Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome
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ABSTRACT:
ORGANISM(S): Mus musculus musculus x Mus musculus castaneus Mus musculus
PROVIDER: GSE181236 | GEO | 2021/10/26
REPOSITORIES: GEO
Similar Datasets
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
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
Project description:Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome
| PRJNA751089 | ENA
Project description:Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome [I]
| PRJNA680314 | ENA
Project description:Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome [II]
| PRJNA751096 | ENA
Project description:The lncRNA Xist forms ∼50 diffraction-limited foci to transcriptionally silence one X chromosome. How this small number of RNA foci and interacting proteins regulate a much larger number of X-linked genes is unknown. We show that Xist foci are locally confined, contain ∼2 RNA molecules, and nucleate supramolecular complexes (SMACs) that include many copies of the critical silencing protein SPEN. Aggregation and exchange of SMAC proteins generate local protein gradients that regulate broad, proximal chromatin regions. Partitioning of numerous SPEN molecules into SMACs is mediated by their intrinsically disordered regions and essential for transcriptional repression. Polycomb deposition via SMACs induces chromatin compaction and the increase in SMACs density around genes, which propagates silencing across the X chromosome. Our findings introduce a mechanism for functional nuclear compartmentalization whereby crowding of transcriptional and architectural regulators enables the silencing of many target genes by few RNA molecules.
| S-EPMC8671326 | biostudies-literature
Project description:There is growing evidence that X-chromosome inactivation is driven by phase-separated supramolecular assemblies. However, among the many proteins recruited to the inactive X chromosome by Xist long non-coding RNA, so far only a minority (CIZ1, CELF1, SPEN, TDP-43, MATR3, PTBP1, PCGF5) have been shown to form Xist-seeded protein assemblies, and of these most have not been analyzed in detail. With focus on CIZ1, here we describe 1) the contribution of intrinsically disordered regions in RNA-dependent protein assembly formation at the inactive X chromosome, and 2) enrichment, distribution, and function of proteins within Xist-seeded assemblies.
| S-EPMC10753822 | biostudies-literature
Project description:The X inactive-specific transcript (Xist) gene is the master regulator of X chromosome inactivation in mammals. Xist produces a long noncoding (lnc)RNA that accumulates over the entire length of the chromosome from which it is transcribed, recruiting factors to modify underlying chromatin and silence X-linked genes in cis Recent years have seen significant progress in identifying important functional elements in Xist RNA, their associated RNA-binding proteins (RBPs), and the downstream pathways for chromatin modification and gene silencing. In this review, we summarize progress in understanding both how these pathways function in Xist-mediated silencing and the complex interplay between them.
| S-EPMC7263139 | biostudies-literature
Project description:Although thousands of long non-coding RNAs (lncRNAs) are encoded in mammalian genomes, their mechanisms of action are poorly understood, in part because they are often expressed at lower levels than their proposed targets. One such lncRNA is Xist, which mediates chromosome-wide gene silencing on one of the two X chromosomes (X) to achieve gene expression balance between males and females. How a limited number of Xist molecules can mediate robust silencing of a much larger number of target genes while maintaining specificity exclusively to genes on the X within each cell is not well understood. Here, we show that Xist drives non-stoichiometric recruitment of the essential silencing protein SHARP (also known as SPEN) to amplify its abundance across the inactive X, including at regions not directly occupied by Xist. This amplification is achieved through concentration-dependent homotypic assemblies of SHARP on the X and is required for chromosome-wide silencing. Expression of Xist at higher levels leads to increased localization at autosomal regions, demonstrating that low levels of Xist are critical for ensuring its specificity to the X. We show that Xist (through SHARP) acts to suppress production of its own RNA which may act to constrain overall RNA levels and restrict its ability to spread beyond the X. Together, our results demonstrate a spatial amplification mechanism that allows Xist to achieve two essential but countervailing regulatory objectives: chromosome-wide gene silencing and specificity to the X. This suggests a more general mechanism by which other low-abundance lncRNAs could balance specificity to, and robust control of, their regulatory targets.
| S-EPMC8969943 | biostudies-literature
Project description:Metals with a high density of nanometre-scale twins have demonstrated simultaneous high strength and good ductility, attributed to the interaction between lattice dislocations and twin boundaries. Maximum strength was observed at a critical twin lamella spacing (∼15 nm) by mechanical testing; hence, an explanation of how twin lamella spacing influences dislocation behaviours is desired. Here, we report a transition of dislocation nucleation from steps on the twin boundaries to twin boundary/grain boundary junctions at a critical twin lamella spacing (12-37 nm), observed with in situ transmission electron microscopy. The local stress concentrations vary significantly with twin lamella spacing, thus resulting in a critical twin lamella spacing (∼18 nm) for the transition of dislocation nucleation. This agrees quantitatively with the mechanical test. These results demonstrate that by quantitatively analysing local stress concentrations, a direct relationship can be resolved between the microscopic dislocation activities and macroscopic mechanical properties of nanotwinned metals.
| S-EPMC4518316 | biostudies-literature