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Genome-wide Kdm1a binding in X chromosome by high throughput sequencing [ChIP-Seq]

ABSTRACT: Genome-wide Kdm1a binding in X chromosome by high throughput sequencing [ChIP-Seq]

PROVIDER: PRJNA661453 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12588745_1.fastq.gz	Fastqsanger.gz
	SRR12588745_2.fastq.gz	Fastqsanger.gz
	SRR12588746_1.fastq.gz	Fastqsanger.gz
	SRR12588746_2.fastq.gz	Fastqsanger.gz
	SRR12588747_1.fastq.gz	Fastqsanger.gz

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Genome-wide Kdm1a binding in X chromosome by high throughput sequencing [ChIP-Seq]

Project description:We analyzed KDM1A (LSD1) occupancy in the Xi during somatic cell reprogramming of female mouse cells. We use MEFs from hybrid embryos by crossing male Mus spretus and female Mus musculus domesticus C57BL/6J to distiguish genome DNA from the Xi. We found a possible physical and/or functional regulation of KDM1A during the X chromosome reactivation in the intiation site on the Xi.

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Project description:KDM1A requires an adaptor protein with specific DNA-binding activity to recognize chromatin sequence. We constructed HepG2 cells stably overexpressing KDM1A-Flag tag using lentivirus. We performed Co-IP with Flag-gel and we used LC-MS to determine the immunoprecipitates of KDM1A.

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Project description:KDM1A-mediated H3K4 demethylation is a well-established mechanism underlying transcriptional gene repression, but its role in gene activation is less clear. Here we report a critical function and novel mechanism of action of KDM1A in glucocorticoid receptor (GR)-mediated gene transcription. Biochemical purification of the nuclear GR complex revealed KDM1A as an integral component. In cell-free assays, GR modulates KDM1A-catalyzed H3K4 progressive demethylation by limiting loss of H3K4me1. Similarly, in cells KDM1A binds to most GR binding sites where it removes preprogrammed H3K4me2 but leaves H3K4me1 untouched. Blocking KDM1A catalytic activity prevents H3K4me2 removal, severely impairs GR binding to chromatin, and dysregulates GR-targeted genes. Taken together, these data suggest KDM1A-mediated H3K4me2 demethylation at GRBSs promotes GR binding and plays an important role in glucocorticoid-induced gene transcription, offering a new mechanism contributing to nuclear receptor mediated gene activation.

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