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Dynamic epigenetic regulation of gene expression during the life cycle of malaria parasite Plasmodium falciparum.

Gupta AP, Chin WH, Zhu L, Mok S, Luah YH, Lim EH, Bozdech Z - PLoS Pathog. (2013)

Bottom Line: While some modifications were found to be associated with the vast majority of the genome and their occupancy was constant, others showed more specific and highly dynamic distribution.In addition, we showed the presence of multivalent domains on the genome carrying more than one histone mark, highlighting the importance of combinatorial effects on transcription.Overall, our work portrays a substantial association between chromosomal locations of various epigenetic markers, transcriptional activity and global stage-specific transitions in the epigenome.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.

ABSTRACT
Epigenetic mechanisms are emerging as one of the major factors of the dynamics of gene expression in the human malaria parasite, Plasmodium falciparum. To elucidate the role of chromatin remodeling in transcriptional regulation associated with the progression of the P. falciparum intraerythrocytic development cycle (IDC), we mapped the temporal pattern of chromosomal association with histone H3 and H4 modifications using ChIP-on-chip. Here, we have generated a broad integrative epigenomic map of twelve histone modifications during the P. falciparum IDC including H4K5ac, H4K8ac, H4K12ac, H4K16ac, H3K9ac, H3K14ac, H3K56ac, H4K20me1, H4K20me3, H3K4me3, H3K79me3 and H4R3me2. While some modifications were found to be associated with the vast majority of the genome and their occupancy was constant, others showed more specific and highly dynamic distribution. Importantly, eight modifications displaying tight correlations with transcript levels showed differential affinity to distinct genomic regions with H4K8ac occupying predominantly promoter regions while others occurred at the 5' ends of coding sequences. The promoter occupancy of H4K8ac remained unchanged when ectopically inserted at a different locus, indicating the presence of specific DNA elements that recruit histone modifying enzymes regardless of their broad chromatin environment. In addition, we showed the presence of multivalent domains on the genome carrying more than one histone mark, highlighting the importance of combinatorial effects on transcription. Overall, our work portrays a substantial association between chromosomal locations of various epigenetic markers, transcriptional activity and global stage-specific transitions in the epigenome.

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Combinatorial histone modifications.(A) PCC-based correlation of the dynamic histone occupancy profiles. The bar charts show examples of pair wise correlation distributions between the dynamic profiles of the individual histone marks calculated analogously to the correlations with steady state mRNA levels (see Figure 3). Line graphs give the randomized distribution of PCC. P value (P) and skewness (S) are shown below each graph. (B) Hierarchical clustering of histone mark associations. The heat maps represent hierarchical clustering of the skewness (S) values of the PCC distributions for every marked histone pair. High positive skew (red) and low negative skew (blue) indicate positive and negative correlations with the marked histone pairs, respectively. (C) Sequential ChIP-on-chip for H3K9ac and H3K56ac. The sequential ChIP-on-chip was carried out with ring stage parasites using anti-H3K56ac antibody followed by anti-H3K9ac antibody. Immunoprecipitation was also done using anti-H3K56ac antibody or anti-H3K9ac antibody separately. Data was averaged from 2 separate experiments and probes with ChIP/input signal ratio above 1 for bead control were subtracted for further analysis. The chart (above) shows the probes overlapping between the sequential ChIP and probes shared in common between both histone marks when used individually (ChIP/input >1). Chromosomal distribution (below) of H3K56ac (orange), H3K9ac (green) and sequential (purple) ChIP enrichment of probes as seen at chromosome 4. Each vertical line depicts the position of a probe on the chromosome.
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ppat-1003170-g006: Combinatorial histone modifications.(A) PCC-based correlation of the dynamic histone occupancy profiles. The bar charts show examples of pair wise correlation distributions between the dynamic profiles of the individual histone marks calculated analogously to the correlations with steady state mRNA levels (see Figure 3). Line graphs give the randomized distribution of PCC. P value (P) and skewness (S) are shown below each graph. (B) Hierarchical clustering of histone mark associations. The heat maps represent hierarchical clustering of the skewness (S) values of the PCC distributions for every marked histone pair. High positive skew (red) and low negative skew (blue) indicate positive and negative correlations with the marked histone pairs, respectively. (C) Sequential ChIP-on-chip for H3K9ac and H3K56ac. The sequential ChIP-on-chip was carried out with ring stage parasites using anti-H3K56ac antibody followed by anti-H3K9ac antibody. Immunoprecipitation was also done using anti-H3K56ac antibody or anti-H3K9ac antibody separately. Data was averaged from 2 separate experiments and probes with ChIP/input signal ratio above 1 for bead control were subtracted for further analysis. The chart (above) shows the probes overlapping between the sequential ChIP and probes shared in common between both histone marks when used individually (ChIP/input >1). Chromosomal distribution (below) of H3K56ac (orange), H3K9ac (green) and sequential (purple) ChIP enrichment of probes as seen at chromosome 4. Each vertical line depicts the position of a probe on the chromosome.

Mentions: The abundance of dynamic temporal regulation of individual histone marks suggests the existence of combinatorial patterns forming a putative “dynamic histone code”. To investigate this possibility, we carried out pair-wise analysis of occupancy profiles with all thirteen histone marks. To this end, we evaluated the concordance of the occupancy profiles using PCC distributions and subsequently the skewness and KS-test P value as described above (Table S2). Figure 6A shows examples of highly positive (S>1), moderately positive (S between 1 and 0) and highly negative PCC distribution (S<0) between the histone marks. Overall our analysis revealed that most of the overlapping marks (present at the same loci) exhibited a high level of correlation between their occupancy profiles. Here it is important to note that the mean size of ChIP DNA product generated by our protocol is 500 bp which corresponds to approximately three nucleosomes positioned in the vicinity of the genetic locus represented by a microarray probe. Hence the correlations in the occupancy profiles represent either a combinatorial histone modification at the same nucleosome or co-occurrence of these at directly adjacent nucleosomes. High correlations of the occupancy profiles are particularly evident for acetylations that exhibited positive correlations at essentially all overlapping loci (Figure 6B). This suggests that, each nucleosome predominantly undergoes only one set of modifications during the IDC, presumably for one purpose (such as transcriptional regulation). This situation contrasted with the lysine methylation profiles that showed loose or no correlations with each other or with acetylations. Interestingly, H4R3me2 exhibited a strong negative correlation with most of the other marks. This methylation is thought to be mediated by PfPRMT1 and might be playing a similar role to H3R2me2a (asymmetrical histone H3 arginine 2 dimethylation) which has been shown to have a mutually exclusive pattern with H3K4me3 in budding yeast [33].


Dynamic epigenetic regulation of gene expression during the life cycle of malaria parasite Plasmodium falciparum.

Gupta AP, Chin WH, Zhu L, Mok S, Luah YH, Lim EH, Bozdech Z - PLoS Pathog. (2013)

Combinatorial histone modifications.(A) PCC-based correlation of the dynamic histone occupancy profiles. The bar charts show examples of pair wise correlation distributions between the dynamic profiles of the individual histone marks calculated analogously to the correlations with steady state mRNA levels (see Figure 3). Line graphs give the randomized distribution of PCC. P value (P) and skewness (S) are shown below each graph. (B) Hierarchical clustering of histone mark associations. The heat maps represent hierarchical clustering of the skewness (S) values of the PCC distributions for every marked histone pair. High positive skew (red) and low negative skew (blue) indicate positive and negative correlations with the marked histone pairs, respectively. (C) Sequential ChIP-on-chip for H3K9ac and H3K56ac. The sequential ChIP-on-chip was carried out with ring stage parasites using anti-H3K56ac antibody followed by anti-H3K9ac antibody. Immunoprecipitation was also done using anti-H3K56ac antibody or anti-H3K9ac antibody separately. Data was averaged from 2 separate experiments and probes with ChIP/input signal ratio above 1 for bead control were subtracted for further analysis. The chart (above) shows the probes overlapping between the sequential ChIP and probes shared in common between both histone marks when used individually (ChIP/input >1). Chromosomal distribution (below) of H3K56ac (orange), H3K9ac (green) and sequential (purple) ChIP enrichment of probes as seen at chromosome 4. Each vertical line depicts the position of a probe on the chromosome.
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Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3585154&req=5

ppat-1003170-g006: Combinatorial histone modifications.(A) PCC-based correlation of the dynamic histone occupancy profiles. The bar charts show examples of pair wise correlation distributions between the dynamic profiles of the individual histone marks calculated analogously to the correlations with steady state mRNA levels (see Figure 3). Line graphs give the randomized distribution of PCC. P value (P) and skewness (S) are shown below each graph. (B) Hierarchical clustering of histone mark associations. The heat maps represent hierarchical clustering of the skewness (S) values of the PCC distributions for every marked histone pair. High positive skew (red) and low negative skew (blue) indicate positive and negative correlations with the marked histone pairs, respectively. (C) Sequential ChIP-on-chip for H3K9ac and H3K56ac. The sequential ChIP-on-chip was carried out with ring stage parasites using anti-H3K56ac antibody followed by anti-H3K9ac antibody. Immunoprecipitation was also done using anti-H3K56ac antibody or anti-H3K9ac antibody separately. Data was averaged from 2 separate experiments and probes with ChIP/input signal ratio above 1 for bead control were subtracted for further analysis. The chart (above) shows the probes overlapping between the sequential ChIP and probes shared in common between both histone marks when used individually (ChIP/input >1). Chromosomal distribution (below) of H3K56ac (orange), H3K9ac (green) and sequential (purple) ChIP enrichment of probes as seen at chromosome 4. Each vertical line depicts the position of a probe on the chromosome.
Mentions: The abundance of dynamic temporal regulation of individual histone marks suggests the existence of combinatorial patterns forming a putative “dynamic histone code”. To investigate this possibility, we carried out pair-wise analysis of occupancy profiles with all thirteen histone marks. To this end, we evaluated the concordance of the occupancy profiles using PCC distributions and subsequently the skewness and KS-test P value as described above (Table S2). Figure 6A shows examples of highly positive (S>1), moderately positive (S between 1 and 0) and highly negative PCC distribution (S<0) between the histone marks. Overall our analysis revealed that most of the overlapping marks (present at the same loci) exhibited a high level of correlation between their occupancy profiles. Here it is important to note that the mean size of ChIP DNA product generated by our protocol is 500 bp which corresponds to approximately three nucleosomes positioned in the vicinity of the genetic locus represented by a microarray probe. Hence the correlations in the occupancy profiles represent either a combinatorial histone modification at the same nucleosome or co-occurrence of these at directly adjacent nucleosomes. High correlations of the occupancy profiles are particularly evident for acetylations that exhibited positive correlations at essentially all overlapping loci (Figure 6B). This suggests that, each nucleosome predominantly undergoes only one set of modifications during the IDC, presumably for one purpose (such as transcriptional regulation). This situation contrasted with the lysine methylation profiles that showed loose or no correlations with each other or with acetylations. Interestingly, H4R3me2 exhibited a strong negative correlation with most of the other marks. This methylation is thought to be mediated by PfPRMT1 and might be playing a similar role to H3R2me2a (asymmetrical histone H3 arginine 2 dimethylation) which has been shown to have a mutually exclusive pattern with H3K4me3 in budding yeast [33].

Bottom Line: While some modifications were found to be associated with the vast majority of the genome and their occupancy was constant, others showed more specific and highly dynamic distribution.In addition, we showed the presence of multivalent domains on the genome carrying more than one histone mark, highlighting the importance of combinatorial effects on transcription.Overall, our work portrays a substantial association between chromosomal locations of various epigenetic markers, transcriptional activity and global stage-specific transitions in the epigenome.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.

ABSTRACT
Epigenetic mechanisms are emerging as one of the major factors of the dynamics of gene expression in the human malaria parasite, Plasmodium falciparum. To elucidate the role of chromatin remodeling in transcriptional regulation associated with the progression of the P. falciparum intraerythrocytic development cycle (IDC), we mapped the temporal pattern of chromosomal association with histone H3 and H4 modifications using ChIP-on-chip. Here, we have generated a broad integrative epigenomic map of twelve histone modifications during the P. falciparum IDC including H4K5ac, H4K8ac, H4K12ac, H4K16ac, H3K9ac, H3K14ac, H3K56ac, H4K20me1, H4K20me3, H3K4me3, H3K79me3 and H4R3me2. While some modifications were found to be associated with the vast majority of the genome and their occupancy was constant, others showed more specific and highly dynamic distribution. Importantly, eight modifications displaying tight correlations with transcript levels showed differential affinity to distinct genomic regions with H4K8ac occupying predominantly promoter regions while others occurred at the 5' ends of coding sequences. The promoter occupancy of H4K8ac remained unchanged when ectopically inserted at a different locus, indicating the presence of specific DNA elements that recruit histone modifying enzymes regardless of their broad chromatin environment. In addition, we showed the presence of multivalent domains on the genome carrying more than one histone mark, highlighting the importance of combinatorial effects on transcription. Overall, our work portrays a substantial association between chromosomal locations of various epigenetic markers, transcriptional activity and global stage-specific transitions in the epigenome.

Show MeSH
Related in: MedlinePlus