Transcriptional regulation in adaptive and developmental processes in malaria parasites: from epigenetic variability to targeted transcriptional responses

Transcriptional regulation plays a key role in the biology of the protozoan parasite Plasmodium falciparum, which causes the most severe forms of malaria. Both the progression of the parasite throughout its life cycle and its adaptation to changes in environmental conditions are regulated primarily at the transcriptional level. Transcriptional variability (epigenetic basis) within isogenic parasite populations plays a fundamental role in the adaptation of parasites to changes in their environment and regulates important processes such as the evasion of immune responses, solute transport, erythrocyte invasion, and sex conversion, among others. More recently, it has been shown that malaria parasites are capable of producing rapid transcriptional responses to cope with changes in their environmental conditions.

Despite enormous progress in recent years, many fundamental questions remain about the molecular mechanisms regulating epigenetic variability and targeted transcriptional responses in malaria parasites. In this project, the research team will address some of these questions. First, the investigators will characterize the role of different genetic elements (promoters and coding sequences) in determining whether a gene exhibits epigenetically regulated variant clonal expression. Considering that epigenetic silencing, which determines variant clonal expression, is mediated by heterochromatin formation, the researchers will analyze the role of different elements in the nucleation, expansion, and maintenance of heterochromatin.

To do this, the team will manipulate the parasite genome using CRISPR-CAS9 technology and analyze it by means of chromosome immunoprecipitation followed by quantitative PCR (ChIP-qPCR) or massive sequencing (ChIP-seq). The investigators will also test the hypothesis that heterochromatin is not formed anew when genes with clonal variant expression are silenced, nor is it completely disassembled when they are activated, but rather that it expands or contracts from nearby reservoirs (accordion model). To identify the specific enzymes involved in heterochromatin formation and dismantling, the researchers will use fusion proteins based on catalytically inactive CAS9 (dCAS9) and proximity labeling followed by proteomics (BioID).

The team will also study the chromatin changes associated with the activation of genes with variant clonal expression and of genes activated in response to changes in environmental conditions. In addition to studying general aspects of variant clonal expression, the investigators will focus on the gene with variant clonal expression PFAP2-G and the process controlled by this gene, sex conversion, which determines the formation of transmissible stages. In the case of directed transcriptional responses, the researchers will focus mainly on the PFAP2-HS gene and the response to heat shock. Finally, to identify important new processes linked to epigenetic variation, the team will test the hypothesis that silencing of CLAG3 genes influences the formation of quiescent stages, which play a key role in the parasite’s resistance to artemisinin.

Overall, this project aims to contribute significantly to advancing the understanding of the mechanisms that regulate transcription in malaria parasites, their adaptation mechanisms to the environment, and sex conversion.

Project details

Enabling Technologies & Assays
Genetics and Genomics

Jan 2019

$311,523

Spain