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Respiratory syncytial virus (RSV) enhances translation of virus-resembling AU-rich host transcripts

GSE268742 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2024/09/03 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 12 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
Homo sapiens (human)
Samples
12 samples: 3 × HEp-2 cells; mock-infected; total RNA; vs 3 × HEp-2 cells; RSV-infected; total RNA; vs 3 × HEp-2 cells; mock-infected; polysomal RNA; vs 3 × HEp-2 cells; RSV-infected; polysomal RNA;Groups 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.
Paper
Respiratory Syncytial Virus (RSV) optimizes the translational landscape during infectionbioRxiv : the preprint server for biology · 2024
Summary (written by the submitters)
Viral infection often triggers eukaryotic initiator factor 2α (eIF2α) phosphorylation, leading to global 5’-cap-dependent translation inhibition. RSV encodes messenger RNAs (mRNAs) mimicking 5’-cap structures of host mRNAs and thus inhibition of cap-dependent translation initiation would likely also reduce viral translation. We confirmed that RSV limits widespread translation initiation inhibition and unexpectedly found that the fraction of ribosomes within polysomes increases during infection, indicating higher ribosome loading on mRNAs during infection.
Read the full summary ↓
We found that AU-rich host transcripts that are less efficiently translated under normal conditions become more efficient at recruiting ribosomes, similar to RSV transcripts. Viral transcripts are transcribed in cytoplasmic inclusion bodies, where the viral AU-rich binding protein M2-1 has been shown to bind viral transcripts and shuttle them into the cytoplasm. We further demonstrated that M2-1 is found on polysomes, and that M2-1 might deliver host AU-rich transcripts for translation.
Published in
Respiratory Syncytial Virus (RSV) optimizes the translational landscape during infection
Kerkhofs K, Guydosh NR, Bayfield MA · bioRxiv : the preprint server for biology 2024 · PMID 39131278 · doi:10.1101/2024.08.02.606199
This dataset
Open GSE268742 in finder → Find more human 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 GSE268742_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 PRJNA1118414 and SRA study SRP510928. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39131278) ↗
Study design
3 × HEp-2 cells; mock-infected; total RNA; vs 3 × HEp-2 cells; RSV-infected; total RNA; vs 3 × HEp-2 cells; mock-infected; polysomal RNA; vs 3 × HEp-2 cells; RSV-infected; polysomal RNA;

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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
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