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Updated: Feb 24, 2026
Genome-wide Surveillance of Transcription Errors in Eukaryotic Organisms
Published on: September 13, 2018
Accurate RNA consensus sequencing for high-fidelity detection of transcriptional mutagenesis-induced epimutations
Kate S Reid-Bayliss1, Lawrence A Loeb2,3
1Department of Pathology, University of Washington School of Medicine, Seattle, WA 98195.
Abstract:
Transcriptional mutagenesis (TM) due to misincorporation during RNA transcription can result in mutant RNAs, or epimutations, that generate proteins with altered properties. TM has long been hypothesized to play a role in aging, cancer, and viral and bacterial evolution. However, inadequate methodologies have limited progress in elucidating a causal association. We present a high-throughput, highly accurate RNA sequencing method to measure epimutations with single-molecule sensitivity. Accurate RNA consensus sequencing (ARC-seq) uniquely combines RNA barcoding and generation of multiple cDNA copies per RNA molecule to eliminate errors introduced during cDNA synthesis, PCR, and sequencing. The stringency of ARC-seq can be scaled to accommodate the quality of input RNAs. We apply ARC-seq to directly assess transcriptome-wide epimutations resulting from RNA polymerase mutants and oxidative stress.
Insights
This study introduces Accurate RNA consensus sequencing (ARC-seq), a novel method to detect RNA epimutations. ARC-seq enables precise measurement of transcriptional mutagenesis, advancing research in aging and disease.
Area of Science:
- Molecular Biology
- Genetics
- Biochemistry
Background:
- Transcriptional mutagenesis (TM) generates epimutations, altering protein properties and potentially contributing to aging, cancer, and evolution.
- Previous methodologies lacked the sensitivity and accuracy to establish causal links for TM.
- Understanding TM is crucial for fields ranging from molecular biology to evolutionary studies.
Purpose of the Study:
- To develop a high-throughput, highly accurate RNA sequencing method for measuring epimutations.
- To enable single-molecule sensitivity in detecting errors during RNA transcription.
- To investigate the role of TM in biological processes like aging and disease.
Main Methods:
- Developed Accurate RNA consensus sequencing (ARC-seq), a novel RNA sequencing technique.
- ARC-seq combines RNA barcoding and multiple cDNA synthesis to minimize errors from cDNA synthesis, PCR, and sequencing.
- The method's stringency is adjustable based on input RNA quality.
Main Results:
- ARC-seq achieves high-throughput and high accuracy in measuring epimutations.
- Single-molecule sensitivity allows for precise detection of transcriptional errors.
- Applied ARC-seq to assess transcriptome-wide epimutations under conditions of RNA polymerase mutation and oxidative stress.
Conclusions:
- ARC-seq provides a powerful new tool for studying transcriptional mutagenesis and epimutations.
- This method overcomes previous technical limitations, facilitating causal association studies.
- The findings open avenues for exploring TM's role in aging, cancer, and microbial evolution.
