Short-read RNA-seq yields lower estimates of A-to-I RNA editing levels than long-read cDNA sequencing

Abstract

A-to-I RNA editing, one of the most frequent RNA modifications, is essential for most aspects of RNA metabolism. However, the accuracy of quantifying A-to-I editing levels has been largely neglected, particularly when contrasting next-generation sequencing (NGS) with long-read sequencing (LRS) RNA-seq. To address it, we performed paired NGS and LRS cDNA RNA-seq of both HEK293T and U2OS cells, revealing that the A-to-I editing levels were estimated to be lower by NGS compared with LRS, a conclusion that was confirmed through full-length amplicon sequencing. Furthermore, the lower estimation of A-to-I editing levels is widespread, while we also identified this consequence using released public both same-study and cross-study NGS and LRS RNA-seq data in various human cancer cell lines. In addition, our analyses indicate that the primary factor contributing to this lower estimation is the sequencing read length difference, and a significantly positive correlation between the quantification and read length is identified by analyzing the public NGS RNA-seq data of various cell lines. We additionally found that shorter sequencing reads are more prone to aligning incorrectly to the reference genome, such as uniquely-to-multiply mapped and uniquely mapped-to-unmapped, inducing the lower estimation of A-to-I editing levels. In summary, our analyses indicate that LRS RNA-seq is preferable for accurately quantifying A-to-I editing levels.

Keywords

A-to-I RNA editing / Short-read RNA-seq / Long-read cDNA sequencing / Editing level / Quantification

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Funding

Key Programme(92269107)

Basic and Applied Basic Research Foundation of Guangdong Province(2023A1515011081)

Funding by Science and Technology Projects in Guangzhou(2024B03J1241)

Grant from MOE Key Laboratory of Gene Function and Regulation

Grant from National Key Laboratory of Respiratory Diseases(J25411010)

Guangdong Medical Research Foundation(B2025244)

Grant from Guangdong Provincial Department of Education

Natural Science Foundation of Guangzhou Municipality(G24151021)

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