The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences

Nucleic Acids Res. 2016 Mar 18;44(5):2110-24. doi: 10.1093/nar/gkv1214. Epub 2015 Nov 17.


In eukaryotes, the chromatin architecture has a pivotal role in regulating all DNA-associated processes and it is central to the control of gene expression. For Plasmodium falciparum, a causative agent of human malaria, the nucleosome positioning profile of regulatory regions deserves particular attention because of their extreme AT-content. With the aid of a highly controlled MNase-seq procedure we reveal how positioning of nucleosomes provides a structural and regulatory framework to the transcriptional unit by demarcating landmark sites (transcription/translation start and end sites). In addition, our analysis provides strong indications for the function of positioned nucleosomes in splice site recognition. Transcription start sites (TSSs) are bordered by a small nucleosome-depleted region, but lack the stereotypic downstream nucleosome arrays, highlighting a key difference in chromatin organization compared to model organisms. Furthermore, we observe transcription-coupled eviction of nucleosomes on strong TSSs during intraerythrocytic development and demonstrate that nucleosome positioning and dynamics can be predictive for the functionality of regulatory DNA elements. Collectively, the strong nucleosome positioning over splice sites and surrounding putative transcription factor binding sites highlights the regulatory capacity of the nucleosome landscape in this deadly human pathogen.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Composition
  • Chromatin Assembly and Disassembly*
  • DNA, Protozoan / chemistry
  • DNA, Protozoan / genetics
  • Erythrocytes / parasitology
  • Exons
  • Gene Expression Regulation
  • Humans
  • Introns
  • Life Cycle Stages / genetics*
  • Nucleosomes / chemistry*
  • Nucleosomes / metabolism
  • Open Reading Frames
  • Plasmodium falciparum / genetics*
  • Plasmodium falciparum / growth & development
  • Promoter Regions, Genetic
  • Protein Binding
  • Protozoan Proteins / genetics*
  • RNA Splice Sites
  • Transcription Factors / genetics
  • Transcription Initiation Site*
  • Transcription, Genetic


  • DNA, Protozoan
  • Nucleosomes
  • Protozoan Proteins
  • RNA Splice Sites
  • Transcription Factors