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piRNA - Piwi-interacting RNAs

piRNA - Piwi-interacting RNAs

PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests...

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Related Experiment Video

Updated: May 6, 2026

Enhanced Crosslinking Immunoprecipitation eCLIP Method for Efficient Identification of Protein-bound RNA in Mouse Testis

Enhanced Crosslinking Immunoprecipitation eCLIP Method for Efficient Identification of Protein-bound RNA in Mouse Testis

Published on: May 10, 2019

HITS-CLIP (CLIP-Seq) for mouse Piwi proteins.

Anastassios Vourekas¹, Zissimos Mourelatos

¹Department of Pathology and Laboratory Medicine, Division of Neuropathology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.

Methods in Molecular Biology (Clifton, N.J.)

|November 2, 2013

Summary

This study details a High Throughput Sequencing after in vivo Crosslinking and Immunoprecipitation (HITS-CLIP) protocol for mouse Piwi proteins Mili and Miwi. This method aids in understanding small RNA interactions and their regulatory roles in germ cells.

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Last Updated: May 6, 2026

Enhanced Crosslinking Immunoprecipitation eCLIP Method for Efficient Identification of Protein-bound RNA in Mouse Testis

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Published on: May 10, 2019

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

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Published on: April 30, 2011

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

Area of Science:

Molecular Biology
Genetics
RNA Biology

Background:

Piwi proteins are crucial Argonaute family members essential for the animal germline.
They bind Piwi-interacting RNAs (piRNAs) to form pi-RiboNucleoProteins (piRNPs).
While piRNAs safeguard germ cell genome integrity by targeting retrotransposons, their regulatory roles on mRNAs are under investigation.

Purpose of the Study:

To present an adapted technical protocol for High Throughput Sequencing after in vivo Crosslinking and Immunoprecipitation (HITS-CLIP) for mouse Piwi proteins Mili and Miwi.
To provide recommendations for applying this HITS-CLIP protocol to other RNA-binding proteins (RBPs).
To offer guidance on bioinformatic analysis of deep sequencing data generated by HITS-CLIP.

Main Methods:

Adaptation of the HITS-CLIP (CLIP-Seq) technique for immunoprecipitation of mouse Piwi proteins Mili and Miwi.
In vivo crosslinking to capture RNA-protein interactions.
High-throughput sequencing for deep sequencing data generation.

Main Results:

A detailed HITS-CLIP protocol optimized for mouse Mili and Miwi proteins is established.
The protocol is presented with general recommendations for broader RBP applications.
Guidelines for the bioinformatic analysis of the resulting deep sequencing data are provided.

Conclusions:

The developed HITS-CLIP protocol enables robust investigation of Piwi protein-RNA interactions in vivo.
This methodology facilitates the study of piRNA-mediated gene regulation beyond retrotransposon control.
The protocol and analysis recommendations support researchers in studying RBP-RNA interactomes.