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NGS based viability screening using haploid cell line

ABSTRACT: Identification of human deubiquitylating enzymes whose knock out result in hypersensitivity to DNA damaging agents, by comparing the sequence reads of ‘barcode region’ from mixed cell culture.

PROVIDER: EGAS00001001095 | EGA |

REPOSITORIES: EGA

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EGAS00001001095-sc-20150702 - samples

Project description:Identification of human deubiquitylating enzymes whose knock out result in hypersensitivity to DNA damaging agents, by comparing the sequence reads of 'barcode region' from mixed cell culture.

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Gene expression in wild type and Cagal102 knockout Candida albicans strains.

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Alpha-ketoglutarate -mediated carnitine synthesis promotes homologous recombination via histone acetylation

Project description:Homologous recombination (HR) deficiency enhances sensitivity to DNA damaging agents commonly used to treat cancer. In HR-proficient cancers, metabolic mechanisms driving response or resistance to DNA damaging agents remain unclear. Here we identified that depletion of alpha-ketoglutarate (αKG) sensitizes HR-proficient cells to DNA damaging agents by metabolic regulation of histone acetylation. αKG is required for the activity of αKG-dependent dioxygenases (αKGDDs), and prior work has shown that changes in αKGDD affect demethylases. Using a targeted CRISPR knockout library consisting of 64 αKGDDs, we discovered that Trimethyllysine Hydroxylase Epsilon (TMLHE), the first and rate-limiting enzyme in de novo carnitine synthesis, is necessary for proliferation of HR-proficient cells in the presence of DNA damaging agents. Unexpectedly, αKG-mediated TMLHE-dependent carnitine synthesis was required for histone acetylation, while histone methylation was affected but dispensable. The increase in histone acetylation via αKG-dependent carnitine synthesis promoted HR-mediated DNA repair through site- and substrate-specific histone acetylation. These data demonstrate for the first time that HR-proficiency is mediated through αKG directly influencing histone acetylation via carnitine synthesis and provide a metabolic avenue to induce HR-deficiency and sensitivity to DNA damaging agents.

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Homo sapiens

Project description:Identifying Novel Predictors of Resistance to DNA Damaging Agents

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Mixed colonies of Aspergillus niger and Aspergillus oryzae cooperatively degrading wheat bran

Project description:A. niger and A. oryzae are two filamentous fungi widely used in industry to produce various enzymes (e.g. pectinases, amylases) and metabolites (e.g. citric acid). Using proteomics, the co-cultivation of these two fungi in wheat bran showed an equal distribution of the two strains forming mixed colonies with a broad range of carbohydrate active enzymes produced. This stable mixed microbial system seems suitable for subsequent commercial processes such as enzyme production. XlnR knock-out strains for both aspergilli were used to study the influence of plant cell wall degrading enzyme production on the fitness of the mixed culture.

2017-02-27 | PXD005532 | Pride

Gene expression in wild type and Cagal102 knockout Candida albicans strains.

Project description:CaGAL102 is a sequence homolog of Rmlb. In Candida knock out of this gene causes abnormal hyphal morphogenesis and increased sensitivity to cell wall damaging agents. The knock out strain is also avirulent in mouse model of systemic infection. To get a larger insight into the function of the protein product of this gene we carried out global transcription analysis through micro array experiment. The gene is expressed under normal growth conditions and the knock out causes the cells to become hyphal under these conditions. Many of the cell wall proteins were upregulated recapitulating the cell morphology. Keywords: Candida albicans, Gene knockout, genome wide transcription profiling study Wild type Sc5314 cells and the mutant CAS12 were grown in YPD till (OD 600nm) 1 following which total RNA was extracted using hot phenol method. The RNA was checked using Bioanalyser (Agilent). Single dye experiment was carried out using Cy3 labelled pooled wild type samples and two independent mutant RNA samples.

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Systematic profiling of lysine lactylation proteome reveals distinct changes in lactylation between the parental AGS cells and cisplatin-resistant AGS cells

Project description:Lactate enable to cause a novel post-translational modification, lactylation of proteins. We are interested in exploring whether lactate modulates DNA-damaging agents resistance in the form of lactylation. To gain a global view of DNA-damaging agents resistance-related lactylation, especially Kla of nonhistone substrates, we used 4D-Label free high-resolution LC-MS/MS, quantitative lysine lactylation analysis to investigate Kla substrates in cisplatin-resistant AGS cells.

2022-12-16 | PXD038880 |

Systematic profiling of lysine lactylation proteome reveals distinct changes in lactylation between the parental AGS cells and cisplatin-resistant AGS cells

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Genome-wide profiling of γH2AX in Arabidopsis

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2019-04-17 | GSE124943 | GEO

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