A biophysical basis for the spreading behavior and limited diffusion of Xist [RNA-Seq]
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ABSTRACT:
PROVIDER: PRJNA1142420 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30049736_1.fastq.gz | Fastqsanger.gz | |||
| SRR30049736_2.fastq.gz | Fastqsanger.gz | |||
| SRR30049737_1.fastq.gz | Fastqsanger.gz | |||
| SRR30049737_2.fastq.gz | Fastqsanger.gz | |||
| SRR30049738_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Here we reveal a biophysical basis for the spreading behavior of Xist RNA on the inactive X-chromosome (Xi). Xist and HNRNPK together drive a liquid-liquid phase separation (LLPS) that encapsulates the Xi. HNRNPK and Xist exert mutual pulling forces that lead to RNA internalization into the condensate. While HNRNPK is sufficient for condensate formation, Xist induces a further phase transition into a "soft" droplet by altering elasticity, adhesiveness, and wetting properties of the condensate in vitro. Once phase transition occurs, other Xist-interacting factors are internalized and concentrated within the condensate. We attribute LLPS to HNRNPK's RGG and Xist's Repeat B (RepB) motifs. Mutating these motifs causes Xist diffusion, disrupts Polycomb recruitment, and precludes the required mixing of Xi chromatin for establishing the Xi superstructure. Thus, phase transitions driven by RepB and HNRNPK create a membrane-less subnuclear compartment for the localization and limited diffusion of Xist ribonucleoprotein complexes on the Xi.
2025-01-17 | GSE273578 | GEO
Project description:Here we reveal a biophysical basis for the spreading behavior of Xist RNA on the inactive X-chromosome (Xi). Xist and HNRNPK together drive a liquid-liquid phase separation (LLPS) that encapsulates the Xi. HNRNPK and Xist exert mutual pulling forces that lead to RNA internalization into the condensate. While HNRNPK is sufficient for condensate formation, Xist induces a further phase transition into a "soft" droplet by altering elasticity, adhesiveness, and wetting properties of the condensate in vitro. Once phase transition occurs, other Xist-interacting factors are internalized and concentrated within the condensate. We attribute LLPS to HNRNPK's RGG and Xist's Repeat B (RepB) motifs. Mutating these motifs causes Xist diffusion, disrupts Polycomb recruitment, and precludes the required mixing of Xi chromatin for establishing the Xi superstructure. Thus, phase transitions driven by RepB and HNRNPK create a membrane-less subnuclear compartment for the localization and limited diffusion of Xist ribonucleoprotein complexes on the Xi.
2025-01-17 | GSE273564 | GEO
Project description:Here we reveal a biophysical basis for the spreading behavior of Xist RNA on the inactive X-chromosome (Xi). Xist and HNRNPK together drive a liquid-liquid phase separation (LLPS) that encapsulates the Xi. HNRNPK and Xist exert mutual pulling forces that lead to RNA internalization into the condensate. While HNRNPK is sufficient for condensate formation, Xist induces a further phase transition into a "soft" droplet by altering elasticity, adhesiveness, and wetting properties of the condensate in vitro. Once phase transition occurs, other Xist-interacting factors are internalized and concentrated within the condensate. We attribute LLPS to HNRNPK's RGG and Xist's Repeat B (RepB) motifs. Mutating these motifs causes Xist diffusion, disrupts Polycomb recruitment, and precludes the required mixing of Xi chromatin for establishing the Xi superstructure. Thus, phase transitions driven by RepB and HNRNPK create a membrane-less subnuclear compartment for the localization and limited diffusion of Xist ribonucleoprotein complexes on the Xi.
2025-01-17 | GSE273563 | GEO
Project description:A biophysical basis for the spreading behavior and limited diffusion of Xist [CHART-seq]
| PRJNA1142421 | ENA
Project description:A biophysical basis for the spreading behavior and limited diffusion of Xist [ChIP-Seq]
| PRJNA1142454 | ENA
Project description:Here we reveal a biophysical basis for the spreading behavior of Xist RNA on the inactive X-chromosome (Xi). Xist and HNRNPK together drive a liquid-liquid phase separation (LLPS) that encapsulates the Xi. HNRNPK and Xist exert mutual pulling forces that lead to RNA internalization into the condensate. While HNRNPK is sufficient for condensate formation, Xist induces a further phase transition into a "soft" droplet by altering elasticity, adhesiveness, and wetting properties of the condensate in vitro. Once phase transition occurs, other Xist-interacting factors are internalized and concentrated within the condensate. We attribute LLPS to HNRNPK's RGG and Xist's Repeat B (RepB) motifs. Mutating these motifs causes Xist diffusion, disrupts Polycomb recruitment, and precludes the required mixing of Xi chromatin for establishing the Xi superstructure. Thus, phase transitions driven by RepB and HNRNPK create a membrane-less subnuclear compartment for the localization and limited diffusion of Xist ribonucleoprotein complexes on the Xi.
2025-01-17 | GSE212696 | GEO
Project description:A biophysical basis for the diffusion-restricted behavior of Xist RNA
| PRJNA877034 | ENA
Project description:During X-inactivation, Xist RNA spreads along an entire chromosome to establish silencing. However, the mechanism and functional RNA elements involved in spreading remain undefined. By performing a comprehensive endogenous Xist deletion screen, we identify Repeat B as crucial for spreading Xist and maintaining Polycomb repressive complexes 1 and 2 (PRC1/PRC2) along the inactive X (Xi). Unexpectedly, spreading of these three factors is inextricably linked. Deleting Repeat B or its direct binding partner, HNRNPK, compromises recruitment of PRC1 and PRC2. In turn, ablating PRC1 or PRC2 impairs Xist spreading. Therefore, Xist and Polycomb complexes require each other to propagate along the Xi, suggesting a positive feedback mechanism between RNA initiator and protein effectors. Perturbing Xist/Polycomb spreading causes failure of de novo Xi silencing, with partial compensatory downregulation of the active X, and also disrupts topological Xi reconfiguration. Thus, Repeat B is a multifunctional element that integrates interdependent Xist/ Polycomb spreading, silencing, and changes in chromosome architecture.
2019-03-01 | GSE107217 | GEO
Project description:The Xist long noncoding RNA (lncRNA) is essential for X-chromosome inactivation (XCI), the process by which mammals compensate for unequal numbers of sex chromosomes. During XCI, Xist coats the future inactive X (Xi) and recruits Polycomb Repressive Complex 2 (PRC2) to the X-inactivation center (Xic). Currently unclear is how Xist spreads silencing on a 150 Mb scale. Here we generate high-resolution maps of Xist binding across a developmental time course using CHART-seq. In female cells undergoing XCI de novo, Xist follows a two-step mechanism in which it initially targets gene-rich islands before spreading to intervening gene-poor domains. Xist is depleted from genes that escape XCI but frequently concentrates near escapee boundaries. Xist binding was linearly proportional to PRC2 density and H3 lysine 27 trimethylation (H3K27me3), suggesting co-migration of Xist and PRC2. Interestingly, when the Xi is acutely stripped of Xist in post-XCI cells, Xist recovers quickly within both gene-rich and -poor domains on a time scale of hours instead of days, suggesting a previously primed Xi chromatin state. We conclude that Xist spreading takes on distinct stage-specific forms: During initial establishment, Xist follows a two-step mechanism, but during maintenance, Xist spreads rapidly to both gene-rich and -poor regions. Capture hybridization analysis of RNA targets (CHART) and input samples of (differentiating) mouse embryonic stem (ES) cells and immortalized mouse embryonic fibroblasts (MEF) using paired-end 75 nt reads on Illumina HiSeq2500, with 2 replicates per sample (# of samples). RNA-seq of the same cell lines with 50 nt reads on Illumina HiSeq2000, with 2 replicates per sample (2 samples, 4 datasets total). CHIP-seq: Data from GSE36905 was aligned and processed as CHART-seq samples. Resulting coverage tracks (EZH2/K27me3) are linked directly to GSE48649 (bedGraphs linked below).
2013-11-04 | E-GEOD-48649 | biostudies-arrayexpress
Project description:The Xist long noncoding RNA (lncRNA) is essential for X-chromosome inactivation (XCI), the process by which mammals compensate for unequal numbers of sex chromosomes. During XCI, Xist coats the future inactive X (Xi) and recruits Polycomb Repressive Complex 2 (PRC2) to the X-inactivation center (Xic). Currently unclear is how Xist spreads silencing on a 150 Mb scale. Here we generate high-resolution maps of Xist binding across a developmental time course using CHART-seq. In female cells undergoing XCI de novo, Xist follows a two-step mechanism in which it initially targets gene-rich islands before spreading to intervening gene-poor domains. Xist is depleted from genes that escape XCI but frequently concentrates near escapee boundaries. Xist binding was linearly proportional to PRC2 density and H3 lysine 27 trimethylation (H3K27me3), suggesting co-migration of Xist and PRC2. Interestingly, when the Xi is acutely stripped of Xist in post-XCI cells, Xist recovers quickly within both gene-rich and -poor domains on a time scale of hours instead of days, suggesting a previously primed Xi chromatin state. We conclude that Xist spreading takes on distinct stage-specific forms: During initial establishment, Xist follows a two-step mechanism, but during maintenance, Xist spreads rapidly to both gene-rich and -poor regions.
2013-11-04 | GSE48649 | GEO