Deciphering chromatin architecture and dynamics in Plasmodium falciparum using the nucDetective pipeline

Abstract

High-resolution analysis of cellular chromatin structure is crucial for uncovering developmental and cell-type-specific regulatory networks. We developed the nucDetective pipeline to provide a comprehensive evaluation of chromatin organisation. This involves assessing nucleosome positioning, occupancy, fuzziness, and array regularity. The pipeline was benchmarked by analysing the chromatin structure of the malaria-causing parasite Plasmodium falciparum (Pf) during its erythrocytic development cycle. Pf is characterised by a unique chromatin landscape, exhibiting unstable nucleosomes and a genomic AT-content exceeding 80%, which presents challenges for standard MNase-seq analysis of chromatin. The nucDetective pipeline provides specific, high-resolution nucleosome profiles for the different asexual stages of Pf, monitoring the dynamics of individual nucleosomes. In contrast to the current view, suggesting an irregular chromatin structure and lack of nucleosomal DNA, we demonstrate that the transcription start sites exhibit typical eukaryotic features, including +1 nucleosomes, nucleosome-free regions upstream, and phased nucleosome arrays downstream of the TSSs. The global mean nucleosome repeat length varies from 176 bp to 185 bp depending on the developmental stage. Stage specific changes in nucleosome positioning occur locally in intergenic regulatory regions, which are characterized by specific histone modifications and variants. Dynamic nucleosomes correlate with DNA accessibility, gene expression and determine the access to transcription factor binding sites in Pf. The highly regular chromatin structure, with stage-specific structural alterations, emphasises the important role of epigenetic mechanisms in regulating the complex life cycles of Pf.