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Specificity, propagation and memory of pericentric heterochromatin in mouse fibroblasts

ABSTRACT: We assembled a quantitative map for the abundance and interactions of 16 factors related to PCH in living cells and found that stably bound complexes of the histone methyltransferase Suv39h1/2 demarcate the PCH state. From the experimental data we developed a predictive mathematical model that explains how chromatin-bound Suv39h1/2 complexes act as nucleation sites and propagate a spatially confined PCH domain with elevated histone H3 trimethylation levels via chromatin dynamics. Enrichment of HP1, Suv39h1/h2, H3K9me3 and H3K36me3 was assessed by ChIP-seq in NPCs derived from ESCs showing differential occupation at intergenic major satellite repeats and enrichment of heterochromatin factors.

ORGANISM(S): Mus musculus

PROVIDER: GSE58555 | GEO | 2014/08/12

SECONDARY ACCESSION(S): PRJNA252865

REPOSITORIES: GEO

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Specificity, propagation and memory of pericentric heterochromatin in mouse fibroblasts

Project description:We assembled a quantitative map for the abundance and interactions of 16 factors related to PCH in living cells and found that stably bound complexes of the histone methyltransferase Suv39h1/2 demarcate the PCH state. From the experimental data we developed a predictive mathematical model that explains how chromatin-bound Suv39h1/2 complexes act as nucleation sites and propagate a spatially confined PCH domain with elevated histone H3 trimethylation levels via chromatin dynamics. Enrichment of HP1, Suv39h1/h2, H3K9me3 and H3K36me3 was assessed by ChIP-seq in NPCs derived from ESCs showing differential occupation at intergenic major satellite repeats and enrichment of heterochromatin factors. ChIP-seq of HP1, Suv39h1, Suv39h2, H3K9me3, H3K36me3 in NPCs

2014-08-12 | E-GEOD-58555 | biostudies-arrayexpress

Specificity, propagation, and memory of pericentric heterochromatin.

Project description: Not available

| S-EPMC4299515 | biostudies-literature

CFDP1 regulates the stability of pericentric heterochromatin thereby affecting RAN GTPase activity and mitotic spindle formation

Project description:The densely packed centromeric heterochromatin at minor and major satellites is comprised of H3K9me2/3 histones, the heterochromatin protein HP1α and histone variants. In the present study we sought to determine the mechanisms by which condensed heterochromatin at major and minor satellites stabilized by the chromatin factor CFDP1 affects the activity of the small GTPase Ran as a requirement for spindle formation. CFDP1 co-localized with heterochromatin at major and minor satellites and was essential for the structural stability of centromeric heterochromatin. Loss of CENPA, HP1α and H2A.Z heterochromatin components resulted in decreased binding of the spindle nucleation facilitator RCC1 to minor and major satellite repeats. Decreased RanGTP levels as a result of diminished RCC1 binding interfered with chromatin-mediated microtubule nucleation at the onset of mitotic spindle formation. Rescuing chromatin H2A.Z levels in cells and mice lacking CFDP1 through knock-down of the histone chaperone ANP32E not only partially restored RCC1 dependent RanGTP levels but also alleviated CFDP1-knockout related craniofacial defects and increased microtubule nucleation in CFDP1/ANP32E co-silenced cells. Together, these studies provide evidence for a direct link between condensed heterochromatin at major and minor satellites and microtubule nucleation through the chromatin protein CFDP1.

2024-03-02 | GSE259307 | GEO

Specificity, propagation and memory of pericentric heterochromatin in mouse fibroblasts: H3S10p

Project description:ChIP-seq of H3S10p in synchronized and asynchronous ESCs and RNA-seq of ESCs after inhibition of AURKB ChIP-seq of H3S10p and RNA-seq for ESCs treated with ZM-447439

2015-06-17 | E-GEOD-67133 | biostudies-arrayexpress

Specificity, propagation and memory of pericentric heterochromatin in mouse fibroblasts: H3S10p

Project description:ChIP-seq of H3S10p in synchronized and asynchronous ESCs and RNA-seq of ESCs after inhibition of AURKB

2015-06-17 | GSE67133 | GEO

ChIP-Seq of FBXO44 and H3K9me3 in MDA-MB-231

Project description:FBXO44 bound H3K9me3-modified nucleosomes at the replication fork and recruited the H3K9me3 methyltransferase SUV39H1 for repetitive element silencing post-DNA replication

2021-03-26 | GSE139973 | GEO

Expression profiles of plasma transfer RNA-derived small RNAs in patients with pathological cardiac hypertrophy

Project description:Aim: To clarify the expression profile of transfer RNA-derived small RNAs (tsRNAs) and disclose the putative role in the pathogenesis of pathological cardiac hypertrophy (PCH). Materials & methods: Small RNA sequencing was conducted in four pairs plasma from PCH patients and healthy volunteers.

2023-12-09 | GSE220617 | GEO

Genome-wide identification of MBD2 and MBD3 binding sites by ChIP-seq

Project description:The heterogeneous collection of NuRD complexes can be grouped into the MBD2 or MBD3 containing complexes MBD2-NuRD and MBD3-NuRD. Although functional differences have been described, a direct comparison of MBD2 and MBD3 in respect to genome-wide binding and function has been lacking. Here we show a strong enrichment for MBD2 at methylated CpG sequences, whereas CpGs bound by MBD3 are devoid of methylation. Gene activity of MBD2 bound genes is four fold lower as compared to genes bound by MBD3. When depleting cells for MBD2, the MBD2 bound genes increase their activity, whereas MBD2 plus MBD3 bound genes reduce their activity. Most strikingly, MBD3 is enriched at active promoters, whereas MBD2 is bound at methylated promoters and enriched at exon sequences of active genes. This suggests a functional connection between MBD2 binding to chromatin and splicing. V5 ChIP followed by high throughput sequencing in HeLa cells transiently transfected with either V5-MBD2b, V5-MBD3 or V5.

2013-02-08 | E-GEOD-41006 | biostudies-arrayexpress

CAMSAP-driven microtubule release from γ-TuRC and its regulation by nucleation-promoting factors

Project description:γ-tubulin ring complex (γ-TuRC) is the major microtubule-nucleating factor. After nucleation, microtubules can be released from γ-TuRC and stabilized by other proteins, such as CAMSAPs, but the biochemical cross-talk between minus-end regulation pathways is poorly understood. Here, we reconstituted this process in vitro using purified components. We found that all CAMSAPs could bind to the minus-ends of γ-TuRC-attached microtubules. CAMSAP2 and CAMSAP3, which decorate and stabilize growing minus ends, but not the minus-end tracking protein CAMSAP1 induced microtubule release from γ-TuRC. CDK5RAP2, a γ-TuRC-interactor, and CLASP2, a regulator of microtubule growth, strongly stimulated γ-TuRC-dependent microtubule nucleation, but only CDK5RAP2 suppressed CAMSAP binding to γ-TuRC-anchored minus ends and their release. CDK5RAP2 also improved selectivity of γ-tubulin-containing complexes for 13- rather than 14-protofilament microtubules in microtubule-capping assays. Knockout and overexpression experiments in cells showed that CDK5RAP2 inhibits formation of CAMSAP2-bound microtubules detached from the microtubule-organizing center. We conclude that CAMSAPs can release newly nucleated microtubules from γ-TuRC, whereas nucleation-promoting factors can differentially regulate this process.

2024-01-30 | PXD048637 | Pride

A role for PchHI as an ABC transporter in iron acquisition by the siderophore pyochelin in Pseudomonas aeruginosa

Project description:Iron is an essential nutrient for bacterial growth but poorly bioavailable. To scavenge ferric iron present in their environment, bacteria synthesize and secrete siderophores, small compounds with a high affinity for iron. Pyochelin (PCH) is one of the two siderophores produced by the opportunistic pathogen Pseudomonas aeruginosa. Once having captured a ferric iron, PCH-Fe is imported back into bacteria first by the outer membrane transporter FptA and afterwards by the inner membrane permease FptX. Here using molecular biology, 55Fe uptake assays and LC-MS/MS quantification of PCH in the different bacterial cell fractions, we show that (i) PCH (probably under its PCH-Fe form) is able to rich bacterial periplasm and cytoplasm when both FptA and FptX are expressed, and (ii) that PchHI (a heterodimeric ABC transporter) plays a role in the translocation of siderophore-free iron siderophore-free iron across the inner membrane into the cytoplasm. Consequently, probably the first fraction of PCH-Fe internalized by FptA may be transported further by FptX in the bacterial cytoplasm to activate the transcriptional regulator PchR, regulating the transcription of all genes of the PCH pathway. The further fractions of PCH-Fe transported by FptA may dissociate in the bacterial periplasm by an unknown mechanism, with the siderophore-free iron being transported into the cytoplasm by PchHI.

2022-03-15 | PXD026833 | Pride

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