CUT&Tag and DiBioCUT&Tag enable investigation of the AT-rich epigenome of Plasmodium falciparum from low-input samples.

Abstract

Phenotypic variation between malaria parasites is a major contributor to the pathogen's success, facilitated by heritable yet dynamic changes in (hetero)chromatin structure. Currently, the chromatin landscape is mostly profiled by chromatin immunoprecipitation sequencing (ChIP-seq), which has several drawbacks: (1) GC-content-related artifacts, (2) substantial material requirement, and (3) a labor-intensive protocol. To overcome these limitations, we adapted cleavage under targets and tagmentation (CUT&Tag) to Plasmodium falciparum. Despite the AT richness of the genome, CUT&Tag results in reproducible heterochromatin profiles concordant with ChIP-seq data while using as little as 10,000 nuclei or crude parasite isolates. We also developed DiBioCUT&Tag, a method utilizing dimerization-induced recruitment of biotin ligase for proximity labeling of core chromatin components during the binding of regulatory proteins followed by anti-biotin CUT&Tag. These methods hence provide substantially improved means for genome-wide profiling of chromatin-associated proteins from low-input samples in the malaria parasite and potentially beyond.