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Related Experiment Video

Updated: Oct 11, 2025

Identification of Circular RNAs using RNA Sequencing

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

Phospho-RNA sequencing with circAID-p-seq.

Alessia Del Piano^1,2, Tea Kecman¹, Michael Schmid³

¹IMMAGINA BioTechnology S.r.l, Via Sommarive 18, Povo, Italy.

Nucleic Acids Research

|December 1, 2021

Summary

This study introduces circAID-p-seq, a novel PCR-free method for sequencing 3' phospho-RNA. This technique accurately profiles ribosome occupancy, offering a versatile strategy for analyzing RNA molecules.

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3' End Sequencing Library Preparation with A-seq2

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Published on: October 10, 2017

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Last Updated: Oct 11, 2025

Identification of Circular RNAs using RNA Sequencing

Identification of Circular RNAs using RNA Sequencing

Published on: November 14, 2019

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

Published on: July 10, 2020

3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

Area of Science:

Molecular Biology
Genomics
Biochemistry

Background:

Traditional RNA footprinting methods produce 3' phosphorylated RNA fragments.
Existing library preparation protocols require a 3' hydroxyl group for adaptor ligation, limiting the analysis of 3' phosphorylated RNA.
This presents a challenge for techniques like ribosome profiling that generate such fragments.

Purpose of the Study:

To develop a novel, PCR-free library preparation method for selective sequencing of 3' phospho-RNA.
To enable accurate and efficient analysis of RNA fragments with a 3' phosphate group.
To provide a versatile tool for studying RNA molecules with endogenous 3'-phospho termini.

Main Methods:

Development of circAID-p-seq, a PCR-free library preparation protocol for selective 3' phospho-RNA sequencing.
Application of circAID-p-seq to ribosome profiling, analyzing RNA fragments protected by ribosomes after endonuclease digestion.
Utilization of a dedicated computational pipeline, circAidMe, for data analysis.

Main Results:

circAID-p-seq enables accurate, fast, and highly efficient sequencing of phospho-RNA fragments from eukaryotic cells and tissues.
The method was successfully applied to ribosome profiling, allowing for the portrayal of ribosome occupancy on transcripts.
Demonstrated versatility in analyzing endogenous 3'-phospho RNA molecules.

Conclusions:

circAID-p-seq is a versatile and efficient PCR-free strategy for selective 3' phospho-RNA sequencing.
This method facilitates accurate ribosome profiling and analysis of other endogenous 3'-phospho RNA molecules.
The developed technique offers a valuable tool for unraveling the complexities of RNA biology.