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Updated: Sep 5, 2025

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

UPA-Seq-Based Search Method for Functional lncRNA Candidates.

Saori Yokoi¹, Shinichi Nakagawa^2,3

¹RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan. yokois@pharm.hokudai.ac.jp.

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

|July 7, 2022

Summary

This summary is machine-generated.

Researchers developed UV-phenol aqueous-phase RNA sequencing (UPA-seq) to identify functional long noncoding RNA (lncRNA) candidates. This method assumes functional lncRNAs interact with proteins, aiding discovery among abundant genomic data.

Keywords:

Phenol-chloroform RNA-Seq UV crosslinking lncRNAs

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Area of Science:

Genomics
Molecular Biology
RNA Biology

Background:

Long noncoding RNAs (lncRNAs) are abundant in mammalian transcriptomes and play roles in various biological processes.
The functional validation of lncRNAs remains limited, with most characterized by sequence and expression data alone.

Purpose of the Study:

To introduce UV-phenol aqueous-phase RNA sequencing (UPA-seq) as a novel method for identifying functional lncRNA candidates.
To leverage protein-RNA interactions as a basis for discovering novel functional lncRNAs.

Main Methods:

Development and description of the UV-phenol aqueous-phase RNA sequencing (UPA-seq) protocol.
Application of UPA-seq to search for functional lncRNA candidates within whole genomes.

Main Results:

UPA-seq enables the identification of potential functional lncRNAs by detecting their association with proteins.
The study provides a methodology to expand the catalog of functionally validated lncRNAs.

Conclusions:

UPA-seq is a valuable tool for discovering functional lncRNA candidates based on protein-binding evidence.
This method facilitates a deeper understanding of lncRNA functions in various biological contexts.