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

Abstract

Phenotypic variation between malaria parasites is one of the major contributors to the pathogens success and is regulated by differences in heterochromatin-mediated gene silencing. Currently, the heterochromatin landscape is mostly profiled utilising chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq). However this technique has drawbacks regarding AT-content-related artifacts and requires substantial material and time investment, severely limiting profiling of scarce sample types (e.g. field isolates). In order to facilitate assessments of epigenetic states in low-input samples, we adopted the epigenetic profiling technique Cleavage Under Targets and Tagmentation (CUT&Tag) to Plasmodium falciparum parasites. Performing the reaction with 100,000 or even only 10,000 nuclei yielded reproducible results coherent with bulk-ChIP-seq data while using significantly less material. We also optimised sample preparation, permitting the use of crude saponin lysates, which decreases sample loss due to inefficient nuclei isolation and increases versatility of the protocol. Finally, we developed DiBioCUT&Tag, a novel way of utilising dimerisation-induced recruitment of biotin ligases for signal amplification prior to anti-biotin CUT&Tag, which we successfully deployed to profile both heterochromatin occupancy and a dynamically chromatin-associated protein (BDP5). Methods described here hence provide substantially improved means for epigenetic profiling of (transiently) chromatin-associated proteins from low-input samples in the malaria parasite and beyond.