|
| Status |
Public on Aug 07, 2023 |
| Title |
PfAP2-P DNA-binding protein is a master regulator of parasite pathogenesis during malaria parasite blood stages (ChIP-Seq II) |
| Organism |
Plasmodium falciparum |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Malarial parasite pathogenicity results from its ability to invade and remodel red blood cells (RBCs), expressing antigenic variant proteins for immune evasion and survival, and then to egress from the host cell. These sequential processes require concerted actions of a large number of proteins during the intraerythrocytic developmental cycle (IDC), but the molecular basis of the required regulation is only partially understood. Here, we have characterized an essential Apicomplexan AP2 (ApiAP2) transcription factor (we refer to it as PfAP2-P; Master Regulator of Pathogenesis) that shows two peaks of expression during the IDC at 16- and 40-hour post invasion (h.p.i.). When expression of PfAP2-P at 40 h.p.i. was disrupted using an inducible gene knockout approach, ∆PfAP2-P parasites unable to form mature merozoites and egress from the host RBCs owing to strong down-regulation of several known egress- and invasion-associated genes, in addition to several novel hypothetical genes of thought to be involved in these key life cycle processes during the IDC. Disruption of PfAP2-P expression at 16 h.p.i. results in transcriptional activation of virtually majority of silenced var genes observed at both bulk and single cell level. This is also reflected by significantly higher level of recognition of the exported proteins on the ∆PfAP2-P parasite-infected RBCs by pooled sera from malaria-exposed individuals from endemic region. In addition, over expression of many early gametocyte marker genes was also observed in ∆PfAP2-P parasites at both 40 h.p.i., and at 16 h.p.i. PfAP2-P directly regulates these genes by binding to their promoter region or indirectly through 14 other down-stream AP2 transcription factors. Taken together, we conclude that PfAP2-P is an upstream transcriptional regulator that participates in mutually exclusive expression pattern shown by the var family of genes and a critical determinant of parasite’s growth during the IDC.
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| |
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| Overall design |
Chip was performed on AP2-P parasites at 40 hour post invasion and 16 hour post invasion using rabbit polyclonal anti H3K9me3 (RRID:AB_310620), rabbit polyclonal anti H3K9ac (RRID:AB_310544), rabbit polyclonal anti H3K4me3(RRID:AB_306649) antibodies . There are two biological replicates for each developmental stages. The input served as the control.
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| |
|
| Contributor(s) |
Kumar SA, Arnab P |
| Citation(s) |
37293082 |
| |
| Submission date |
Apr 20, 2023 |
| Last update date |
Aug 08, 2023 |
| Contact name |
AMIT KUMAR SUBUDHI |
| E-mail(s) |
amit.subudhi@kaust.edu.sa
|
| Phone |
+96540375986
|
| Organization name |
King Abdullah University of Science and Technology
|
| Department |
BESE
|
| Lab |
Pathogen Genomics
|
| Street address |
Level4, Builiding, 2, KAUST
|
| City |
Thuwal |
| State/province |
Thuwal |
| ZIP/Postal code |
239556900 |
| Country |
Saudi Arabia |
| |
|
| Platforms (1) |
| GPL26836 |
Illumina NovaSeq 6000 (Plasmodium falciparum) |
|
| Samples (32)
|
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| This SubSeries is part of SuperSeries: |
| GSE190519 |
PfAP2-P DNA-binding protein is a master regulator of parasite pathogenesis during malaria parasite blood stages |
|
| Relations |
| BioProject |
PRJNA957828 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE230206_RAW.tar |
255.5 Mb |
(http)(custom) |
TAR (of BED, BW) |
| GSE230206_intersect_20D-12-12-22-H3K4ME3_rep1_rep2.bed.gz |
178.2 Kb |
(ftp)(http) |
BED |
| GSE230206_intersect_20D-12-12-22-H3K9ME3_rep1_rep2.bed.gz |
23.8 Kb |
(ftp)(http) |
BED |
| GSE230206_intersect_20D-21-11-22-H3K9ac_rep1_rep2.bed.gz |
127.3 Kb |
(ftp)(http) |
BED |
| GSE230206_intersect_20R-12-12-22-H3K4ME3_rep1_rep2.bed.gz |
168.7 Kb |
(ftp)(http) |
BED |
| GSE230206_intersect_20R-12-12-22-H3K9ME3_rep1_rep2.bed.gz |
11.3 Kb |
(ftp)(http) |
BED |
| GSE230206_intersect_20R-21-11-22-H3K9ac_rep1_rep2.bed.gz |
72.7 Kb |
(ftp)(http) |
BED |
| GSE230206_intersect_20R-H3K4ME3_rep1_rep3.bed.gz |
167.2 Kb |
(ftp)(http) |
BED |
| GSE230206_intersect_20R-H3K9ME3_rep1_rep3.bed.gz |
18.8 Kb |
(ftp)(http) |
BED |
| GSE230206_intersect_40D-22-02-22-H3K4ME3_rep1_rep2.bed.gz |
210.4 Kb |
(ftp)(http) |
BED |
| GSE230206_intersect_40D-22-02-22-H3K9ME3_rep1_rep2.bed.gz |
7.4 Kb |
(ftp)(http) |
BED |
| GSE230206_intersect_40D-22-02-22-H3K9ac_rep1_rep2.bed.gz |
17.4 Kb |
(ftp)(http) |
BED |
| GSE230206_intersect_40R-22-02-22-H3K4ME3_rep1_rep2.bed.gz |
222.1 Kb |
(ftp)(http) |
BED |
| GSE230206_intersect_40R-22-02-22-H3K9ME3_rep1_rep2.bed.gz |
29.1 Kb |
(ftp)(http) |
BED |
| GSE230206_intersect_40R-22-02-22-H3K9ac_rep1_rep2.bed.gz |
39.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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