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FMRP Regulates Neuronal RNA Granules Containing Stalled Ribosomes, Not Where Ribosomes Stall

GSE291701 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2026/06/18 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 36 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
36 samples: 8 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Summary (written by the submitters)
Local protein synthesis is a crucial process that maintains synaptic proteostasis. Ribosomes stalled at elongation make up a sizable percentage of mRNAs translated in developing neurons. The protein lost in Fragile X syndrome (FMRP) is highly enriched in RNA granules containing stalled ribosomes, both of which play crucial roles in regulating forms of synaptic plasticity such as metabotropic glutamate receptor-dependent long-term depression (mGLUR-LTD).
Read the full summary ↓
Previous examination of ribosome protected fragments (RPFs) from neuronal stalled ribosomes have identified motifs matching those found in mRNAs associated with FMRP, as recognized by FMRP cross-linking immunoprecipitation (CLIP) (Anadolu et al., 2023, Journal of Neuroscience doi: 10.1523/JNEUROSCI.1002-22.2023). To investigate if FMRP recognition of these sequences is important for determining where mRNAs are stalled, we examined stalled ribosomes RPFs isolated from P5 mice lacking the FMRP protein. We found that the loss of FMRP had no effect on the proteins associated with RNA granules, structure of the ribosomes and stalling sites, or where accumulations of RPFs occurred. However, there was a significant decrease in the amount of stalling on mRNAs previously shown to be associated with FMRP by cross-linking immunoprecipitation (CLIP). In addition, there was a decrease in the number of RNA granules containing stalled polysomes as assayed by ribopuromycylation in distal neurites and, unlike RNA granules in WT neurons, the remaining distal RNA granules were resistant to reactivation by stimuli that induce mGLuR-LTD. These results show important roles for FMRP in regulating RNA granules containing stalled ribosomes, but not in determining where ribosomes are stalled.
This dataset
Open GSE291701 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE291701_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1234679 and SRA study SRP569688. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
8 conditions, mostly in triplicate
M-WT Granule Sample single-end M-protocol, ×3 M-FMR1-KO Granule Sample single-end M-protoco… ×3 M-WT Polysome Sample single-end M-protocol, ×3 M-FMR1-KO Polysome Sample single-end M-protoc… ×3 WT Granule Sample single-end, ×3 FMR1-KO Granule Sample single-end, ×3 WT Polysome Sample single-end, ×3 FMR1-KO Polysome Sample single-end, ×3 +12 more

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 36 sample titles; they account for 24 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
Datasets on a similar topic

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