CRISPR CAPTURE for multi-omic probing of genomic loci

Burgess, Darren J.

doi:10.1038/nrg.2017.79

Research Highlight
Published: 03 October 2017

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CRISPR CAPTURE for multi-omic probing of genomic loci

Darren J. Burgess

Nature Reviews Genetics volume 18, page 641 (2017)Cite this article

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Liu et al. sought to direct the CRISPR-associated protein Cas9 to regulatory elements as an affinity tag to enable subsequent molecular characterization of the surrounding chromatin. Onto a nuclease-dead Cas9 (dCas9), they engineered a biotin acceptor site so that locus-bound dCas9 could be biotinylated in vivo by the biotin ligase BirA and isolated by streptavidin-based capture, followed by analysis of the locus-associated proteins and nucleic acids by various methodologies. They termed their approach CRISPR affinity purification in situ of regulatory elements (CAPTURE). Key features are that the high-affinity biotin–streptavidin interaction provides higher sensitivity and specificity than antibody-based strategies to isolate locus-bound proteins, and that guide RNA (gRNA)-based targeting enables multiple regulatory loci to be targeted simultaneously.

The team primarily focused on using CAPTURE to dissect regulation at the human β-globin locus, which consists of five β-like globin genes that are controlled by a shared cluster of five enhancers. The authors co-expressed dCas9, gRNAs and BirA in human K562 cells, and optimized proteomic analysis following CAPTURE of individual enhancers or promoters. They found known erythroid transcription factors and chromatin remodellers at β-globin enhancers, but also identified novel regulators such as nucleoporin nuclear pore components. Functional relevance was confirmed by showing that knockdown of these components altered β-globin gene expression. Furthermore, the authors classified the different regulatory elements based on their associated proteins, proposing a hierarchical arrangement with different enhancers and promoters in distinct subdomains.

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