GEO series

Widespread microRNA degradation elements in target mRNAs can assist the encoded proteins

GSE178943 Homo sapiens (human) Non-coding RNA profiling 12 samples Submitted 2024/06/25 Platform GPL24676

At a glance

Non-coding RNA profiling · human · 12 samples

What it is: Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
Organism: Homo sapiens (human)
Samples: 12 samples: 12 samples, each with a distinct title — no replicated groupsGroups 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: Widespread microRNA degradation elements in target mRNAs can assist the encoded proteinsGenes & development · 2021

Summary (written by the submitters)

Binding of microRNAs (miRNA) to mRNAs normally results in post-transcriptional repression. However, extensive base-pairing between miRNAs and target RNAs can trigger miRNA degradation, a phenomenon called target RNA-directed miRNA degradation (TDMD). Here, we systematically analyzed Argonaute-CLASH (crosslinking, ligation, and sequencing of miRNA-target RNA hybrids) data, and identified numerous candidate TDMD triggers based on their ability to induce non-templated nucleotide addition at the miRNA 3 end.

Read the full summary ↓

When overexpressed in HEK293T cells, nine highly conserved triggers induce degradation of corresponding miRNAs. Consistent with previous reports, both the TDMD base-pairing and surrounding sequences are important for TDMD. CRISPR knockout of endogenous trigger or ZSWIM8, a ubiquitin ligase essential for TDMD, reduce miRNA degradation. Furthermore, degradation of miR-221 and miR-222 by a trigger in BCL2L11, which encodes an apoptotic protein, enhances apoptosis. Therefore, we uncovered widespread TDMD triggers in target RNAs and demonstrated that they can functionally cooperate with the encoded proteins.

Published in

Widespread microRNA degradation elements in target mRNAs can assist the encoded proteins

Li L, Sheng P, Li T et al. · Genes & development 2021 · PMID 34819352 · doi:10.1101/gad.348874.121

This dataset

Open GSE178943 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 GSE178943_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 ↗

Also filed as BioProject PRJNA741532 and SRA study SRP325666. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 34819352) ↗

Study design

12 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 12 sample titles: 12 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

GSM5401677 S1_GFP_sRNA
GSM5401678 S2_BCL2L11_sRNA
GSM5401679 S3_TRIM9_sRNA
GSM5401680 S4_GFP_sRNA
GSM5401681 S5_BCL2L11_sRNA
GSM5401682 S6_TRIM9_sRNA
GSM5401683 M1_GFP_mRNA
GSM5401684 M2_BCL2L11_mRNA
GSM5401685 M3_TRIM9_mRNA
GSM5401686 M4_GFP_mRNA
GSM5401687 M5_BCL2L11_mRNA
GSM5401688 M6_TRIM9_mRNA

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