Functional annotation of native enhancers with a Cas9-histone demethylase fusion

Nature Methods
Nicola A KearnsRené Maehr

Abstract

Understanding of mammalian enhancers is limited by the lack of a technology to rapidly and thoroughly test the cell type-specific function. Here, we use a nuclease-deficient Cas9 (dCas9)-histone demethylase fusion to functionally characterize previously described and new enhancer elements for their roles in the embryonic stem cell state. Further, we distinguish the mechanism of action of dCas9-LSD1 at enhancers from previous dCas9-effectors.

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Datasets Mentioned

BETA
GSE64059

Methods Mentioned

BETA
PCR
transfection
RNASeq
immunoprecipitation
Assay
chip

Software Mentioned

MACS
Bowtie
bowtie2
R package limma
ATACseq
Elements
Elements Analysis
NIS
R
Adobe Photoshop

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