A5059797893- CRISPR and Genetic Engineering
- DNA Repair Mechanisms
- Genomics and Chromatin Dynamics
- HIV Research and Treatment
- Cancer Genomics and Diagnostics
- Plant Virus Research Studies
- Pluripotent Stem Cells Research
- RNA Research and Splicing
- DNA and Nucleic Acid Chemistry
Oncode Institute
2019-2024
The Netherlands Cancer Institute
2019-2024
Babraham Institute
2019
DNA double-strand break (DSB) repair is mediated by multiple pathways. It thought that the local chromatin context affects pathway choice, but underlying principles are poorly understood. Using a multiplexed reporter assay in combination with Cas9 cutting, we systematically measure relative activities of three DSB pathways as function >1,000 genomic locations. This reveals non-homologous end-joining (NHEJ) broadly biased toward euchromatin, while contribution microhomology-mediated (MMEJ)...
Extrachromosomal circular DNA (eccDNA) facilitates adaptive evolution by allowing rapid and extensive gene copy number variation is implicated in the pathology of cancer ageing. Here, we demonstrate that yeast aged under environmental copper accumulate high levels eccDNA containing copper-resistance CUP1. Transcription tandemly repeated CUP1 causes accumulation, which occurs absence phenotypic selection. We have developed a sensitive quantitative sequencing pipeline reveals accumulation on...
DNA double-strand breaks are repaired by multiple pathways, including non-homologous end-joining (NHEJ) and microhomology-mediated (MMEJ). The balance of these pathways is dependent on the local chromatin context, but underlying mechanisms poorly understood. By combining knockout screening with a dual MMEJ:NHEJ reporter inserted in 19 different environments, we identified dozens repair proteins that modulate pathway state. Proteins favor NHEJ mostly synergize euchromatin, while MMEJ...
Cells respond to double-strand breaks (DSBs) by activating DNA damage response pathways, including cell cycle arrest. We have previously shown that a single break generated via CRISPR/Cas9 is sufficient delay progression and compromise viability. However, we also found the cellular DSBs can vary, independent of number lesions. This implies not all are equally toxic, raises question if location could influence its toxicity. To systematically investigate DSB-location determinant toxicity...
Abstract The efficiency and outcome of CRISPR/Cas9 editing depends on the chromatin state at cut site. It has been shown that changing can influence both repair outcome, epigenetic drugs have used to improve Cas9 editing. However, because target proteins these are not homogeneously distributed across genome, efficacy may be expected vary from locus locus. Here, we systematically analyzed this context-dependency for 160 drugs. We a human cell line with 19 stably integrated reporters induce...
Extrachromosomal circular DNA (eccDNA) facilitates adaptive evolution by allowing rapid and extensive gene copy number variation, is implicated in the pathology of cancer ageing. Here, we demonstrate that yeast aged under environmental copper accumulate high levels eccDNA containing resistance CUP1 . Transcription causes accumulation, which occurs absence phenotypic selection. We have developed a sensitive quantitative sequencing pipeline reveals accumulation on exposure to be exquisitely...
ABSTRACT DNA double-strand breaks are repaired by multiple pathways, including non-homologous end-joining (NHEJ) and microhomology-mediated (MMEJ). The balance of these pathways is dependent on the local chromatin context, but underlying mechanisms poorly understood. By combining knockout screening with a dual MMEJ:NHEJ reporter inserted in 19 different environments, we identified dozens repair proteins that modulate pathway state. Proteins favor NHEJ mostly synergize euchromatin, while MMEJ...
Abstract DNA double-strand break (DSB) repair is mediated by multiple pathways, including classical non-homologous end-joining pathway (NHEJ) and several homology-driven pathways. This particularly important for Cas9-mediated genome editing, where the outcome critically depends on that repairs break. It thought local chromatin context affects choice, but underlying principles are poorly understood. Using a newly developed multiplexed reporter assay in combination with Cas9 cutting, we...
ABSTRACT The efficiency and outcome of CRISPR/Cas9 editing depends on the chromatin state at cut site. It has been shown that changing can influence both repair outcome, epigenetic drugs have used to improve Cas9 editing. However, because target proteins these are not homogeneously distributed across genome, efficacy may be expected vary from locus locus. Here, we systematically analyzed this context-dependency for 160 drugs. We a human cell line with 19 stably integrated reporters induce...