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RNA-seq of Xist deletion mouse models

ABSTRACT: RNA-seq of Xist deletion mouse models

PROVIDER: PRJEB33688 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3452830_1.fastq.gz	Fastqsanger.gz
	ERR3452830_2.fastq.gz	Fastqsanger.gz
	ERR3452840_1.fastq.gz	Fastqsanger.gz
	ERR3452840_2.fastq.gz	Fastqsanger.gz
	ERR3452831_1.fastq.gz	Fastqsanger.gz

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RNA-seq of Xist deletion mouse models

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Project description:In this study, we have investigated the role of Xist upstream region located near the Xist-TAD boundary in maintenance of imprinted X-chromosome inactivation in extraembryonic endoderm stem cells (XEN). We found that deletion of Xist upstream region(~6Kb) leads to the alterations of Xist intra-TAD contacts and upregulate Xist expression. Moreover, it impaired the interactions of the Xist locus across X-chromosomes and autosomes. Moreover, Xist upstream deletion resulted dispersal of Xist coating and loss of accumulation of diffrent repressive chromatin marks on the inactive-X. Surprisingly there was no effect on inactive-X gene silencing, however, it affeted the autosomal gene expression.

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Probing Xist RNA structure in cells using Targeted Structure-Seq

Project description:The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5'-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function. Examination of dimethylsufate reactivity of Xist lncRNA and 18S rRNA in cells using targeted reverse transcription to determine reactivity, and comparisons with untreated control samples.

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Perturbed maintenance of transcriptional repression on the inactive X-chromosome in the mouse brain after XIST deletion

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