Landscape and Dynamics of Transcription Initiation in the Malaria Parasite Plasmodium falciparum

Publication date: Available online 3 March 2016
Source:Cell Reports
Author(s): Sophie H. Adjalley, Christophe D. Chabbert, Bernd Klaus, Vicent Pelechano, Lars M. Steinmetz
A comprehensive map of transcription start sites (TSSs) across the highly AT-rich genome of P. falciparum would aid progress toward deciphering the molecular mechanisms that underlie the timely regulation of gene expression in this malaria parasite. Using high-throughput sequencing technologies, we generated a comprehensive atlas of transcription initiation events at single-nucleotide resolution during the parasite intra-erythrocytic developmental cycle. This detailed analysis of TSS usage enabled us to define architectural features of plasmodial promoters. We demonstrate that TSS selection and strength are constrained by local nucleotide composition. Furthermore, we provide evidence for coordinate and stage-specific TSS usage from distinct sites within the same transcription unit, thereby producing transcript isoforms, a subset of which are developmentally regulated. This work offers a framework for further investigations into the interactions between genomic sequences and regulatory factors governing the complex transcriptional program of this major human pathogen.

Graphical abstract

Teaser

The genome of P. falciparum is characterized by an extremely AT-biased nucleotide composition. Adjalley et al. conducted a survey of transcription initiation events throughout the malaria parasite’s blood cycle. They detect coordinate and stage-specific transcription initiation and extract sequence and chromatin signatures from promoter regions.


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