Fig. 2

H3K4me1 is significantly enriched at the intergenic peaks. a Enrichment of H3K9ac, H3K4me1, H3K4me3 and Histone H4ac over the intergenic peaks and 500 strongly and weakly expressed promoters is calculated. H3K9ac, H3K4me3 and histone H4ac are enriched at the active promoters whereas the distal peaks are enriched with H3K4me1 (P < 0.05). IR: Intergenic regions; SP: Strong Promoters; WP: Weak Promoters. P values were computed using the Wilcoxon test (two-sided). b Profiles of H3K9ac, H3K4me 1, H3K4me3 and histone H4ac over the intergenic peaks and 500 strongly and weakly expressed promoters (+/− 0.5 kb). Intergenic peaks have bell shaped distribution of all histone modifications. c One of the characteristic features of the enhancer histone modifications in higher eukaryotes, the ratio of H3K4me1 to H3K4me3 tag density is also higher on intergenic peaks as compared to strongly expressed promoters (P < 0.05). Weak promoters showed higher ratio of H3K4me1 to H3K4me3 as compared to IRs, most probably due to absence of active histone modification (i.e. H3K4me3) on weak promoters d. Furthermore, one of the hallmarks of the regulatory elements is the nucleosome-depleted regions, which can be assessed by Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE)-sequencing. To assess if the identified IRs can function in vivo as regulatory elements globally; we integrated available FAIRE-seq data in Plasmodium with enrichment of H3K4me1 on identified IRs. Overlapping peaks of H3K4me1 and FAIRE-sequencing over the 462 intergenic peaks suggests that identified IRs are depleted of nucleosomes and that the intergenic peaks are indeed regulatory elements