Characterization of the Plasmodium falciparum var gene interactome

We adapted a CRISPR-based immunoprecipitation-mass spectrometry technique for de novo identification of factors associated with specific transcription control regions of var genes. Tagged, catalytically inactive Cas9 (“dCas9”) was targeted to the promoters or introns of var genes, cross-linked, and immunoprecipitated with all DNA, proteins, and RNA associated with the targeted DNA locus. Chromatin immunoprecipitation followed by sequencing demonstrated that genome-wide dCas9 binding was specific and robust. Proteomics analysis of dCas9-immunoprecipitates identified specific proteins for each target region, including known and novel factors such as DNA binding factors, chromatin remodelers, and structural proteins. We also demonstrate the ability to immunoprecipitate RNA that is closely associated to the targeted DNA locus.