ArticleMethods in molecular biology (Clifton, N.J.)2021
Transcript Isoform-Specific Estimation of Poly(A) Tail Length by Nanopore Sequencing of Native RNA.
Article in Methods in molecular biology (Clifton, N.J.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed, 10 citations in OpenAlex.
- Poly(A) Profiling for Euglenozoans Using Oxford Nanopore Direct RNA Sequencing, Illustrated by the Example of Euglena gracilis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Article
- An extended wave of global mRNA deadenylation sets up a switch in translation regulation across the mammalian oocyte-to-embryo transition.Cell reports · 2024Article
- Nanopore Direct RNA Sequencing Data Processing and Analysis Using MasterOfPores.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Drought induces epitranscriptome and proteome changes in stem-differentiating xylem of Populus trichocarpa.Plant physiology · 2022Article
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Authors and funding
3 authors at 1 institution in 1 country.
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Abstract
The poly(A) tail is a homopolymeric stretch of adenosine at the 3'-end of mature RNA transcripts and its length plays an important role in nuclear export, stability, and translational regulation of mRNA. Existing techniques for genome-wide estimation of poly(A) tail length are based on short-read sequencing. These methods are limited because they sequence a synthetic DNA copy of mRNA instead of the native transcripts. Furthermore, they can identify only a short segment of the transcript proximal to the poly(A) tail which makes it difficult to assign the measured poly(A) length uniquely to a single transcript isoform. With the introduction of native RNA sequencing by Oxford Nanopore Technologies, it is now possible to sequence full-length native RNA. A single long read contains both the transcript and the associated poly(A) tail, thereby making transcriptome-wide isoform-specific poly(A) tail length assessment feasible. We developed tailfindr-an R-based package for estimating poly(A) tail length from Oxford Nanopore sequencing data. In this chapter, we describe in detail the pipeline for transcript isoform-specific poly(A) tail profiling based on native RNA Nanopore sequencing-from library preparation to downstream data analysis with tailfindr.
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