Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Apparent RNA bridging between PRC2 and chromatin is an artifact of non-specific chromatin precipitation upon RNA degradation

ABSTRACT: Apparent RNA bridging between PRC2 and chromatin is an artifact of non-specific chromatin precipitation upon RNA degradation

PROVIDER: PRJNA1003467 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR25572404_1.fastq.gz	Fastqsanger.gz
	SRR25572404_2.fastq.gz	Fastqsanger.gz
	SRR25572405_1.fastq.gz	Fastqsanger.gz
	SRR25572405_2.fastq.gz	Fastqsanger.gz
	SRR25572406_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 40

Similar Datasets

Apparent RNA bridging between PRC2 and chromatin is an artifact of non-specific chromatin precipitation upon RNA degradation

Project description:Polycomb repressive complex 2 (PRC2) modifies chromatin to maintain repression of genes specific for other cell lineages and is essential for development. In vitro, RNA inhibits PRC2 catalytic activity and interaction with nucleosomes but the effect of RNA on PRC2 in cells has been unclear, with studies concluding that RNA either antagonises or promotes the association of PRC2 with chromatin. Suggesting the existence of an RNA bridge that connects PRC2 to chromatin, treatment of formaldehyde-crosslinked, sonicated nuclear extracts with RNase A reduces co-precipitation of polycomb target sites with PRC2. Here, we show that this apparent loss of PRC2 chromatin association after RNase A treatment is due to non-specific chromatin precipitation. RNA degradation causes chromatin to precipitate out of solution, thereby reducing the enrichment of specific DNA sequences in chromatin immunoprecipitation reactions. Maintaining chromatin solubility by the addition of poly-L-glutamic acid (PGA) rescues detection of PRC2 chromatin association upon RNA degradation. These findings undermine support for the model that RNA bridges PRC2 and chromatin in cells.

2024-02-22 | GSE240380 | GEO

Apparent loss of PRC2 chromatin occupancy as an artefact of RNA depletion

Project description:RNA has been implicated in the recruitment of chromatin modifiers, and previous studies have provided evidence in favour and against this idea. RNase treatment of chromatin is a prevalent tool for the study of RNA-mediated regulation of chromatin modifiers, but the limitations of this approach remain unclear. One of the most studied chromatin modifiers in the context of RNA-mediated regulation is the H3K27me3 methyltransferase Polycomb Repressive Complex 2 (PRC2). RNase A treatment during chromatin immunoprecipitation (rChIP) reduces the occupancy of PRC2 on chromatin. This led to suggestions of an “RNA bridge" between PRC2 and chromatin. Here we show that RNase A treatment during chromatin immunoprecipitation leads to the apparent loss of all facultative heterochromatin, including both PRC2 and its H3K27me3 mark genome-wide. This phenomenon persists in mouse embryonic stem cells, human cancer cells and human-induced pluripotent stem cells. We track this observation to a global gain of chromatin that artificially reduces ChIP signals from facultative heterochromatin. Our results point to substantial limitations in RNase A treatment for mapping RNA-dependent chromatin occupancy and invalidate conclusions that were previously established for PRC2 based on this assay.

2024-02-21 | GSE240079 | GEO

Apparent loss of PRC2 chromatin occupancy as an artefact of RNA depletion

Project description:Apparent loss of PRC2 chromatin occupancy as an artefact of RNA depletion

| PRJNA1002261 | ENA

Dynamic and flexible bridging of H3K9me3-nucleosomes via HP1β-dimerization establishes a plastic state of condensed chromatin

Project description:Histone H3 trimethylation of lysine 9 (H3K9me3) and heterochromatin proteins 1 (HP1) are hallmarks of heterochromatin, a state of compacted DNA essential for genome stability and long-term transcriptional silencing. The mechanisms by which H3K9me3 and HP1 contribute to chromatin compaction have been speculative and controversial. We demonstrate that mammalian HP1β is a prototypic HP1 protein exemplifying most basal chromatin binding and effects. These are caused by dimeric and dynamic interaction with highly enriched H3K9me3 and are modulated by various electrostatic interfaces. Via internucleosomal bridging HP1β specifically interacts with condensed chromatin, which we postulate stabilizes the compacted state. In agreement, HP1β genome-wide localization follows enrichment of H3K9me3 and bridging of chromatin fibers in a cellular context is sufficient for maintaining heterochromatic conformation. Overall, our findings define a fundamental mechanism for chromatin higher order structural changes caused by HP1 proteins, which may contribute to the plastic nature of condensed chromatin.

2017-02-10 | GSE71114 | GEO

An archaeal chromatin protein condenses DNA through bridging-induced phase separation

Project description:An archaeal chromatin protein condenses DNA through bridging-induced phase separation

| PRJNA1046133 | ENA

The interactome of multiprotein bridging factor 1 in Beauveria bassiana

Project description:Beauveria basiana is a well-known filamentous entomopathogenic fungus. Oxidation tolerance is an important determinant to fungal pathogenicity and biocontrol potential. B. bassiana transcriptional co-activator multiprotein bridging factor 1 (BbMBF1) contributes to fungal resistance to the oxidative stress. The interactome of BbMBF1 was revealed by the qualitative proteomic analysis integrated with the immuno-precipitation. This study is sought to unveil the comprehensive protein interaction of BbMBF1 and isolate the BbMBF1-mediated transcription factor under oxidative stress.

2017-09-11 | PXD005660 | Pride

NANOG prion-like assembly mediates DNA bridging

Project description:NANOG is a key stem cell pluripotency factor. NANOG’s unique ability to form prion-like assemblies provides a cooperative and concerted DNA bridging mechanism essential for chromatin reorganization and dose-sensitive activation of ground state pluripotency. We take advantage of Hi-C and ChIP-seq experiments to directly address whether NANOG can bridge DNA elements together in human cells, and our results support this.

2022-02-15 | GSE190567 | GEO

Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping [RNA-Seq]

Project description:Intrinsically disordered regions (IDRs) in DNA-associated proteins have recently been shown to play important roles in gene regulation. To better understand these domains we developed an antibody-independent assay to map disordered proteins genome-wide by combining b-isox mediated precipitation and next-generation sequencing (DisP-seq, disordered protein precipitation followed by DNA sequencing). We first analyzed Ewing sarcoma cells as a proof of principle given that the prion-like IDR of the oncogenic fusion protein EWS-FLI1 has been shown to play a critical role in this cancer. We find that DisP-seq produces thousands of strong peaks associated with diverse chromatin states in Ewing sarcoma and other cell types tested. These locations are highly enriched for DNA binding motifs matching EWS-FLI1 and other transcription factors with prominent IDRs. Moreover, depletion of EWS-FLI1 in Ewing sarcoma cells leads to a widespread reorganization of DisP-seq signals, including decreases at EWS-FLI1 binding sites and marked increases at sites associated with mesenchymal differentiation. Analysis of these new DisP-seq signals shows that they arise from redistribution of the transcription factor NFIB, which initially overlaps EWS-FLI1 and has an IDR that is required for proper localization and function. Our results thus show that antibody-independent precipitation mapping can enable genome-wide profiling and identification of disordered transcription factors to uncover their roles in complex gene regulation programs.

2023-02-20 | GSE190962 | GEO

The interaction of PRC2 with RNA or chromatin is mutually antagonistic.

Project description:Polycomb repressive complex 2 (PRC2) modifies chromatin to maintain genes in a repressed state during development. PRC2 is primarily associated with CpG islands at repressed genes and also possesses RNA binding activity. However, the RNAs that bind PRC2 in cells, the subunits that mediate these interactions, and the role of RNA in PRC2 recruitment to chromatin all remain unclear. By performing iCLIP for PRC2 in comparison with other RNA binding proteins, we show here that PRC2 binds nascent RNA at essentially all active genes. Although interacting with RNA promiscuously, PRC2 binding is enriched at specific locations within RNAs, primarily exon-intron boundaries and the 3' UTR. Deletion of other PRC2 subunits reveals that SUZ12 is sufficient to establish this RNA binding profile. Contrary to prevailing models, we also demonstrate that the interaction of PRC2 with RNA or chromatin is mutually antagonistic in cells and in vitro. RNA degradation in cells triggers PRC2 recruitment to CpG islands at active genes. Correspondingly, the release of PRC2 from chromatin in cells increases RNA binding. Consistent with this, RNA and nucleosomes compete for PRC2 binding in vitro. We propose that RNA prevents PRC2 recruitment to chromatin at active genes and that mutual antagonism between RNA and chromatin underlies the pattern of PRC2 chromatin association across the genome.

| S-EPMC4937559 | biostudies-literature

Bridging the gap: Defining the non-cultivable microbiota fraction in Cannabis seeds

Project description:Bridging the gap

| PRJEB83654 | ENA