Exploring the virulence gene interactome with CRISPR/dCas9 in the human malaria parasite

Mol Syst Biol. 2020 Aug;16(8):e9569. doi: 10.15252/msb.20209569.


Mutually exclusive expression of the var multigene family is key to immune evasion and pathogenesis in Plasmodium falciparum, but few factors have been shown to play a direct role. We adapted a CRISPR-based proteomics approach to identify novel factors associated with var genes in their natural chromatin context. Catalytically inactive Cas9 ("dCas9") was targeted to var gene regulatory elements, immunoprecipitated, and analyzed with mass spectrometry. Known and novel factors were enriched including structural proteins, DNA helicases, and chromatin remodelers. Functional characterization of PfISWI, an evolutionarily divergent putative chromatin remodeler enriched at the var gene promoter, revealed a role in transcriptional activation. Proteomics of PfISWI identified several proteins enriched at the var gene promoter such as acetyl-CoA synthetase, a putative MORC protein, and an ApiAP2 transcription factor. These findings validate the CRISPR/dCas9 proteomics method and define a new var gene-associated chromatin complex. This study establishes a tool for targeted chromatin purification of unaltered genomic loci and identifies novel chromatin-associated factors potentially involved in transcriptional control and/or chromatin organization of virulence genes in the human malaria parasite.

Keywords: CRISPR; Plasmodium falciparum; chromatin; epigenetics; var genes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphatases / metabolism*
  • Animals
  • Antigens, Protozoan / genetics
  • Antigens, Protozoan / metabolism
  • CRISPR-Cas Systems
  • Chromatin Immunoprecipitation Sequencing
  • Humans
  • Introns
  • Mass Spectrometry
  • Plasmodium falciparum / genetics
  • Plasmodium falciparum / immunology
  • Plasmodium falciparum / pathogenicity*
  • Promoter Regions, Genetic
  • Protein Interaction Maps
  • Proteomics / methods*
  • Transcription Factors / metabolism*
  • Virulence Factors / genetics*
  • Virulence Factors / metabolism


  • Antigens, Protozoan
  • ISWI protein
  • Transcription Factors
  • Virulence Factors
  • Adenosine Triphosphatases

Associated data

  • GEO/GSE104075