A bisulfite-assisted and ligation-based qPCR amplification technology for locus-specific pseudouridine detection at base resolution

TL;DR

This paper introduces a new method called pseU-TRACE for detecting pseudouridine in RNA at base resolution using bisulfite and qPCR.

Contribution

The novel pseU-TRACE method enables base-resolution detection of pseudouridine in RNA with high sensitivity and specificity.

Findings

pseU-TRACE successfully detects known pseudouridine sites in 28S, 18S, 5.8S, and mRNA.

The method allows quantification of pseudouridine fractions and analysis of pseudouridine synthase activity.

pseU-TRACE is a reliable, time-efficient, and sensitive technique for pseudouridine detection.

Abstract

Over 150 types of chemical modifications have been identified in RNA to date, with pseudouridine (Ψ) being one of the most prevalent modifications in RNA. Ψ plays vital roles in various biological processes, and precise, base-resolution detection methods are fundamental for deep analysis of its distribution and function. In this study, we introduced a novel base-resolution Ψ detection method named pseU-TRACE. pseU-TRACE relied on the fact that RNA containing Ψ underwent a base deletion after treatment of bisulfite (BS) during reverse transcription, which enabled efficient ligation of two probes complementary to the cDNA sequence on either side of the Ψ site and successful amplification in subsequent real-time quantitative PCR (qPCR), thereby achieving selective and accurate Ψ detection. Our method accurately and sensitively detected several known Ψ sites in 28S, 18S, 5.8S, and even mRNA. Moreover, pseU-TRACE could be employed to measure the Ψ fraction in RNA and explore the Ψ metabolism of different pseudouridine synthases (PUSs), providing valuable insights into the function of Ψ. Overall, pseU-TRACE represents a reliable, time-efficient and sensitive Ψ detection method.

Graphical Abstract

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