Nucleosome landscape and control of transcription in the human malaria parasite

Abstract

In eukaryotic cells, chromatin reorganizes within promoters of active genes to allow the transcription machinery and various transcription factors to access DNA. In this model, promoter-specific transcription factors bind DNA to initiate the production of mRNA in a tightly regulated manner. In the case of the human malaria parasite, Plasmodium falciparum, specific transcription factors are apparently underrepresented with regards to the size of the genome, and mechanisms underlying transcriptional regulation are controversial. Here, we investigate the modulation of DNA accessibility by chromatin remodeling during the parasite infection cycle. We have generated genome-wide maps of nucleosome occupancy across the parasite erythrocytic cycle using two complementary assays-the formaldehyde-assisted isolation of regulatory elements to extract protein-free DNA (FAIRE) and the MNase-mediated purification of mononucleosomes to extract histonebound DNA (MAINE), both techniques being coupled to high-throughput sequencing. We show that chromatin architecture undergoes drastic upheavals throughout the parasite's cycle, contrasting with targeted chromatin reorganization usually observed in eukaryotes. Chromatin loosens after the invasion of the red blood cell and then repacks prior to the next cycle. Changes in nucleosome occupancy within promoter regions follow this genome-wide pattern, with a few exceptions such as the var genes involved in virulence and genes expressed at early stages of the cycle. We postulate that chromatin structure and nucleosome turnover control massive transcription during the erythrocytic cycle. Our results demonstrate that the processes driving gene expression in Plasmodium challenge the classical eukaryotic model of transcriptional regulation occurring mostly at the transcription initiation level.

DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome

“…The stereotypical nucleosome array that has been previously observed near transcription start sites in aggregate plots remains somewhat of a mystery. This organization has been observed in diverse eukaryotes (Yuan et al 2005;Mavrich et al 2008b;Lantermann et al 2010;Ponts et al 2010;Chen et al 2013b;Zhang et al 2014), suggesting that it is established by a widely conserved mechanism. However, the functional relationship between the stereotypical nucleosome array and gene transcription is unclear, since even highly expressed genes exhibit this nucleosome organization (Shivaswamy et al 2008;Lantermann et al 2010).…”

Epigenetics in Plasmodium: What Do We Really Know?

“…Analyses of physical chromatin characteristics, including nucleosomal occupancy (87,108) and the distribution of heterochromatin protein 1 (HP1) (42,84), have also been made. Nucleosomal occupancy is highest around telomeres and lowest in housekeeping genes but it is not more generally correlated with levels of transcription throughout the genome.…”

Chromatin-Mediated Epigenetic Regulation in the Malaria Parasite Plasmodium falciparum

“…This is accomplished through the use of high-throughput technologies such as the combination of ChIP with DNA microarrays (ChIP-chip) and with massive parallel sequencing (ChIP-seq). Recently, the global nucleosomal occupancy in P. falciparum during the parasite's IDC has been mapped using a tiling array (154), and the formaldehyde-assisted isolation of regulatory elements to extract protein-free DNA (FAIRE) and the MNase-mediated purification of mononucleosomes to extract histone-bound DNA (MAINE) coupled to high-throughput sequencing (119). These studies have revealed that coding regions are generally densely packed with nucleosomes, while telomeres harbor a region with the highest nucleosomal density.…”