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PfSET2 is involved in genome organization of var gene family in Plasmodium falciparum [RNAseq]

ABSTRACT: PfSET2 is involved in genome organization of var gene family in Plasmodium falciparum [RNAseq]

PROVIDER: PRJNA714924 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13979009_1.fastq.gz	Fastqsanger.gz
	SRR13979009_2.fastq.gz	Fastqsanger.gz
	SRR13979010_1.fastq.gz	Fastqsanger.gz
	SRR13979010_2.fastq.gz	Fastqsanger.gz
	SRR13979011_1.fastq.gz	Fastqsanger.gz

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PfSET2 is involved in genome organization of var gene family in Plasmodium falciparum [HiC]

Project description:The three-dimensional (3D) genome structure of human malaria parasite Plasmodium falciparum is highly organized and plays important roles in regulating coordinated expression patterns of specific genes such as virulence genes which are involved in antigenic variation and immune escape. However, the molecular mechanisms that control 3D genome of the parasite remain elusive. Here by analyzing genome organization in P. falciparum, we identify high-interacting regions (HIRs) with strong chromatin interactions telomeres and virulence genes loci. Specifically, HIRs are highly enriched with repressive histone marks (H3K36me3 and H3K9me3) and form the transcriptional repressive center. Deletion of PfSETvs, which controls H3K36me3 level, results in marked reduction of both intra-chromosomal and inter-chromosomal interactions for HIRs. Importantly, such chromatin reorganization coordinates with dymamic changes in epigenetic feature in HIRs and specifically activation of var genes. Our results uncover a fundamental mechanism that the epigenetic factor PfSETvs controls the 3D organization of heterochromatin in regulating the transcription activities of var genes family in P. falciparum.

2022-12-16 | GSE169028 | GEO

PfSET2 is involved in genome organization of var gene family in Plasmodium falciparum [RNAseq]

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PfSET2 is involved in genome organization of var gene family in Plasmodium falciparum [ChIPseq_HP1]

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PfSET2 is involved in genome organization of var gene family in Plasmodium falciparum [HiC]

Project description:PfSET2 is involved in genome organization of var gene family in Plasmodium falciparum [HiC]

| PRJNA714925 | ENA

PfSET2 is involved in genome organization of var gene family in Plasmodium falciparum [ChIPseq_HP1]

Project description:PfSET2 is involved in genome organization of var gene family in Plasmodium falciparum [ChIPseq_HP1]

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Expression analysis of Plasmodium falciparum 3D7 delta-PfPuf2 mutant

Project description:Investigation of whole genome gene expression level changes in Plasmodium falciparum 3D7 delta-PfPuf2 mutant, compared to the wild-type strain 3D7. The mutation engineered into this strain render tanslational control. The mutants analyzed in this study are further described in Miao J, Li J, Fan Q, Li X, Li X, Cui L.2010. The Puf-family RNA-binding protein PfPuf2 regulates sexual development and sex differentiation in the malaria parasite Plasmodium falciparum. J Cell Sci. 123(7):1039-49 (PMID 20197405). A 12 chip study using total RNA recovered from six separate wild-type cultures of Plasmodium falciparum 3D7 at gametocyte stage III (three cultures) and stage V (three cultures) and six separate cultures of dalta PfPuf2 mutant at gametocyte stage III (three cultures) and stage V (three cultures). Each chip measures the expression level of 5,367 genes from Plasmodium falciparum 3D7 with 45-60 mer probes with two replicates on final array of 71618 probes.

2012-07-05 | E-GEOD-39124 | biostudies-arrayexpress

Expression analysis of Plasmodium falciparum 3D7 delta-PfPuf2 mutant

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Plasmodium falciparum NF54 Transcriptome

Project description:Transcriptomic Analysis of Cultured Sporozoites of P. falciparum RNA-seq reads from each of three developmental stages (2 replicates per sample) were mapped to the reference Plasmodium falciparum genome, and gene expression levels were calculated for each sample.

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Plasmodium falciparum

Project description:Plasmodium falciparum Epigenomics

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Expression data of gene knockout Plasmodium falciparum clones

Project description:The variant antigen, Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), expressed on the surface of P. falciparum infected Red Blood Cells (iRBCs) is a critical virulence factor for malaria. Each parasite encodes 60 antigenically distinct var genes encoding PfEMP1s, but during infection the clonal parasite population expresses only one gene at a time before switching to the expression of a new variant antigen as an immune evasion mechanism to avoid the hostM-bM-^@M-^Ys antibody responses. The mechanism by which 59 of the 60 var genes are silenced remains largely unknown. We used microarrays to detail the global programme changes of gene expression caused by each gene knockout with a particular view towards which gene knockout results in transcriptional upregulation of the entire var gene family. Plasmodium falciparum clones, in each of which one of different histone lysine methylation modification enzyme genes was knocked out, were synchronized in the asexual stage and collected at indicated time points post invasion of erythrocytes for RNA extraction and hybridization on Affymetrix microarrays. We sought to identify the key epigenetic enzyme that controls silencing of the whole var gene family.

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