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The 3’-5’ exoribonuclease ISG20L2 contributes to 3’ terminus maturation of 18S and 28S ribosomal RNAs (revision)

GSE292922 Homo sapiens (human) RNA-seq (gene expression) 60 samples Submitted 2025/10/16 Platform GPL15520
At a glance

RNA-seq (gene expression) · human · 60 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
60 samples: 48 distinct titles, 9 of them repeatedGroups 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
The 3'-5' exoribonuclease ISG20L2 contributes to 3' terminus maturation of 18S and 28S ribosomal RNAsNucleic acids research · 2025
Summary (written by the submitters)
Ribosome biogenesis is a nodal process in cell growth and proliferation, and its dysfunction is associated to human congenital diseases and tumorigenesis. Despite extensive mechanistic characterization, several processing steps of human pre-ribosomal RNAs remain elusive. The 47S primary transcript contains 3 out of 4 ribosomal RNAs flanked by external (5’ETS, 3’ETS) and internal (ITS1, ITS2) transcribed spacers.
Read the full summary ↓
The molecular processes leading to the removal of the 3’ETS, one of the earliest maturation steps, is not fully understood. Combining loss-of-function experiments and 3’-RACE high-throughput sequencing, we showed that the vertebrate-specific 3’-5’ exoribonuclease ISG20L2, a DEDDh RNase T superfamily member, is critical for efficient removal of the 3’ETS and formation of large ribosomal subunits. ISG20L2 inactivation led to accumulation of various forms of 3’-extented pre-rRNAs and disorganized PDFC, a sub-nucleolar compartment recently linked to 3’ETS processing. The function of ISG20L2 also extends to the trimming of ITS1 after endonucleolytic cleavage at site 2 and its knockdown reveals the precise location of site 2. Altogether, the present work uncovers the landscape of two pre-rRNA processing steps at nucleotide resolution, and restricts the function of ISG20L2 to the nucleoli where it contributes to the maturation of 18S and 28S 3’ ends.
Published in
The 3'-5' exoribonuclease ISG20L2 contributes to 3' terminus maturation of 18S and 28S ribosomal RNAs
Aubert M, Zuber H, Mommert-Tripon M et al. · Nucleic acids research 2025 · PMID 41261865 · doi:10.1093/nar/gkaf1180
This dataset
Open GSE292922 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 GSE292922_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 PRJNA1241877 and SRA study SRP573069. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41261865) ↗
Study design
48 distinct titles, 9 of them repeated
Primer2_mut+_siISG20L2 ×4 Primer2_control ×3 Primer2_wt-_siISG20L2 ×2 Primer2_siURB1 ×2 Primer2_mut-_siISG20L2 ×2 Primer1_siRPL26 ×2 Primer1_wt+_siISG20L2 ×2 Primer1_siRPL3 ×2 +1 more

How we read this: Read from 60 sample titles: 48 distinct titles with little repetition. 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

+ 20 more — browse all 60 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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