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Polycomb-dependent differential chromatin compartmentalization determines gene co-regulation in Arabidopsis

ABSTRACT: Polycomb-dependent differential chromatin compartmentalization determines gene co-regulation in Arabidopsis

PROVIDER: PRJNA649954 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12361548_1.fastq.gz	Fastqsanger.gz
	SRR12361548_2.fastq.gz	Fastqsanger.gz
	SRR12361549_1.fastq.gz	Fastqsanger.gz
	SRR12361549_2.fastq.gz	Fastqsanger.gz
	SRR12361550_1.fastq.gz	Fastqsanger.gz

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Polycomb-dependent differential chromatin compartmentalization determines gene co-regulation in Arabidopsis

Project description:Previous studies in animals have shown that polycomb targets marked with H3K27me3 can establish interactions between them, forming a repressive chromatin hub (Lanzuolo et al., 2007; Cheutin and Cavalli, 2014). In plants few studies suggested that H3K27me3 may act directly or indirectly to regulate the interactivity of polycomb marked genes. However, several aspects of the molecular function of the H3K27me3 histone modification on the 3D chromatin architecture remained obscure. To decipher the impact of H3K27me3 levels on loop formation, we combined genetics, 3D epigenomics and transcriptomic approaches. By using the ref6 mutant, defective for a histone demethylase, that displays ectopic accumulation of H3K27me3, we demonstrated that H3K27me3 is important to trigger chromatin loop formation. Reciprocally, using clf mutant, a histone methyltransferase mutant that displays a strong reduction of H3K27me3 we found that a reduction of the H3K27me3 leads to the decrease of interactions inside the polycomb repressive domain. Surprisingly, we observed that regions losing H3K27me3 in clf establish new interactions with regions marked with the H3K9ac active histone modification, showing that a reduction in H3K27me3 levels induces a global reconfiguration of chromatin architecture. Altogether our results demonstrate that the 3D organization of the genome is tightly linked to histone modifications that trigger the formation of chromatin domains associated with gene co-regulation, thereby allowing proper plant development and in which H3K27me3 is a key regulator of chromatin topology at global and local scales.

2021-04-29 | GSE155502 | GEO

Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in <i>Arabidopsis</i>.

Project description:In animals, distant H3K27me3-marked Polycomb targets can establish physical interactions forming repressive chromatin hubs. In plants, growing evidence suggests that H3K27me3 acts directly or indirectly to regulate chromatin interactions, although how this histone modification modulates 3D chromatin architecture remains elusive. To decipher the impact of the dynamic deposition of H3K27me3 on the Arabidopsis thaliana nuclear interactome, we combined genetics, transcriptomics, and several 3D epigenomic approaches. By analyzing mutants defective for histone H3K27 methylation or demethylation, we uncovered the crucial role of this chromatin mark in short- and previously unnoticed long-range chromatin loop formation. We found that a reduction in H3K27me3 levels led to a decrease in the interactions within Polycomb-associated repressive domains. Regions with lower H3K27me3 levels in the H3K27 methyltransferase clf mutant established new interactions with regions marked with H3K9ac, a histone modification associated with active transcription, indicating that a reduction in H3K27me3 levels induces a global reconfiguration of chromatin architecture. Altogether, our results reveal that the 3D genome organization is tightly linked to reversible histone modifications that govern chromatin interactions. Consequently, nuclear organization dynamics shapes the transcriptional reprogramming during plant development and places H3K27me3 as a key feature in the coregulation of distant genes.

| S-EPMC8256866 | biostudies-literature

Chromatin localization of nucleophosmin determines the sorting and compartmentalization of ribosome biogenesis

Project description:Chromatin localization of nucleophosmin determines the sorting and compartmentalization of ribosome biogenesis

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Chromatin localization of nucleophosmin determines the sorting and compartmentalization of ribosome biogenesis

Project description:Assembly of eukaryotic ribosomes begins in the nucleolus, a compartmentalized membraneless organelle. Although the two ribosomal subunits, 40S and 60S, assemble independently, it remains unknown if these particles are physically sorted as they assemble and how they partition from the central chromatin compartment into the outer nucleolar regions, where maturation occurs. In this study, we show that nucleophosmin specifically mediates the assembly of nascent 60S subunits and that this specificity is determined by its chromatin localization at the rDNA sites encoding for 60S subunit rRNA. Nucleophosmin dissociates from chromatin to bind nascent 60S subunits, causing their partitioning away from chromatin and from nascent 40S subunits through liquid-liquid phase separation. This directs translocation of nascent 60S subunits towards the nucleophosmin-rich granular component, where biogenesis continues. Notably, this compartmentalization increases the efficiency of 60S subunit assembly, specifically the incorporation of the 60S domain III. Our data reveal that the chromatin localization of nucleophosmin determines its specificity in sorting and coordinates the movement of ribosomal subunits into specialized assembly compartments.

2023-03-01 | GSE156203 | GEO

MLL4-associated condensates counterbalance Polycomb-mediated nuclear mechanical stress in Kabuki Syndrome

Project description:The genetic elements required to tune gene expression are partitioned in active and repressive nuclear condensates. Chromatin compartments include transcriptional clusters whose dynamic establishment and functioning depends on multivalent interactions occurring among transcription factors, cofactors and basal transcriptional machinery. However how chromatin players contribute to the assembly of transcriptional condensates has not been addressed. By interrogating the effect of KMT2D haploinsufficiency in Kabuki Syndrome, we found that MLL4 contributes in the assembly of transcriptional condensates through liquid-liquid phase separation. MLL4 loss-of-function impaired Polycomb-dependent chromatin compartmentalization, altering nuclear architecture. By releasing the nuclear mechanical stress through the inhibition of the mechano-sensor ATR, we re-established the mechano-signaling of mesenchymal stem cells and their commitment towards chondrocytes both in vitro and in vivo. This study supports the notion that in Kabuki Syndrome the haploinsufficiency of MLL4 causes an altered functional partitioning of chromatin, which determines the architecture and mechanical properties of the nucleus.

2020-09-22 | PXD021616 | Pride

Differential ageing of growth plate cartilage determines skeletal proportions

Project description:Differential ageing of growth plate cartilage determines skeletal proportions

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Differential contributions of nuclear lamina association and genome compartmentalization to gene regulation

Project description:Differential contributions of nuclear lamina association and genome compartmentalization to gene regulation

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Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome

Project description:Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome

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A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina

Project description:This SuperSeries is composed of the following subset Series: GSE35777: A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina [Tiling Array] GSE36048: A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina [ChIP-seq] Refer to individual Series

2012-02-24 | E-GEOD-36049 | biostudies-arrayexpress

Poised RNA polymerase II co-localises with Polycomb repression at multi-lineage developmental regulator genes in differentiated neurons

Project description:Polycomb repression is tightly associated with promoter co-occupancy of poised RNA polymerase II (RNAPII) in mouse Embryonic Stem Cells (ESCs). However, it remains unclear whether poising is a specific feature of ESCs or also associated with Polycomb during cell differentiation. Here, we show that RNAPII poising at Polycomb repressed genes is found in five stages of ESC differentiation to dopaminergic neurons. We find that key transcription factor genes of non-neuronal lineages are kept silent in the neuronal lineage through Polycomb repression in co-association with poised RNAPII in the absence of DNA methylation within DNA Methylation Valleys (DMVs). This group of poised transcription factors are preferential candidate master regulators for trans-differentiation of neurons into different lineages. We conclude that RNAPII poising is a general feature of Polycomb repression and cell plasticity in pluripotent stem cells and terminally differentiated neurons.

2017-09-29 | GSE94364 | GEO

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