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Inheritance of Repressed Chromatin Domains during S-phase Requires the Histone Chaperone NPM1

ABSTRACT: Inheritance of Repressed Chromatin Domains during S-phase Requires the Histone Chaperone NPM1

PROVIDER: PRJNA759176 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18855282_1.fastq.gz	Fastqsanger.gz
	SRR18855282_2.fastq.gz	Fastqsanger.gz
	SRR18855283_1.fastq.gz	Fastqsanger.gz
	SRR18855283_2.fastq.gz	Fastqsanger.gz
	SRR18855284_1.fastq.gz	Fastqsanger.gz

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Inheritance of Repressed Chromatin Domains during S-phase Requires the Histone Chaperone NPM1

Project description:The epigenetic process safeguards cell identity during cell division through the inheritance of appropriate gene expression profiles. We demonstrated previously that parental nucleosomes are inherited by the same chromatin domains during DNA replication only in the case of repressed chromatin. We now show that this specificity is conveyed by NPM1, a histone H3/H4 chaperone. Proteomic analyses of late S-phase chromatin revealed NPM1 in association with both H3K27me3, an integral component of facultative heterochromatin and MCM2, an integral component of the DNA replication machinery; moreover NPM1 interacts directly with PRC2 and with MCM2. Given that NPM1 is essential, the inheritance of repressed chromatin domains was examined anew using mESCs expressing an auxin-degradable version of endogenous NPM1. Upon NPM1 degradation, cells accumulated in S-phase of the cell-cycle and parental nucleosome inheritance from repressed chromatin domains was markedly compromised. Appropriate inheritance required the NPM1 acidic patches that function in chaperone activity, pointing to NPM1 being integral to the epigenetic process.

2022-04-27 | GSE183090 | GEO

Inheritance of repressed chromatin domains during S phase requires the histone chaperone NPM1.

Project description:The epigenetic process safeguards cell identity during cell division through the inheritance of appropriate gene expression profiles. We demonstrated previously that parental nucleosomes are inherited by the same chromatin domains during DNA replication only in the case of repressed chromatin. We now show that this specificity is conveyed by NPM1, a histone H3/H4 chaperone. Proteomic analyses of late S-phase chromatin revealed NPM1 in association with both H3K27me3, an integral component of facultative heterochromatin, and MCM2, an integral component of the DNA replication machinery; moreover, NPM1 interacts directly with PRC2 and with MCM2. Given that NPM1 is essential, the inheritance of repressed chromatin domains was examined anew using mESCs expressing an auxin-degradable version of endogenous NPM1. Upon NPM1 degradation, cells accumulated in the G1-S phase of the cell cycle and parental nucleosome inheritance from repressed chromatin domains was markedly compromised. NPM1 chaperone activity may contribute to the integrity of this process as appropriate inheritance required the NPM1 acidic patches.

| S-EPMC9045712 | biostudies-literature

A replisome-associated parental histone H3-H4 tetramer chaperone required for faithful epigenetic inheritance

Project description:Faithful transfer of parental histones to newly replicated daughter DNA strands is critical for inheritance of epigenetic states. Although replication proteins that facilitate parental histone transfer have been identified, how intact histone H3-H4 tetramers travel relatively large distances from the front to the back of the replication fork remains unknown. Here, we use AlphaFold-Multimer structural predictions combined with biochemical and genetic approaches to identify the Mrc1/CLASPIN subunit of the replisome as a histone chaperone. Mrc1 contains a conserved histone binding domain that forms a brace around the H3-H4 tetramer mimicking nucleosomal DNA and H2A-H2B histones, is required for heterochromatin inheritance, and promotes parental histone recycling during replication. We further identify binding sites for the FACT histone chaperone in Swi1/TIMELESS and DNA polymerase α that are required for heterochromatin inheritance. We propose that Mrc1, in concert with FACT acting as a mobile co-chaperone, coordinates the distribution of parental histones to newly replicated DNA.

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Stable transgenerational epigenetic inheritance requires a DNA methylation-sensing circuit

Project description:Stable transgenerational epigenetic inheritance requires a DNA methylation-sensing circuit

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Transcriptome analysis using Quant-RNAseq after NPM1 or HIF-1α silencing under normoxia or Hypoxia

Project description:Hypoxia inducible factor-1 (HIF-1) is a central transcriptional regulator of genes associated with adaptive responses to hypoxia. NPM1 is a histone chaperone found to associate with HIF-1α in a phosphorylation dependent manner and increase its activty. The aim of this study was to find if HIF-1α and NPM1 regualate gene expression under hypoxia. Transcriptome analysis using Quant-RNA-seq after HIF-1α or NPM1 silencing under hypoxia reveals a significant number of genes, the hypoxic expression of which depends on both proteins.

2021-12-15 | GSE158890 | GEO

Efficient DNA binding of NF-κB requires the chaperone-like function of NPM1.

Project description:NPM1/nucleophosmin is frequently overexpressed in various tumors, although the oncogenic role of NPM1 remains unclear. Here we revealed the link between NPM1 and nuclear factor-κB (NF-κB), a master regulator of inflammation. We found that NPM1 knockdown decreased NF-κB-mediated transcription of selected target genes by decreasing the recruitment of NF-κB p65 to the gene promoters. NPM1 is directly associated with the DNA binding domain of p65 to enhance its DNA binding activity without being a part of the DNA-NF-κB complex. This result suggests that NF-κB requires the chaperone-like function of NPM1 for DNA binding. Furthermore, we demonstrated that NPM1 was required for efficient inflammatory gene expression induced by tumor necrosis factor alpha (TNF-α) and lipopolysaccharide in fibroblasts and macrophages. The NF-κB-mediated invasion of breast cancer cells was significantly decreased by NPM1 knockdown. Our study suggests a novel mechanistic insight into the NF-κB-mediated transcription and an oncogenic role of NPM1 in both tumor cells and the tumor micro-environment through the regulation of NF-κB.

| S-EPMC5397172 | biostudies-literature

HA-GABARAPL1 immunoprecipitation with siRNA-mediated NPM1 depletion

Project description:The nucleolar scaffold protein NPM1 acts as a multifunctional regulator of cellular homeostasis, genome integrity, and stress response. We and others show that NPM1 is also involved in regulation of the autophagic pathway. As NPM1 binds to members of the GABARAP protein family, important for autophagy, we anticipate that this interaction is important for the role of NPM1 in autophagy. In order to identify NPM1-dependent GABARAPL1 interactors we performed HA-GABARAPL1 immunoprecipitation with siRNA-mediated NPM1 depletion.

2023-10-28 | PXD040220 | Pride

A replisome-associated parental histone H3-H4 tetramer chaperone required for faithful epigenetic inheritance

Project description:A replisome-associated parental histone H3-H4 tetramer chaperone required for faithful epigenetic inheritance

| PRJNA1121313 | ENA

ChIP-seq analysis about Dot1l and Npm1 samples

Project description:To identify whether Dot1l or Npm1 were enriched in MERVL directly, we performed Dot1l and Npm1 ChIP-seq in wildtype ESCs. We conclude that Dot1l and Npm1 binding were enriched on MERVL-int region, suggesting a direct regulatory role of Dot1l and Npm1 on MERVL expression.

2023-07-18 | GSE201848 | GEO

DHX9 and NPM1 silencing RNA-seq

Project description:In our study, we valided DHX9 and NPM1 interact with KIMAT1, whereas DHX9 also interacts with HIF1A-As2. DHX9 is a highly conserved DEAD-box protein expressed in the nucleus and the cytoplasm, involved in many processes including transcriptional activation, miRNA biogenesis and tumor cell maintenance. NPM1 is predominantly localized in the nucleoplasm, where it associates with active RNA polymerase II and transcriptionally activates genes involved in cancer. We silenced DHX9 and NPM1 and performed RNA-seq to examine the dysregulated genes by DHX9 and NPM1.

2020-12-17 | GSE124626 | GEO

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