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An ISWI-related chromatin remodeler orchestrates parasite lifecycle progression by insulating gene expression in a densely packed genome [ATAC-seq]

ABSTRACT: An ISWI-related chromatin remodeler orchestrates parasite lifecycle progression by insulating gene expression in a densely packed genome [ATAC-seq]

PROVIDER: PRJNA1133890 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29760711_1.fastq.gz	Fastqsanger.gz
	SRR29760711_2.fastq.gz	Fastqsanger.gz
	SRR29760712_1.fastq.gz	Fastqsanger.gz
	SRR29760712_2.fastq.gz	Fastqsanger.gz
	SRR29760713_1.fastq.gz	Fastqsanger.gz

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Project description:An ISWI-related chromatin remodeler orchestrates parasite lifecycle progression by insulating gene expression in a densely packed genome [RNA-seq]

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Project description:An ISWI-related chromatin remodeler orchestrates parasite lifecycle progression by insulating gene expression in a densely packed genome [ChIP-seq]

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Project description:In eukaryotic cells, ATP-dependent chromatin remodelers are specialized multiprotein machines that organize the genome and rule its accessibility by repositioning, ejecting or modifying nucleosomes, but their role in Toxoplasma gondii is still poorly understood. Phylogenetic analyzes show that the parasite retains the four commonly recognized remodeler families and has evolved two divergent proteins within the ISWI family: TgSNF2h and TgSNF2L. These proteins are structurally divergent and form distinct complexes. TgSNF2h specifically forms a core complex with the transcription factor AP2VIII-2 and the scaffold protein TgRFTS. Depletion of TgRFTS phenocopies the knockdown of TgSNF2h, restricting access to chromatin and altering local gene expression. At the genomic level, TgSNF2h actively insulates highly transcribed genes from their minimally expressed or silenced neighbors. This ISWI complex establishes and maintains stage-specific gene expression by regulating the chromatin accessibility to transcription factors. Using MORC as a proxy, we have shown that TgSNF2h rules DNA accessibility and thereby exerts an epistatic control over a key regulator of sexual commitment. In a parasite characterized by high phenotypic plasticity and a compact genome, this dedicated ISWI complex orchestrates the partitioning of developmental genes and ensures transcriptional fidelity throughout its life cycle.

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Identification and Characterization of Splenic Adherent Cells forming Densely-Packed Colony

Project description:As a first step for identifying hypothetical splenic stem cells for nonhematopoietic cells, densely-packed colony-forming cells were isolated from mouse spleen. Those which we designated as Splenic Adherent Colony-Forming Cells (SACCs) are positive for some of stem cell markers such as alkaline phosphatase and SSEA-1 antigen. We herewith determined global expression profiles of SACCs and control splenic adherent cells.

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Affinity Purification of ISWI chromatin remodeler in Trypanosoma cruzi

Project description:Chromatin remodeling is a general mechanism involved in DNA-dependent processes, including gene expression regulation. ISWI ATPase is the catalytic subunit in diverse chromatin remodeling complexes that changing histone–DNA interactions and therefore play a pivotal role in different nuclear processes. Here, the ISWI remodeler was fused to GFP (NH and CO fusions) and its partners were determined by affinity purification-mass spectrometry (MS) assay. This approach identified known ISWI partners (NLP, RCCP and FYRP), previously characterized in T. brucei, and new components of TcISWI complex (DRBD2, DHH1 and proteins containing SMC domains).

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Identification and Characterization of Splenic Adherent Cells forming Densely-Packed Colony

Project description:Identification and Characterization of Splenic Adherent Cells forming Densely-Packed Colony

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Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 1)

Project description:Chromatin remodelers influence genetic processes by altering nucleosome occupancy, positioning, and composition. In vitro, yeast ISWI and CHD remodelers require > 20 bp of extranucleosomal DNA for remodeling, but linker DNA in S. cerevisiae averages < 20 bp. To resolve this paradox, we have mapped the genomic distributions of the yeast Isw1, Isw2, and Chd1 remodelers at base-pair resolution. Surprisingly, remodelers are highly enriched at promoter nucleosome depleted regions (5' NDRs), where they bind to regions of extended linker DNA. Remodelers are also enriched in the bodies of genes displaying high nucleosome turnover. We hypothesize that remodelers bind but do not act at 5' NDRs, remaining in physical proximity to gene bodies, where they act on regions of transient nucleosome depletion following transcriptional elongation. We have analyzed the dynamics of yeast ISWI and CHD chromatin remodeler genomic association at base-pair resolution using native chromatin immunoprecipitation followed by sequencing (N-ChIP-seq).

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Dynamics of yeast ISWI and CHD chromatin remodeler genomic association (part 2)

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