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The role of HNRNPU and the nuclear matrix in human pluripotent stem cells [MAR-Seq]

ABSTRACT: The role of HNRNPU and the nuclear matrix in human pluripotent stem cells [MAR-Seq]

PROVIDER: PRJNA1013374 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25918258_1.fastq.gz	Fastqsanger.gz
	SRR25918258_2.fastq.gz	Fastqsanger.gz
	SRR25918259_1.fastq.gz	Fastqsanger.gz
	SRR25918259_2.fastq.gz	Fastqsanger.gz
	SRR29879759_1.fastq.gz	Fastqsanger.gz

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The role of HNRNPU and the nuclear matrix in human pluripotent stem cells [MAR-Seq]

Project description:During early embryogenesis the fertilized zygote proceeds through an intricate developmental program, accompanyed by DNA and chromatin remodelling. However, the mechanisms governing this reconfiguring are poorly understood. Parts of the embryogenesis developmental program can be captured in vitro in the form of two types of human pluripotent stem cells (hPSC): naïve and primed hPSCs. Naïve hPSCs resemble the inner cell mass of the blastocyst, whilst primed hPSCs resemble the post-implantation embryo. The nucleus is made of DNA wrapped around chromatin, and the nuclear matrix, a proteinaceous gel that provides structure. Here, we show that disruptions in the nuclear matrix caused primed hPSCs to spontaneously convert to the naïve, earlier embryonic state.

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Identifying Nuclear Matrix–attached DNA across the Genome (MAR-seq)

Project description:Experimental approaches to define the relationship between gene expression and nuclear matrix attachment regions (MARs) have given contrasting and method-specific results. We have developed a next generation sequencing strategy to identify MARs across the human genome (MAR-Seq). The method is based on crosslinking chromatin to its nuclear matrix attachment sites to minimize changes during biochemical processing. We used this method to compare nuclear matrix organization in MCF-10A mammary epithelial-like cells and MDA-MB-231 breast cancer cells and evaluated the results in the context of global gene expression (array analysis) and positional enrichment of gene-regulatory histone modifications (ChIP-Seq). In the normal-like cells, nuclear matrix–attached DNA was enriched in expressed genes, while in the breast cancer cells, it was enriched in non-expressed genes. In both cell lines, the chromatin modifications that mark transcriptional activation or repression were appropriately associated with gene expression. Using this new MAR-Seq approach, we provide the first genome-wide characterization of nuclear matrix attachment in mammalian cells and reveal that the nuclear matrix–associated genome is highly cell-context dependent.

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The role of HNRNPU and the nuclear matrix in human pluripotent stem cells

Project description:The role of HNRNPU and the nuclear matrix in human pluripotent stem cells

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The role of HNRNPU and the nuclear matrix in human pluripotent stem cells [ATAC]

Project description:The role of HNRNPU and the nuclear matrix in human pluripotent stem cells [ATAC]

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The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [ChIP-Seq 2]

Project description:Here we show that HNRNPU, the major nuclear matrix attachment factor, is necessary to maintain proper nuclear architecture in mouse hepatocytes. Upon HNRNPU depletion, the interactions between chromatin and nuclear lamina have been changed dramatically；chromatin organization is globally changed; boundaries of topologically associating domains (TADs) become weaker; inter-TAD interactions are increased; thousands of genes are significantly altered coincident with 3D chromatin changes. Mechanically, HNRNPU interacts with CTCF and RAD21, which affects the binding of RAD21 to the chromatin significantly, whereas CTCF bindings are almost unchanged, what’ more, the decrease of binding strengths are highly correlated with the weakness of loop bounded by Rad21. Taken together, we identify HNRNPU as a key regulator of chromatin architecture, and our data suggest the importance of nuclear matrix associating factors in 3D genome organization.

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Project description:The role of HNRNPU and the nuclear matrix in human pluripotent stem cells [scRNA-Seq]

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The role of HNRNPU and the nuclear matrix in human pluripotent stem cells [RNA-Seq]

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The role of HNRNPU and the nuclear matrix in human pluripotent stem cells [RIP-Seq]

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The role of HNRNPU and the nuclear matrix in human pluripotent stem cells [Hi-C]

Project description:The role of HNRNPU and the nuclear matrix in human pluripotent stem cells [Hi-C]