Remodeling ◽  
Cell Cycle Progression ◽  
Histone Deacetylation ◽  
Dna Double Strand Breaks ◽  
Nucleosome Remodeling ◽  
Chromatin Remodeling Complex ◽  
Genome Wide ◽  
A Genome ◽  
A Subunit

Cells respond to ionizing radiation (IR)–induced DNA double-strand breaks (DSBs) by orchestrating events that coordinate cell cycle progression and DNA repair. How cells signal and repair DSBs is not yet fully understood. A genome-wide RNA interference screen in Caenorhabditis elegans identified egr-1 as a factor that protects worm cells against IR. The human homologue of egr-1, MTA2 (metastasis-associated protein 2), is a subunit of the nucleosome-remodeling and histone deacetylation (NuRD) chromatin-remodeling complex. We show that knockdown of MTA2 and CHD4 (chromodomain helicase DNA-binding protein 4), the catalytic subunit (adenosine triphosphatase [ATPase]) of NuRD, leads to accumulation of spontaneous DNA damage and increased IR sensitivity. MTA2 and CHD4 accumulate in DSB-containing chromatin tracks generated by laser microirradiation. Directly at DSBs, CHD4 stimulates RNF8/RNF168-dependent formation of ubiquitin conjugates to facilitate the accrual of RNF168 and BRCA1. Finally, we show that CHD4 promotes DSB repair and checkpoint activation in response to IR. Thus, the NuRD chromatin–remodeling complex is a novel regulator of DNA damage responses that orchestrates proper signaling and repair of DSBs.

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