Fig. 4

Clustering of P. falciparum genes based on histone modification profiles. a Heat map of the signal density using k-means clustering observed on 3750 P. falciparum genes for IgG control and histone modifications (H3K4me3, H3K9ac, H4ac, H3K9me3, H3K36me2, and H3K36me3). Genes were clustered into four distinct categories based on the distribution of histone modifications in the gene body: (1) Cluster 1 (411 genes), peaks at the 5′ end of the gene (red squared and labeled 1), Cluster 2 (562 genes), peaks at the 3′ end of the genes (green squared and labeled 2), Cluster 3 (335 genes), peaks observed at the center of the gene body (blue squared and labeled 3) and Cluster 4 (2442 genes), with very low levels of histone modifications (black squared and labeled 4). b RNA sequencing (RNA-seq) profiles of the respective cluster plotted as average gene unit. RNA-seq reads correlate with the histone modifications. c Levels of naturally anti-sense transcript calculated for cluster 1, 2 and 3 using publicly available data. Cluster 2 shows maximum anti-sense transcript levels as predicted with histone modification profiles. d Sense and anti-sense transcript were measured for PF11_0468 and PF10_0287 genes from cluster 2. Actin (from cluster 1) was used as control. Both these genes showed significant anti-sense transcript production. e UCSC snapshot of a representative gene having histone modifications at the center of the gene unit. The intragenic region was cloned in a dual promoter reporter vector in which mCherry and EGFP were cloned in sense and anti-sense orientation. f Intragenic region showed both EGFP and mCherry expression suggesting bidirectional promoter activity from the two randomly selected genes. Differential levels of mCherry and EGFP between two intragenic sequences indicate differential promoter strength of these sequences. Empty vector backbone was used a negative control