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Chromatin context-dependent effects of epigenetic drugs on CRISPR-Cas9 editing

ABSTRACT: We sought to find if epigenetic drugs had chromatin context-dependent effects on CRISPR-Cas9 efficiency and DNA double-strand break repair. We performed a multiplexed drug screen in a reporter cell line containing 19 sequencing based pathway reporters. This submission contains high throughput sequencing data of the pathway reporters, their mapping and mutation readout. It also contains the raw pA-DamID data for H3K27me3, H3K9me2, H3K9me3 and "Dam-only" samples in RPE-1 cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE248980 | GEO | 2023/11/30

REPOSITORIES: GEO

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Dam mutants provide improved sensitivity and spatial resolution for profiling transcription factor binding

Project description:DamID, in which a protein of interest is fused to Dam methylase, enables mapping of protein-DNA binding through readout of adenine methylation in genomic DNA. DamID offers a compelling alternative to chromatin immunoprecipitation sequencing (ChIP-Seq), particularly in cases where cell number or antibody availability are limiting. This comes at a cost, however, of high non-specific signal and a lowered spatial resolution of several kb, limiting its application to transcription factor-DNA binding. Here we show that mutations in Dam, when fused to the transcription factor Tcf7l2, greatly reduce non-specific methylation. Combined with a simplified DamID sequencing protocol, we find that these Dam mutants allow for accurate detection of transcription factor binding at a sensitivity and spatial resolution closely matching that seen in ChIP-seq.

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Genome-wide binding patterns of group B Sox proteins in four Drosophila species

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