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Transcriptome-wide RNA binding analysis of C9orf72 poly(PR) dipeptides

ABSTRACT: Transcriptome-wide RNA binding analysis of C9orf72 poly(PR) dipeptides

PROVIDER: PRJNA877223 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21440131.fastq.gz	Fastqsanger.gz
	SRR21440132.fastq.gz	Fastqsanger.gz
	SRR21440133.fastq.gz	Fastqsanger.gz
	SRR21440134.fastq.gz	Fastqsanger.gz

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Similar Datasets

Transcriptome-wide RNA binding analysis of C9orf72 poly(PR) dipeptides

Project description:An intronic GGGGCC repeat expansion in C9orf72 is a common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. The repeats are transcribed in both sense and antisense directions to generate distinct dipeptide repeat proteins, of which poly(GA), poly(GR) and poly(PR) have been implicated in contributing to neurodegeneration. Poly(PR) binding to RNA may contribute to toxicity, but analysis of poly(PR)-RNA binding on a transcriptome-wide scale has not yet been carried out. We therefore performed crosslinking and immunoprecipitation (CLIP) analysis in human cells to identify the RNA binding sites of poly(PR). We found that poly(PR) binds to nearly 600 RNAs, with the sequence GAAGA enriched at the binding sites. In vitro experiments showed that poly(GAAGA) RNA binds poly(PR) with higher affinity than control RNA and induces phase-separation of poly(PR) into condensates. These data indicate that poly(PR) preferentially binds to poly(GAAGA)-containing RNAs, which may have physiological consequences.

2023-07-10 | GSE212761 | GEO

Translation deficits drive C9orf72 associated poly-GR/PR toxicity

Project description:Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) patients with the C9orf72 mutation show predominantly cytoplasmic aggregates of poly-GR and poly-PR proteins that are acutely toxic in various model systems. To identify the molecular mediators of neurotoxicity of poly-GR/PR, we analyzed their interactomes in primary neurons. GFP-(GR)149 and (PR)175-GFP preferentially interacted with RNA-binding proteins, including stress granule-associated and nucleolar proteins, as well as ribosomes. Overexpression of the poly-GR/PR interactors Staufen 1/2 (STAU1/2) and YBX1 led to cytoplasmic aggregation of poly-GR/PR into large stress granule-like inclusions, while the poly-GR/PR interactor nucleophosmin (NPM1) recruited poly-GR into the nucleolus. In addition, poly-PR expression reduced ribosome levels and translation, which is consistent with the widespread reduction of synaptic proteins detected by proteomics. Surprisingly, only GFP-(GR)53, but not GFP-(GR)149, localized to the nucleolus and reduced ribosome levels and translation in neurons, suggesting impaired ribosome biogenesis is driving the acute toxicity commonly observed in vitro. In C9orf72 patient brains, we detected co-aggregation of poly-GR/PR inclusions with ribosomes, but not stress granules. Partial sequestration of ribosomes may chronically impair protein synthesis and contribute to C9orf72 ALS/FTD pathogenesis.

2018-06-27 | PXD008691 | Pride

Toxic C9orf72 poly(PR) binds heterochromatin, disrupts HP1α and causes dsRNA accumulation

Project description:How G4C2 repeat expansions in C9orf72 cause frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) is not understood. Here, we report the first mouse model to express poly(PR), a dipeptide repeat protein synthesized from expanded G4C2 repeats. Expression of GFP-(PR)50 throughout the mouse brain yielded progressive brain atrophy, neuron5 loss, loss of poly(PR)-positive cells and gliosis, culminating in motor and memory impairments. We found that poly(PR) bound DNA, localized to heterochromatin, and caused abnormal histone methylation, lamin invaginations, decreases in HP1α expression, and disruptions of HP1α liquid phases. These aberrations of histone methylation, lamins and HP1α, which regulate heterochromatin structure and gene expression, were accompanied by repetitive element10 expression and double-stranded RNA accumulation. Thus, we uncover new mechanisms by which poly(PR) contributes to c9FTD/ALS pathogenesis.

2019-05-29 | GSE124834 | GEO

p53 is a central regulator driving neurodegeneration caused by C9orf72 poly(PR)

Project description:To analyze the epigenomic landscape of neurodegeneration caused by ALS-associated protein aggregation, we developed a modified version of ATAC-seq that works on primary neurons. We discovered that C9orf72-ALS/FTD associated poly(PR) activated a remarkably specific signature of chromatin accessibility, involving transcriptional targets of the tumor suppressor gene p53. Our findings reveal an unexpected role of p53 as a mediator of neurodegeneration elicited by poly(PR) and provide an example of how ATAC-seq can now be applied to neurons to define mechanisms of neurodegeneration.

2020-12-09 | GSE162048 | GEO

Proximity proteomics of C9orf72 dipeptide repeat proteins

Project description:Profiling of proximity proteomes of C9orf72-derived dipeptide repeat proteins (poly-GA, poly-GR, poly-PR) in HEK293 cells using BioID assay

2021-12-17 | MSV000088581 | MassIVE

Toxic C9orf72 poly(PR) binds heterochromatin, disrupts HP1α and causes dsRNA accumulation

Project description:Toxic C9orf72 poly(PR) binds heterochromatin, disrupts HP1α and causes dsRNA accumulation

| PRJNA513973 | ENA

p53 is a central regulator driving neurodegeneration caused by C9orf72 poly(PR)

Project description:p53 is a central regulator driving neurodegeneration caused by C9orf72 poly(PR)

| PRJNA680362 | ENA

Motor dysfunction and neurodegeneration in a C9orf72 mouse line expressing poly-PR

Project description:Motor dysfunction and neurodegeneration in a C9orf72 mouse line expressing poly-PR

| PRJNA545960 | ENA

Transcriptome-wide RNA binding analysis of C9orf72 poly(PR) dipeptides.

Project description:An intronic GGGGCC repeat expansion in C9orf72 is a common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. The repeats are transcribed in both sense and antisense directions to generate distinct dipeptide repeat proteins, of which poly(GA), poly(GR), and poly(PR) have been implicated in contributing to neurodegeneration. Poly(PR) binding to RNA may contribute to toxicity, but analysis of poly(PR)-RNA binding on a transcriptome-wide scale has not yet been carried out. We therefore performed crosslinking and immunoprecipitation (CLIP) analysis in human cells to identify the RNA binding sites of poly(PR). We found that poly(PR) binds to nearly 600 RNAs, with the sequence GAAGA enriched at the binding sites. In vitro experiments showed that poly(GAAGA) RNA binds poly(PR) with higher affinity than control RNA and induces the phase separation of poly(PR) into condensates. These data indicate that poly(PR) preferentially binds to poly(GAAGA)-containing RNAs, which may have physiological consequences.

| S-EPMC10338859 | biostudies-literature

Arginine valency in C9ORF72 dipolypeptides mediates promiscuous proteome binding that transmits multiple modes of toxicity

Project description:Motor Neuron Disease patients with the C9ORF72 hexanucleotide expansion mutations feature abnormal expression of 5 different dipeptide repeat polymers (DPRs). Two of these, poly-GR and poly-PR, have proven highly toxic to cell and animal models. To investigate the mechanisms, we defined the interactomes of the DPRs in 10× and 101× repeat lengths as fusions to GFP in Neuro2a cells using quantitative proteomics. Relative to the more inert poly-GA and poly-PA peptides, poly-PR and poly-GR of both repeat lengths were promiscuous binders to the proteome and especially ribosomal proteins, translation initiation factors and translation elongation factors including ribosome recycling factor ABCE1, suggesting a role in ribosome stalling. The PR101 and GR101 DPRs robustly stalled the ribosome compared to the other DPRs and an unrelated mutant protein (Huntingtin) that causes neurodegeneration. Poly-GR also bound to arginine methylases and led to hypomethylation of endogenous proteins, with a profound destabilization of the actin cytoskeleton. Our findings point to arginine in the GR and PR polymers as multivalent toxins to translation as well as arginine methylation with concomitant downstream effects on widespread biological processes including ribosome biogenesis, mRNA splicing and cytoskeleton assembly.

2020-02-25 | PXD015177 | Pride

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