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METTL3-mediated chromatin contacts promote phase separation during senescence [KAS-seq]

ABSTRACT: METTL3-mediated chromatin contacts promote phase separation during senescence [KAS-seq]

PROVIDER: PRJNA1016281 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26049145.fastq.gz	Fastqsanger.gz
	SRR26049146.fastq.gz	Fastqsanger.gz
	SRR26049147.fastq.gz	Fastqsanger.gz
	SRR26049148.fastq.gz	Fastqsanger.gz
	SRR26049149.fastq.gz	Fastqsanger.gz

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METTL3-mediated chromatin contacts promote phase separation during senescence.

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METTL3-mediated chromatin contacts promote phase separation during senescence [KAS-seq]

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.

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METTL3-mediated chromatin contacts promote phase separation during senescence [Mettl3-HiChIP-seq]

Project description:METTL3-mediated chromatin contacts promote phase separation during senescence [Mettl3-HiChIP-seq]

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METTL3-mediated chromatin contacts promote phase separation during senescence [fastGro-seq]

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METTL3-mediated chromatin contacts promote phase separation during senescence [H3K27Ac-HiChIP-seq]

Project description:METTL3-mediated chromatin contacts promote phase separation during senescence [H3K27Ac-HiChIP-seq]

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METTL3-mediated chromatin contacts promote phase separation during senescence [Mettl3-HiChIP-seq]

2024-04-22 | GSE243044 | GEO

METTL3-mediated chromatin contacts promote phase separation during senescence [fastGro-seq]

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METTL3-mediated chromatin contacts promote phase separation during senescence [H3K27Ac-HiChIP-seq]

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METTL3-mediated chromatin contacts promote phase separation during senescence.

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

2024-04-22 | GSE243047 | GEO

KAS-Analyzer: an integrated toolkit for exploring KAS-seq data

Project description:Kethoxal-assisted ssDNA sequencing (KAS-seq) is gaining popularity as a robust and effective approach to study the dynamics of transcriptionally engaged RNA polymerases through profiling of genome-wide single-stranded DNA (ssDNA). Its latest variant, spKAS-seq, a strand-specific version of KAS-seq, has been developed to map genome-wide R-loop structures by detecting imbalances of ssDNA on two strands. However, user-friendly, open-source, and specific bioinformatic analyzer for KAS-seq data are still lacking. Here we present KAS-Analyzer as a flexible and integrated toolkit to facilitate the analysis and interpretation of KAS-seq data. KAS-Analyzer can perform standard analyses such as quality control, read alignment, and differential RNA polymerase activity analysis. In addition, KAS-Analyzer introduces many novel features, including, but not limited to: calculation of transcriptional indexes, identification of single-stranded transcribing enhancers, and high-resolution mapping of R-loops. We use benchmark datasets to demonstrate that KAS-Analyzer provides a powerful framework to study transient transcriptional regulatory programs. KAS-Analyzer is available at https://github.com/Ruitulyu/KAS-Analyzer.

2022-07-27 | GSE202044 | GEO

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