Abstract
BackgroundIn eukaryotic organisms, packaging of DNA into nucleosomes controls gene expression by regulating access of the promoter to transcription factors. The human malaria parasite Plasmodium falciparum encodes relatively few transcription factors, while extensive nucleosome remodeling occurs during its replicative cycle in red blood cells. These observations point towards an important role of the nucleosome landscape in regulating gene expression. However, the relation between nucleosome positioning and transcriptional activity has thus far not been explored in detail in the parasite.ResultsHere, we analyzed nucleosome positioning in the asexual and sexual stages of the parasite’s erythrocytic cycle using chromatin immunoprecipitation of MNase-digested chromatin, followed by next-generation sequencing. We observed a relatively open chromatin structure at the trophozoite and gametocyte stages, consistent with high levels of transcriptional activity in these stages. Nucleosome occupancy of genes and promoter regions were subsequently compared to steady-state mRNA expression levels. Transcript abundance showed a strong inverse correlation with nucleosome occupancy levels in promoter regions. In addition, AT-repeat sequences were strongly unfavorable for nucleosome binding in P. falciparum, and were overrepresented in promoters of highly expressed genes.ConclusionsThe connection between chromatin structure and gene expression in P. falciparum shares similarities with other eukaryotes. However, the remarkable nucleosome dynamics during the erythrocytic stages and the absence of a large variety of transcription factors may indicate that nucleosome binding and remodeling are critical regulators of transcript levels. Moreover, the strong dependency between chromatin structure and DNA sequence suggests that the P. falciparum genome may have been shaped by nucleosome binding preferences. Nucleosome remodeling mechanisms in this deadly parasite could thus provide potent novel anti-malarial targets.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-347) contains supplementary material, which is available to authorized users.
Highlights
In eukaryotic organisms, packaging of DNA into nucleosomes controls gene expression by regulating access of the promoter to transcription factors
To extend and complement existing nucleosome occupancy data sets [17,18,20], we performed two variants of chromatin immunoprecipitation coupled to generation sequencing (ChIP-Seq) for nucleosome mapping using either sonication or micrococcal nuclease (MNase) digestion (MNase Chromatin immunoprecipitation (ChIP)-Seq) to fragment crosslinked chromatin into mononucleosomes (Additional file 1: Figure S1)
Antibodies used for immunoprecipitations were either directed against H4, which is universally present in all nucleosomes, or against an epitope shared between H3 and H3.3, which enabled pull-down of all nucleosomes with the exception of centromeric nucleosomes that contain the variant histone CenH3
Summary
In eukaryotic organisms, packaging of DNA into nucleosomes controls gene expression by regulating access of the promoter to transcription factors. The human malaria parasite Plasmodium falciparum encodes relatively few transcription factors, while extensive nucleosome remodeling occurs during its replicative cycle in red blood cells. These observations point towards an important role of the nucleosome landscape in regulating gene expression. The positioning of these nucleosomes along the genome is important for control of gene expression by regulating access of DNA to transcription factors and other DNA binding proteins [2,3,4,5]. Another nucleosome-depleted region is present at the 3′ end of the gene where RNA polymerase II terminates transcription
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