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LncRNA 5430416N02Rik Promotes the Proliferation of Mouse Embryonic Stem Cells by Activating Mid1 expression through 3D chromatin Architecture

ABSTRACT: lncRNA 5430416N02Rik Promotes the Proliferation of Mouse Embryonic Stem Cells by Activating Mid1 expression through 3D chromatin Architecture

PROVIDER: PRJNA551451 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9608420_1.fastq.gz	Fastqsanger.gz
	SRR9608420_2.fastq.gz	Fastqsanger.gz
	SRR9608430_1.fastq.gz	Fastqsanger.gz
	SRR9608430_2.fastq.gz	Fastqsanger.gz
	SRR9608440_1.fastq.gz	Fastqsanger.gz

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lncRNA 5430416N02Rik Promotes the Proliferation of Mouse Embryonic Stem Cells by Activating Mid1 expression through 3D chromatin Architecture

Project description:Both three-dimensional chromatin architecture and long non-coding RNAs (lncRNAs) play essential roles in pluripotency maintenance. However, whether lncRNAs are involved in organizing 3D chromatin structure remains largely unexplored. Here, we identified 39 lncRNAs bound by Klf4, a pluripotency factor mediating long-range chromatin interactions. Among these 39 Klf4-bound lncRNAs, we further investigated the function of 5430416N02Rik. 4C-seq and capture-C experiments revealed that the 5430416N02Rik promoter is a chromatin interaction hub, and 5430416N02Rik RNA functions to facilitate chromatin interactions with the 5430416N02Rik promoter. Knockout of 5430416N02Rik reduces the proliferation rate of embryonic stem cells (ESCs). Moreover, compared to deletion of the gene body alone, deleting both the promoter and the gene body of 5430416N02Rik causes a more severe proliferation defect and a more profound impact on the transcriptome. The reduced proliferation of 5430416N02Rik knockout ESCs is mainly due to the down-regulation of Mid1 transcription, the activation of which requires the inter-chromosomal interaction between Mid1 and 5430416N02Rik loci. In summary, our data demonstrated that lncRNA 5430416N02Rik maintains the proliferation of ESCs by activating the expression of Mid1 through its function of mediating chromatin interaction.

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lncRNA 5430416N02Rik Promotes the Proliferation of Mouse Embryonic Stem Cells by Activating Mid1 Expression through 3D Chromatin Architecture.

Project description:Both 3D chromatin architecture and long non-coding RNAs (lncRNAs) play essential roles in pluripotency maintenance. However, whether lncRNAs are involved in organizing 3D chromatin structure remains largely unexplored. We identified 39 lncRNAs bound by Klf4, among which we further revealed the 5430416N02Rik promoter is a chromatin interaction hub. Knockout of the 5430416N02Rik locus reduces the proliferation rate of embryonic stem cells (ESCs). Moreover, deleting both the promoter and the gene body of 5430416N02Rik causes a more severe proliferation defect and has a more profound impact on the transcriptome than deleting the gene body alone. The reduced proliferation of the 5430416N02Rik locus knockout ESCs is mainly due to the downregulation of Mid1, the expression of which requires the inter-chromosomal interaction between Mid1 and 5430416N02Rik loci. In summary, our data demonstrated that the lncRNA 5430416N02Rik gene locus maintains the fast proliferation of ESCs by activating the expression of Mid1 through chromatin interaction.

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