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

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.

Public datasets used and analyzed
Reference genomes
Plasmodium falciparum (Pfal3D7) – PlasmoDB v9.0
Script to download — All chromosomes — Chromosome lengths (canonical names)
Human genome (hg19)
Script to download

Plasmodium genes
Annotations (GFF) — Coding genes — Virulence (VRSM) genes and clusters — rDNA genes — Histone genes

Plasmodium centromere coordinates
Publication information — Published coordinates in PlasmoDB v8.0 — Coordinates in PlasmoDB v9.0

Plasmodium telomere coordinates
Coordinates in PlasmoDB v9.0 — Telomeric regions are defined as the region starting from the chromosome end until the first var, rif or stevor gene is encountered.

Plasmodium mappability/alignability tracks
Description — Mappability track for 50bp reads

Gene expression datasets
Le Roch et al. Science, 2003 – Microarray data
Publication info. — Supp. Table 1 — Sorbitol treated dataset — Expression clusters
Otto TD et al. Mol Microbiology, 2010 (RNA-Seq)
Publication link — Expression values
Lopez-Barragan et al. BMC Genomics, 2011 (cDNA)
Publication link — Expression values
Bunnik et al. Genome Biology, 2013 (RNA-Seq)
Publication link — Expression values

GO term enrichment and gene set enrichment analysis (GSEA)
Broad Institute GSEA tool — GO Term Finder — .GAF file for PlasmoDB v9.0

Other links
Fit-Hi-C: Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts.
Contact
For questions about the project and/or this supplementary page please e-mail Ferhat Ay.
Ferhat Ay ferhatay@lji.org