NADs identification under heat-stress
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB36061 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR14364900.fastq.gz | Fastqsanger.gz | |||
| ERR14364901.fastq.gz | Fastqsanger.gz | |||
| ERR14364902.fastq.gz | Fastqsanger.gz | |||
| ERR14364903.fastq.gz | Fastqsanger.gz | |||
| ERR14364904.fastq.gz | Fastqsanger.gz |
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Project description:Repressive chromatin domains often localize to the nuclear lamina or nucleolus. Although nucleolar-associated domains (NADs) have recently been mapped, their mechanisms of nucleolar association and functional significance remain unclear. Here, we show that nucleophosmin (NPM1), a factor located in the granular component of the nucleolus, mediates NAD association in mouse embryonic stem cells. NPM1 binds NADs, interacts with the histone methyltransferase G9a (EHMT2), and is required for establishing H3K9me2 at NADs. Loss of NPM1 or expression of a DNA-binding-deficient mutant disrupts NAD-nucleolus association and reduces H3K9me2 specifically at NADs. G9a is dispensable for NAD-nucleolus contacts, indicating that H3K9me2 is acquired after NADs associate with NPM1 at nucleoli. These findings reveal mechanistic insights into how genomic domains associate with nucleoli and form repressive chromatin and indicate that the nucleolus not only serves as a scaffold for positioning repressive domains but also plays a direct role in establishing their repressive chromatin states.
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Project description:Repressive chromatin domains often localize to the nuclear lamina or nucleolus. Although nucleolar-associated domains (NADs) have recently been mapped, their mechanisms of nucleolar association and functional significance remain unclear. Here, we show that nucleophosmin (NPM1), a factor located in the granular component of the nucleolus, mediates NAD association in mouse embryonic stem cells. NPM1 binds NADs, interacts with the histone methyltransferase G9a (EHMT2), and is required for establishing H3K9me2 at NADs. Loss of NPM1 or expression of a DNA-binding-deficient mutant disrupts NAD-nucleolus association and reduces H3K9me2 specifically at NADs. G9a is dispensable for NAD-nucleolus contacts, indicating that H3K9me2 is acquired after NADs associate with NPM1 at nucleoli. These findings reveal mechanistic insights into how genomic domains associate with nucleoli and form repressive chromatin and indicate that the nucleolus not only serves as a scaffold for positioning repressive domains but also plays a direct role in establishing their repressive chromatin states.
2025-05-22 | GSE270572 | GEO
Project description:Repressive chromatin domains often localize to the nuclear lamina or nucleolus. Although nucleolar-associated domains (NADs) have recently been mapped, their mechanisms of nucleolar association and functional significance remain unclear. Here, we show that nucleophosmin (NPM1), a factor located in the granular component of the nucleolus, mediates NAD association in mouse embryonic stem cells. NPM1 binds NADs, interacts with the histone methyltransferase G9a (EHMT2), and is required for establishing H3K9me2 at NADs. Loss of NPM1 or expression of a DNA-binding-deficient mutant disrupts NAD-nucleolus association and reduces H3K9me2 specifically at NADs. G9a is dispensable for NAD-nucleolus contacts, indicating that H3K9me2 is acquired after NADs associate with NPM1 at nucleoli. These findings reveal mechanistic insights into how genomic domains associate with nucleoli and form repressive chromatin and indicate that the nucleolus not only serves as a scaffold for positioning repressive domains but also plays a direct role in establishing their repressive chromatin states.
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Project description:Maintenance of the epigenome is of utmost importance to warrant appropriate cellular functioning Here we analyzed PRC1/2 function, in response to cellular stress. We observe that heat shock (HS) leads to nucleolar accumulation of CBX proteins, and are strongly immobilized in a 1,6-hexanediol insensitive manner, suggestive of a HS-induced liquid-to-solid phase transition of the nucleolus. CBX protein recovery from the nucleolus is dependent on heat shock protein (HSP) activity. LC-MS/MS analyses of nucleoli shows HS-induced nucleolar accumulation of PRC1/2 subunits, various chromatin regulators, HSPs, and the 26S proteasome. Finally, we find that HS leads to a strong reduction of PRC1/2 chromatin binding at target genes and loss of H2AK119ub and H3K27me3. Our findings demonstrate that thermal stress results in a rapid accumulation of epigenetic regulators in the nucleolus, and a concomitant loss of PRC1/2 complex chromatin binding and associated epimarks, underlining that environmental stress directly alters the epigenome.
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Project description:Metazoan chromosomes in interphase nucleus are partitioned into discrete three dimensional physical domains which confine epigenetically modified chromatin and are relative stable across different cell types even species1-4. Physical domains are segregated preferentially at DNase I hypersensitive sequences of high density of active gene and insulator proteins which are hypothesized contributing together to domain border formation3,4. However, whether physical domain structure can be maintained without insulator proteins and transcription is unknown5-8. Transcription of most genes and the insulator proteins binding can be severely impaired in heat shocked (HS) fruit fly nuclei9. Here we show that chromatin contact frequency increases within and decreases beyond ~100kb after HS respectively accompanied by repartitioning of the Drosophila chromosomes into a different array of physical domain. Prominently, domains tend to merge because borders disappeared are more than borders newly emerged which are located more frequently in repressive chromatin. In contrast to previous hypothesis1,3,4, changes in insulator proteins enrichment and RNAPII show no noticeable difference at lost or emerged borders. Our results show a metazoan genome can be quickly reconfigured as cells undergo brief physiological stress. In addition to insulator proteins and transcription, we speculate that extra trans-factors binding and various biological activities are required for the establishment and maintenance of physical domains. Moreover, we found long-range chromatin interaction network is reshaped after HS implying long-range chromatin interactions can be formed due to domain level reorganization of chromosomes despite functional relevance. We anticipate our analysis to be a starting point for more intensive experimental investigation into the elusive mechanisms behind the physical domain partition and dynamic reconfiguration of metazoan genomes.
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