Locus-specific histone deacetylation using a synthetic CRISPR-Cas9-based HDAC

Nature Communications
Deborah Y KwonZhaolan Zhou

Abstract

Efforts to manipulate locus-specific histone acetylation to assess their causal role in gene expression and cellular and behavioural phenotypes have been impeded by a lack of experimental tools. The Cas9 nuclease has been adapted to target epigenomic modifications, but a detailed description of the parameters of such synthetic epigenome remodellers is still lacking. Here we describe a Cas9-based histone deacetylase (HDAC) and the design principles required to achieve locus-specific histone deacetylation. We assess its range of activity and specificity, and analyse target gene expression in two different cell types to investigate cellular context-dependent effects. Our findings demonstrate that the chromatin environment is an important element to consider when utilizing this synthetic HDAC.

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Datasets Mentioned

BETA
GSE91043

Methods Mentioned

BETA
acetylation
histone acetylation
histone
immunoprecipitation
RNA-seq
reverse-transcription PCR
ChIP-seq
transfections
fluorescence-activated cell sorting
ChIP

Software Mentioned

STAR
house Perl programmes
edgeR
Bowtie

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