Ontology highlight
ABSTRACT:
PROVIDER: PRJNA598331 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10809227_1.fastq.gz | Fastqsanger.gz | |||
| SRR10809227_2.fastq.gz | Fastqsanger.gz | |||
| SRR10809228_1.fastq.gz | Fastqsanger.gz | |||
| SRR10809228_2.fastq.gz | Fastqsanger.gz | |||
| SRR10809229.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 26 |
Similar Datasets
Project description:Cellular senescence is a stable state of growth arrest that emerges as a response to stress. The methyltransferase complex (MTC) has been shown to facilitate the expression of the senescence-associated secretion phenotype (SASP) factors via genome-wide redistribution. However, whether and how MTC impacts on the three-dimensional (3D) chromatin organization and its functional implications during senescence remain largely unknown. Here we show that the MTC complex coordinates its enzymatic activity-dependent and -independent functions to enforce cellular senescence. Specifically, METTL3-mediated chromatin loops induce Hexokinase 2 (HK2) expression during senescence. The elevated HK2 expression subsequently promotes liquid-liquid phase separation (LLPS), manifesting as stress granules. These phase-separated stress granules act as reservoirs to sequester cell-cycle related mRNAs harboring polymethylated m6A sites, impeding their efficient translation. Overall, we uncover a mechanism by which senescent cells utilize phase-separated stress granules, facilitated by MTC-mediated HK2 activation, to sequester cell-cycle related mRNAs in governing senescence-associated stable growth arrest.
2024-04-22 | GSE243044 | GEO
Project description:Cellular senescence is a stable state of growth arrest that emerges as a response to stress. The methyltransferase complex (MTC) has been shown to facilitate the expression of the senescence-associated secretion phenotype (SASP) factors via genome-wide redistribution. However, whether and how MTC impacts on the three-dimensional (3D) chromatin organization and its functional implications during senescence remain largely unknown. Here we show that the MTC complex coordinates its enzymatic activity-dependent and -independent functions to enforce cellular senescence. Specifically, METTL3-mediated chromatin loops induce Hexokinase 2 (HK2) expression during senescence. The elevated HK2 expression subsequently promotes liquid-liquid phase separation (LLPS), manifesting as stress granules. These phase-separated stress granules act as reservoirs to sequester cell-cycle related mRNAs harboring polymethylated m6A sites, impeding their efficient translation. Overall, we uncover a mechanism by which senescent cells utilize phase-separated stress granules, facilitated by MTC-mediated HK2 activation, to sequester cell-cycle related mRNAs in governing senescence-associated stable growth arrest.
2024-04-22 | GSE243043 | GEO
Project description:Cellular senescence is a stable state of growth arrest that emerges as a response to stress. The methyltransferase complex (MTC) has been shown to facilitate the expression of the senescence-associated secretion phenotype (SASP) factors via genome-wide redistribution. However, whether and how MTC impacts on the three-dimensional (3D) chromatin organization and its functional implications during senescence remain largely unknown. Here we show that the MTC complex coordinates its enzymatic activity-dependent and -independent functions to enforce cellular senescence. Specifically, METTL3-mediated chromatin loops induce Hexokinase 2 (HK2) expression during senescence. The elevated HK2 expression subsequently promotes liquid-liquid phase separation (LLPS), manifesting as stress granules. These phase-separated stress granules act as reservoirs to sequester cell-cycle related mRNAs harboring polymethylated m6A sites, impeding their efficient translation. Overall, we uncover a mechanism by which senescent cells utilize phase-separated stress granules, facilitated by MTC-mediated HK2 activation, to sequester cell-cycle related mRNAs in governing senescence-associated stable growth arrest.
2024-04-22 | GSE243046 | GEO
Project description:Cellular senescence is a stable state of growth arrest that emerges as a response to stress. The methyltransferase complex (MTC) has been shown to facilitate the expression of the senescence-associated secretion phenotype (SASP) factors via genome-wide redistribution. However, whether and how MTC impacts on the three-dimensional (3D) chromatin organization and its functional implications during senescence remain largely unknown. Here we show that the MTC complex coordinates its enzymatic activity-dependent and -independent functions to enforce cellular senescence. Specifically, METTL3-mediated chromatin loops induce Hexokinase 2 (HK2) expression during senescence. The elevated HK2 expression subsequently promotes liquid-liquid phase separation (LLPS), manifesting as stress granules. These phase-separated stress granules act as reservoirs to sequester cell-cycle related mRNAs harboring polymethylated m6A sites, impeding their efficient translation. Overall, we uncover a mechanism by which senescent cells utilize phase-separated stress granules, facilitated by MTC-mediated HK2 activation, to sequester cell-cycle related mRNAs in governing senescence-associated stable growth arrest.
2024-04-22 | GSE243042 | GEO
Project description:Stress response by phase-separated p62
| PRJNA955674 | ENA
Project description:Stress granules are phase separated assemblies formed around mRNAs that have now been identified after stress granule purification from cell culture. Here, we present a purification free method to detect stress granules RNAs in single cells and in tissues, including those displaying cell heterogeneity. We adapted TRIBE (Target of RNA-binding proteins Identified by Editing) to detect stress-granule RNAs by fusing a stress-granule RNA-binding protein (FMR1) to the catalytic domain of an RNA-editing enzyme (ADAR). RNAs colocalized with this fusion are edited, producing mutations that are detectable by sequencing. We then show that this “in situ" method can reliably identify stress granule RNAs in single S2 cells and in Drosophila neurons, and that they encode cell cycle, transcription and splicing factors. The identification of stress granule RNAs without perturbation opens the possibility to examine cell-to-cell variability and identify the RNA content not only in stress granules, but also in other RNA based assemblies in single cells derived from tissues.
2021-05-30 | GSE175782 | GEO
Project description:N6-methyladenosine (m6A) is a dynamic and reversible nucleotide modification in mRNA. m6A alters mRNA fate, but it is unclear why the effects of m6A can vary in different cellular contexts. Here we show that methylated mRNAs are catalysts for liquid-liquid phase separation of the YTHDF family of m6A-binding proteins. RNAs that contain multiple, but not single, m6A residues recruit multiple YTHDF proteins, causing them to undergo a proximity-induced phase separation. YTHDF proteins show liquid-like properties upon binding polymethylated mRNAs in cells, and partition into endogenous phase-separated compartments, such as P-bodies, neuronal RNA granules, and stress granules. The complexes of YTHDF proteins and polymethylated mRNAs are targeted to different compartments depending on the cell context, leading to different effects on m6A mRNAs. These studies reveal a role for nucleotide modifications in regulating phase separation and indicate that the cellular properties of m6A-modified mRNAs can be explained by liquid-liquid phase separation principles.
2019-07-15 | GSE125725 | GEO
Project description:Combining RNAi in cultured cells and analysis of mutant animals, we probed roles of known piRNA pathway components in the initiation and effector phases of transposon silencing.
2010-10-25 | GSE24108 | GEO
Project description:The ability of proteins and RNA to coalesce into phase-separated assemblies is an emergent principle in organizing membraneless cellular compartments such as stress granules (SGs) and the nucleolus. While the individual constituents of these compartments have become increasingly well documented, the mechanisms underlying their rapid and reversible formation are only partially understood. Here, we report that the ubiquitin related modifier Urm1 functions in promoting the assembly of phase-separated compartments in yeast. Through its intrinsic ability to self-associate and interact with target proteins in a pH-sensitive manner, stress-induced Urm1 conjugation, mediated by the E1-like enzyme Uba4, drives efficient deposition of target proteins into phase-separated assemblies, including SGs and the nucleolus. Yeast cells lacking urmylation exhibit condensate assembly defects, causing reduced fitness upon exposure to stress-induced challenges. We propose that Urm1 acts as a reversible molecular “adhesive” to drive condensate formation of a wide range of proteins under various stress conditions.
2024-06-28 | PXD044486 | Pride
Project description:N6-methyladenosine (m6A) is the most abundant nucleotide modification found on mRNA. m6A has been previously shown to facilitate recruitment of mRNAs to stress granules due to interactions between m6A and the YTHDF proteins. Although protein-RNA interactions are known to contribute to the recruitment of mRNAs to stress granules, the predominant driver of mRNA recruitment to stress granules is thought to be RNA-RNA interactions between long RNAs. Here, we show that m6A contributes significantly to the length-dependent effect of mRNA enrichment in stress granules and that upon depletion of METTL3, the enzyme responsible for adding m6A to nascent transcripts, the nature of the stress granule transcriptome is fundamentally altered by greatly reducing the propensity of long mRNAs to enter stress granules. This reveals that not only does m6A enhance the phase separation of mRNAs, but that it is a driving force underpinning length-dependent enrichment of mRNAs in stress granules.
2023-06-01 | GSE190121 | GEO