Chromatin structure dynamics including the modification of histones and the exchange of core histones with histone variants can control gene expression and regulate critical processes in malaria pathogenesis. Promoters and enhancers are regulatory DNA elements that are important for gene expression. Only a few enhancers have been characterized in Plasmodium falciparum.
Recent studies indicate that the presence of specific histone modifications at enhancers precedes and controls changes in gene expression and that histone variants are associated with regulatory elements within dynamic chromatin. We have used chromatin immunoprecipitation of H3K4me1, H3K18ac, H3K27ac and H2A.Z combined with sequencing to identify putative regulatory elements in the P. falciparum genome.
Genes possibly regulated by elements defined by chromatin structure dynamics were identified by correlating dynamic patterns of gene expression generated by RNAseq at different points in the lifecycle with dynamic patterns of enhancer-associated chromatin characteristics. These chromatin characteristics were enriched in the intergenic regions and some showed dynamic enrichment upstream of expressed genes, indicating that they could play a role in regulating these genes. Conserved sequences found in putative regulatory elements could act as transcription factor binding sites and sequences that significantly matched ApiAP2 transcription factor binding motifs were found in putative enhancers. Functionally related sets of genes were enriched in putative motifs suggesting these may be specifically regulated through enhancer-like sequences.
In summary, mapping chromatin structural elements that are dynamically associated with expression of downstream genes provided a library of putative regulatory sequences. We are in the process of validating the function of these regulatory elements. These sequences can eventually be used to identify their cognate transcription factors and further elucidate gene regulation in P. falciparum.