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Related Experiment Video

Updated: Feb 2, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

A secondary structure within a human piRNA modulates its functionality.

Sumirtha Balaratnam¹, Madara Hettiarachchilage², Nicole West¹

¹Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA.

|November 12, 2018

Summary

This summary is machine-generated.

G-quadruplex (GQ) structures in piwi-interacting RNAs (piRNAs) can hinder their function. This study confirms GQ formation in piRNAs and shows it prevents PIWI protein binding and target gene silencing, revealing a new regulatory mechanism.

Keywords:

G-quadruplex Gene silencing HIWI binding Piwi-interacting RNAs Secondary structure

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Area of Science:

Molecular Biology
RNA Biology
Bioinformatics

Background:

Piwi-interacting RNAs (piRNAs) are small non-coding RNAs crucial for gene regulation.
Conserved secondary structures or sequence motifs in piRNAs are not well-established.
G-quadruplexes (GQs) are non-canonical RNA secondary structures.

Purpose of the Study:

To investigate the presence and functional implications of G-quadruplex (GQ) forming sequences in human piRNAs.
To determine if GQ formation affects piRNA binding to PIWI proteins and target RNA.
To assess the impact of GQ structures on piRNA-mediated gene silencing in vivo.

Main Methods:

Bioinformatic analysis to identify putative GQ forming sequences in human piRNAs.
Biochemical and biophysical techniques (e.g., EMSA) to confirm GQ formation in a specific piRNA (piR-48164/piR-GQ).
Reporter assays to evaluate the effect of GQ formation on gene silencing activity in vivo.

Main Results:

Putative GQ forming sequences were identified in human piRNAs.
Human piR-48164/piR-GQ was confirmed to form a GQ structure.
GQ formation inhibited piRNA binding to the HIWI-PAZ domain and complementary base pairing to target RNA.
piR-GQ failed to inhibit reporter gene expression, while a non-GQ forming mutant did, indicating GQ is detrimental to function.

Conclusions:

Piwi-interacting RNAs can form G-quadruplex structures.
GQ formation in piRNAs inhibits their interaction with PIWI proteins and target RNAs.
The presence of GQ structures in piRNAs is detrimental to their gene silencing function, adding a new layer of RNA regulation.