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GSE276985

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Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [eCLIP-seq]

Organism: Mus musculus
Platform: GPL24676
Samples: 31
Experiment Types:
Other
Submitted: Sep 11 2024
Last Updated: Feb 19 2025
Status: Public on Feb 18 2025
Contact: Kevin,,Rhine (University of Arizona)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1159891

Summary

Aging is one of the most prominent risk factors for neurodegeneration, yet the molecular mechanisms underlying the deterioration of old neurons are mostly unknown. To efficiently study neurodegeneration in the context of aging, we transdifferentiated primary human fibroblasts from aged healthy donors directly into neurons, which retained their aging markers. Here we show that aged neurons are broadly depleted of RNA-binding proteins, especially spliceosome components. Intriguingly, splicing proteins – like the dementia and ALS-associated protein TDP-43 – mislocalize to the cytoplasm in aged neurons, which leads to widespread alternative splicing. Cytoplasmic spliceosome components typically are recruited to stress granules, but aged neurons suffer from chronic stress that prevents this sequestration. We link chronic stress to the malfunctioning ubiquitylation machinery, poor HSP90α chaperone activity, and the failure to respond to new stress events. Together our data demonstrates that aging-linked deterioration of RNA biology is a key driver of poor resiliency in aged neurons.

Overall Design

Enhanced immunoprecipitation and crosslinking followed by sequencing (eCLIP-seq) of RNA-binding proteins in neuron and tissues

Analysis (2 steps)

View Data Processing
Processing steps for GSE276985
  1. eCLIP data was analyzed using Skipper with default settings.
  2. The kDa of each ORF was matched to the closest input sample beginning at that range; for example, a 78 kDa ORF would be paired with the input sample covering the range of 75 to 150 kDa.

Supplementary Files (1)

GSE276985_RAW.tar Download
GEO Samples (31)

Potentially Related Publications (1)

This accession was text-mined from the PMC full text of these publications. It may be referenced for comparison or reused from another study rather than generated for them.

Data Files (10)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— G3BP1_Mid-Age_HumanBrain-131G-IP_S24_L001_R1_001.fastq… RIP-Seq 337.2 MB link
— G3BP1_Mid-Age_HumanBrain-20G-IP_S19_L001_R1_001.fastq.… RIP-Seq 162.4 MB link
— G3BP1_Mid-Age_HumanBrain-26G-IP_S20_L001_R1_001.fastq.… RIP-Seq 320.2 MB link
— G3BP1_Ngn2_Stress-KR_2A_G3BP1_S_IP_S44_L001_R1_001.fas… RIP-Seq 236.9 MB link
— G3BP1_Ngn2_Stress-KR_2B_G3BP1_S_IP_S46_L001_R1_001.fas… RIP-Seq 174.2 MB link
— G3BP1_Ngn2_Unstress-KR_1A_G3BP1_U_IP_S40_L001_R1_001.f… RIP-Seq 190.1 MB link
— G3BP1_NK_Unstress-KR_C_IP_S42_L004_R1_001.fastq.gz RIP-Seq 425.1 MB link
— G3BP1_Old-Age_HumanBrain-105G-IP_S23_L001_R1_001.fastq… RIP-Seq 493.1 MB link
— G3BP1_Old-Age_HumanBrain-65G-IP_S21_L001_R1_001.fastq.… RIP-Seq 461.1 MB link
— G3BP1_Old-Age_HumanBrain-67G-IP_S22_L001_R1_001.fastq.… RIP-Seq 186.1 MB link