Three-dimensional modeling of the <i>P. falciparum</i> genome during the erythrocytic cycle

Three-dimensional modeling of the P. falciparum* genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression*

Ferhat Ay*, Evelien M. Bunnik*, Nelle Varoquaux*, Sebastiaan M. Bol, Jacques Prudhomme, Jean-Philippe Vert, William Stafford Noble+, Karine G. Le Roch+. 2014. Genome Research

The development of the human malaria parasite Plasmodium falciparum is controlled by coordinated changes in gene expression throughout its complex life cycle, but the corresponding regulatory mechanisms are incompletely understood. To study the relationship between genome architecture and gene regulation in Plasmodium, we used chromosome conformation capture coupled with next-generation sequencing technology (Hi-C) and generated 3D models of Plasmodium falciparum genome at three time points during its erythrocytic (asexual) cycle.

Data generated for this project

Raw reads files (fastq) and contact maps for each stage are available via GSE50199.

File: Number of MboI (restriction enzyme) cleavage sites, GC content and mappability values for each 10 kb of Plasmodium falciparum genome (PlasmoDB v9.0). Each 10 kb window is represented by its midpoint coordinate. Mappability is calculated using GEM tools with 50 basepair reads.

Stage	GEO entry	3D coordinates of	3D distance of genes to landmarks	3D structures

Ring	GSM1215592	Windows(10 kb) Genes	Dist. to Landmarks	Image PDB
Trophozoite	GSM1215593	Windows(10 kb) Genes	Dist. to Landmarks	Image PDB
Schizont	GSM1215594	Windows(10 kb) Genes	Dist. to Landmarks	Image PDB
Trophozoite (Non-crosslinked Control)	GSM1215595