Document Type
Article
Publication Date
11-18-2021
Abstract
Direct sequencing of single, native RNA molecules through nanopores has a strong potential to transform research in all aspects of RNA biology and clinical diagnostics. The existing platform from Oxford Nanopore Technologies is unable to sequence the very 5′ ends of RNAs and is limited to polyadenylated molecules. Here, we develop True End-to-end RNA Sequencing (TERA-Seq), a platform that addresses these limitations, permitting more thorough transcriptome characterization. TERA-Seq describes both poly-and non-polyadenylated RNA molecules and accurately identifies their native 5′ and 3′ ends by ligating uniquely designed adapters that are sequenced along with the transcript. We find that capped, full-length mRNAs in human cells show marked variation of poly(A) tail lengths at the single molecule level. We report prevalent capping downstream of canonical transcriptional start sites in otherwise fully spliced and polyadenylated molecules. We reveal RNA processing and decay at single molecule level and find that mRNAs decay cotranslationally, often from their 5′ ends, while frequently retaining poly(A) tails. TERA-Seq will prove useful in many applications where true end-to-end direct sequencing of single, native RNA molecules and their isoforms is desirable.
Recommended Citation
Ibrahim, Fadia; Oppelt, Jan; Maragkakis, Manolis; and Mourelatos, Zissimos, "TERA-Seq: true end-to-end sequencing of native RNA molecules for transcriptome characterization" (2021). Department of Biochemistry and Molecular Biology Faculty Papers. Paper 202.
https://jdc.jefferson.edu/bmpfp/202
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License
PubMed ID
34428294
Language
English
Comments
This article is the author’s final published version in Nucleic Acids Research, Volume 49, Issue 20, November 2021, Page E115.
The published version is available at https://doi.org/10.1093/nar/gkab713. Copyright © Ibrahim et al.