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Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome [II]

ABSTRACT: Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome [II]

PROVIDER: PRJNA751096 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15309300_1.fastq.gz	Fastqsanger.gz
	SRR15309300_2.fastq.gz	Fastqsanger.gz
	SRR15309301_1.fastq.gz	Fastqsanger.gz
	SRR15309301_2.fastq.gz	Fastqsanger.gz
	SRR15309302_1.fastq.gz	Fastqsanger.gz

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Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome

Project description:Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome

| PRJNA751089 | ENA

Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome [I]

Project description:Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome [I]

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Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome [I]

Project description:The long non-coding RNA Xist exploits numerous effector proteins to gradually induce gene silencing across the X chromosome. Here, we show that formation of the inactive X (Xi)-compartment is induced by ~50 locally confined granules, where two Xist RNA molecules nucleate supra-molecular complexes (SMCs) of interacting proteins. Xist-SMCs are dynamic structures that concentrate rapidly recycling proteins on the X by increasing their binding affinity, thereby facilitating their access to the entire chromosome. We find that gene silencing originates at Xist-SMCs and propagates across the entire X chromosome over time. The propagation of silencing is achieved by Polycomb-mediated coalescence of chromatin regions and aggregation of the critical silencing enzyme SPEN, via its intrinsically disordered domains. Our observations suggest a new model for X Chromosome Inactivation, whereby Xist RNA triggers macromolecular crowding of heterochromatinizing proteins at distinct sites to ultimately increase their occupancy throughout the X chromosome . This mechanism enables deterministic gene silencing across an entire chromosome without the need for Xist ribonucleoprotein complex-chromatin interactions at each target gene. Our findings uncover a spatial organization mechanism by which few RNA molecules can regulate a broad nuclear compartment through the recruitment and local concentration of dynamic effector proteins, and provide a quantitative framework for studying such compartments.

2021-10-27 | GSE162011 | GEO

Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome [II]

Project description:The long non-coding RNA Xist exploits numerous effector proteins to gradually induce gene silencing across the X chromosome. Here, we show that formation of the inactive X (Xi)-compartment is induced by ~50 locally confined granules, where two Xist RNA molecules nucleate supra-molecular complexes (SMCs) of interacting proteins. Xist-SMCs are dynamic structures that concentrate rapidly recycling proteins on the X by increasing their binding affinity, thereby facilitating their access to the entire chromosome. We find that gene silencing originates at Xist-SMCs and propagates across the entire X chromosome over time. The propagation of silencing is achieved by Polycomb-mediated coalescence of chromatin regions and aggregation of the critical silencing enzyme SPEN, via its intrinsically disordered domains. Our observations suggest a new model for X Chromosome Inactivation, whereby Xist RNA triggers macromolecular crowding of heterochromatinizing proteins at distinct sites to ultimately increase their occupancy throughout the X chromosome. This mechanism enables deterministic gene silencing across an entire chromosome without the need for Xist ribonucleoprotein complex-chromatin interactions at each target gene. Our findings uncover a spatial organization mechanism by which few RNA molecules can regulate a broad nuclear compartment through the recruitment and local concentration of dynamic effector proteins, and provide a quantitative framework for studying such compartments.

2021-10-27 | GSE181235 | GEO

Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome

Project description:This SuperSeries is composed of the SubSeries listed below.

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Transcriptomic analysis of XIST+ and XIST- hES cells

Project description:Purpose: Compare the transcriptome of homogeneous XIST+ and XIST- hES cell populations. Methods: We isolated homogeneous XIST+ and XIST- cell populations. The XIST+ cells correspond to cells with a XIST cloud and one ATRX pinpoint. The XIST- cells correspond to cells with no XIST cloud and one ATRX pinpoint. Results: We took advantage of the clonal pattern of X-chromosome inactivation in H9 cells and analyzed the data in an allelic manner. By comparing the RNA-Seq data with known H9 SNPs, we identified genomic positions which were relaxed from XCI in XIST- cells compared to XIST+ cells. Conclusions: Genic as well as unannotated transcripts are massively relaxed from XCI in H9 cells when XIST expression is lost, however, this reactivation is only partial and a large region around the centromere is protected from relaxation of silencing. Total RNA (rRNA depleted) profiles of XIST+ and XIST- human embryonic stem cells

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XIST CHIRP-MS in GM12878 and K562 cell line

Project description:Identification of cell type-specific XIST co-factors during maintenance of X chromosome inactivation by XIST CHIRP-MS

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Transcriptomic analysis of XIST+ and XIST- hES cells

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Project description:In this project, we have studied the role of Chd8 in Xist regulation and XCI initiation by means of Chd8 Knock-Downs (KD) and Knock-Out (KO).

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