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MetabolomicsMetabolic responses induced by DNA damage and poly (ADP-ribose) polymerase (PARP) inhibition in MCF-7 cells
Genomic instability is one of the hallmarks of cancer. Several chemotherapeutic drugs and radiotherapy induce DNA damage to prevent cancer cell replication. Cells in turn activate different DNA damage response (DDR) pathways to either repair the damage or induce cell death. These DDR pathways also e...
2015-08-01 | MTBLS177 | MetaboLights
ProteomicsIdentification of proteins in the interactomes of 4 DNA-repair proteins of Deinococcus radiodurans
Project includes identification of the interacting partners of the four important DNA-repair proteins (DdrA, DdrB, RecA, Ssb) of the extremophile D. radiodurans. The interacting proteins were crosslinked with DSP, immunoprecipitated using antibodies against the four DNA repair proteins, followed by...
ORGANISM(S): Deinococcus radiodurans R1 
2021-05-07 | PXD021822 | Pride
Deinococcus radiodurans dna damage repair 
ProteomicsPAXX and its paralogues synergistically direct DNA polymerase I activity in DNA repair
In this study, we characterised the interactomes of PAXX and its paralogs, XLF and XRCC4, to show that these factors share the ability to interact with DNA polymerase lambda (Poll), stimulate its activityand are required for the recruitment of Poll to laser-induced DNA damage sites.
ORGANISM(S): Homo sapiens (Human) 
2018-09-24 | PXD010891 | Pride
Polymerase lambda Xrcc4 Double strand breaks Nhej Paxx Dna repair Xlf Dna-pkcs 
ProteomicsProteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links part 2 of 2: AP-MS DATA (QUBIC)
DNA interstrand crosslinks (ICLs) block replication fork progression by inhibiting DNA strand separation. Repair of ICLs requires sequential incisions, translesion DNA synthesis, and homologous recombination, but the full set of factors involved in these transactions remains unknown. Here we establi...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-03-13 | MSV000079577 | MassIVE
MetabolomicsWe characterize the anti-phage function of a type IV TA system, ShosTA toxin-antitoxin system provides phage defense via DNA damage and repair
Widespread in bacteria and archaea, Toxin-antitoxin (TA) systems have been recently demonstrated to function in phage defense. Here we characterize the anti-phage function of a type IV TA system, ShosTA. Using structural and biochemical approaches, we show that ShosT couples phosphoribosyltransferas...
2025-02-17 | MTBLS11212 | MetaboLights
ProteomicsDNA repair in Mycoplasma gallisepticum
In the current study, we attempted to characterize the DNA repair system of Mycopalsma gallisepticum. We identified members of different DNA repair pathways based on genomic data and publications. We quantified mRNA of respective proteins per cell in a set of adverse conditions and identified most o...
ORGANISM(S): Mycoplasma gallisepticum 
2014-07-30 | PXD000249 | Pride
Dna repair Tof Mycoplasma 
TranscriptomicsDNA repair and recovery of RNA synthesis following exposure to ultraviolet light are delayed in long genes
The kinetics of DNA repair and RNA synthesis recovery in human cells following UV-irradiation were assessed using nascent RNA Bru-seq and quantitative long PCR. It was found that UV light inhibited transcription elongation and that recovery of RNA synthesis occurred as a wave in the 5’-3’ direction ...
ORGANISM(S): Homo sapiens 
2015-03-03 | E-GEOD-65985 | biostudies-arrayexpress
GenomicsCovalent linkage of the DNA repair template to the CRISPR-Cas9 nuclease enhances homology-directed repair
Based on the hypothesis that, enhancing the local concentration of donor oligos could increase the correction rates, we generated and tested novel CRISPR-Cas9 systems, in which the DNA repair template is covalently conjugated to Cas9 (RNPD system). To validate our results from the HEK293T reporter c...
ORGANISM(S): Mus musculus 
2018-06-04 | E-MTAB-6808 | biostudies-arrayexpress
TranscriptomicsExpanding epigenomics to archived FFPE tissues: An evaluation of DNA repair methodologies
A study to evaluate techniques for repairing DNA from formalin-fixed paraffin-embedded (FFPE) tissue samples by direct comparison of FFPE DNA repair methods prior to analysis on genome-wide methylation array to matched fresh frozen (FF) tissues. Formalin-fixed paraffin-embedded tissue from three col...
ORGANISM(S): Homo sapiens 
2014-12-17 | E-GEOD-59038 | biostudies-arrayexpress
TranscriptomicsCPD-seq mapping of UV damage formation and repair in yeast
UV-induced DNA lesions are an important contributor to mutagenesis and cancer, but it is not fully understood how the chromosomal landscape influences UV lesion formation and repair. We have used a novel high-throughput sequencing method to precisely map UV-induced cyclobutane pyrimidine dimers (CPD...
ORGANISM(S): Saccharomyces cerevisiae 
2016-08-19 | E-GEOD-79977 | biostudies-arrayexpress
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