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A Reporter Assay to Analyze Intronic microRNA Maturation in Mammalian Cells

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Published on: June 16, 2022

Short intron-derived ncRNAs.

Florent Hubé^1,2, Damien Ulveling^1,2, Alain Sureau^1,2

¹Université Paris Diderot, Sorbonne Paris Cité, Paris, France.

Nucleic Acids Research

|January 6, 2017

Summary

This summary is machine-generated.

Researchers discovered novel Short Intron-Derived ncRNAs (SID) that can produce microRNAs (miRNAs) through alternative splicing. Some SID depend on DBR1, while others reveal new non-canonical miRNA biogenesis pathways.

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Area of Science:

Genomics
Molecular Biology
RNA Biology

Background:

Introns constitute a significant portion of the human genome but are typically removed during RNA splicing.
Non-canonical microRNAs (miRNAs) have been suggested to arise directly from intron splicing events.
Alternative splicing of introns presents a potential source for developmental regulation of miRNA production.

Purpose of the Study:

To computationally predict novel Short Intron-Derived ncRNAs (SID) as precursors for small non-coding RNAs (ncRNAs).
To investigate the biogenesis pathways of these SID, including their dependence on key factors in canonical and alternative miRNA biogenesis.
To validate predicted SID and identify novel endogenous miRNAs produced via non-canonical pathways.

Main Methods:

Computational prediction of Short Intron-Derived ncRNAs (SID).
Testing the dependence of SID biogenesis on canonical and alternative miRNA processing factors (Drosha, DGCR8, DBR1, snRNP70, U2AF65, PRP8, Dicer, Ago2).
Validation of selected SID as miRNA precursors and identification of endogenous miRNAs using molecular biology techniques.

Main Results:

Approximately half of the predicted SID require the enzyme DBR1 for debranching, similar to mirtrons.
New classes of SID were identified, suggesting intermingling between canonical and alternative miRNA biogenesis pathways.
Several SID were validated as miRNA precursors, yielding novel endogenous miRNAs, including one from the SRA gene intron.

Conclusions:

Alternative splicing of introns is a viable source for generating novel miRNAs through Short Intron-Derived ncRNAs (SID).
The study reveals diverse non-canonical miRNA biogenesis pathways, some involving DBR1 and others integrating canonical and alternative mechanisms.
Dysregulation of SRA intron-derived miRNA processing was observed in myotonic dystrophy patients, highlighting the clinical relevance of these non-canonical pathways.