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| Status |
Public on Jan 16, 2018 |
| Title |
Comparative profiling of the heterochromatin landscape in different life cycle stages, strains and species of malaria parasites |
| Organisms |
Plasmodium berghei; Plasmodium chabaudi; Plasmodium falciparum; Plasmodium knowlesi; Plasmodium vivax; Plasmodium yoelii |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Heterochromatin is a tightly packaged form of DNA that leads to permanent or temporal gene silencing. In P. falciparum heterochromatin is formed after trimethylation of lysine 9 on histone H3 and consequent binding of heterochromatin protein 1 (HP1). Genome-wide profiling studies established that in P. falciparum blood stage schizonts heterochromatin is formed at subtelomeres and some intra-chromosomal islands. Reversible silencing of genes located in these regions has been shown to be key to, among others, antigenic variation, invasion pathway selection or commitment to gametocytogenesis. However, heterochromatic gene silencing has not been investigated in many other Plasmodium species, strains or life cycle stages, yet. Here, we used ChIP-seq to profile HP1 occupancy in asexual parasites of six different species (P. falciparum, P. knowlesi, P. vivax, P. berghei, P. yoelii, and P. chabaudi) and of four different P. falciparum strains (3D7, PF2004, NF54, NF135) as well as two different P. knowlesi clones (A1C1, A1H1). Additionally, we performed HP1 ChIP-seq on three asexual stages (ring, trophozoite and schizont stage) and two sexual stages of P. falciparum parasites. Collectively, the generated HP1 profiles provide a detailed catalog of heterochromatic genes and reveal conserved and specialized features of epigenetic control at different life cycle stages, strains and species across the genus Plasmodium.
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| Overall design |
In total, we sequenced 26 samples (14 HP1-ChIP-seq samples and 12 inputs) generated from chromatin from six different Plasmodium species (P. chabaudi, P. berghei, P. yoelii, P. knowlesi, P. vivax and P. falciparum), four different strains of P. falciparum (3D7, NF54, NF135 and Pf2004) and two different strains of P. knowlesi (A1.C1 and A1.H1) as well as three different intraerythrocytic stages of the P. falciparum 3D7 strain (ring, trophozoite and schizont stages) and three different stages of the P. falciparum Pf2004 strain (schizont stages, stage II/III gametocytes and stage IV/V gametocytes).
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| Contributor(s) |
Fraschka SA, Filarsky M, Hoo R, Niederwieser I, Yan Yam X, Brancucci NB, Mohring F, Mushunje AT, Huang X, Christensen PR, Nosten F, Russell B, Moon RW, Marti M, Preiser PR, Bartfai R, Voss TS |
| Citation(s) |
29503181 |
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| Submission date |
Aug 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sabine Fraschka |
| Organization name |
Radboud University Nijmegen
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| Department |
Molecular Biology
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| Lab |
Richárd Bártfai
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| Street address |
Geert Grooteplein 28
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| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
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| Platforms (6)
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| GPL21298 |
Illumina NextSeq 500 (Plasmodium falciparum) |
| GPL23133 |
Illumina NextSeq 500 (Plasmodium berghei) |
| GPL23913 |
Illumina NextSeq 500 (Plasmodium chabaudi) |
| GPL23914 |
Illumina NextSeq 500 (Plasmodium yoelii) |
| GPL23915 |
Illumina NextSeq 500 (Plasmodium knowlesi) |
| GPL23916 |
Illumina NextSeq 500 (Plasmodium vivax) |
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| Samples (26)
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| Relations |
| BioProject |
PRJNA398396 |
| SRA |
SRP115493 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE102695_P.berghei-HP1_over_P.berghei-Input.Bedgraph.gz |
125.5 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE102695_P.chabaudi-HP1_over_P.chabaudi-Input.Bedgraph.gz |
140.1 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE102695_P.knowlesi-A1C1-HP1_over_P.knowlesi-A1C1-Input.Bedgraph.gz |
160.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE102695_P.knowlesi-A1H1-HP1_over_P.knowlesi-A1H1-Input.Bedgraph.gz |
160.6 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE102695_P.vivax-HP1_over_P.vivax-Input.Bedgraph.gz |
123.8 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE102695_P.yoelii-HP1_over_P.yoelii-Input.Bedgraph.gz |
143.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE102695_Pf-3D7-Ring-HP1_over_Pf-3D7-Schizont-Input.Bedgraph.gz |
124.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE102695_Pf-3D7-Schizont-HP1_over_Pf-3D7-Schizont-Input.Bedgraph.gz |
116.5 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE102695_Pf-3D7-Trophozoite-HP1_over_Pf-3D7-Schizont-Input.Bedgraph.gz |
109.8 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE102695_Pf-NF135-Schizont-HP1_over_Pf-NF135-Schizont-Input.Bedgraph.gz |
107.8 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE102695_Pf-NF54-Schizont-HP1_over_Pf-NF54-Schizont-Input.Bedgraph.gz |
118.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE102695_Pf-Pf2004-GamII-III-HP1_over_Pf-Pf2004-GamII-III-Input.Bedgraph.gz |
86.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE102695_Pf-Pf2004-GamII-III-HP1_over_Pf-Pf2004-GamII-III-Input_Pf2004-assembly.Bedgraph.gz |
92.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE102695_Pf-Pf2004-GamIV-V-HP1_over_Pf-Pf2004-GamIV-V-Input.Bedgraph.gz |
124.1 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE102695_Pf-Pf2004-GamIV-V-HP1_over_Pf-Pf2004-GamIV-V-Input_Pf2004-assembly.Bedgraph.gz |
129.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE102695_Pf-Pf2004-Schizont-HP1_over_Pf-Pf2004-Schizont-Input.Bedgraph.gz |
92.4 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE102695_Pf-Pf2004-Schizont-HP1_over_Pf-Pf2004-Schizont-Input_Pf2004-assembly.Bedgraph.gz |
98.8 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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