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         

Public datasets used and analyzed

Other links

Fit-Hi-C: Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts.


For questions about the project and/or this supplementary page please e-mail Ferhat Ay.

Ferhat Ay < ferhatay at uw period edu >