RT Journal Article
SR Electronic
T1 Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore sequencing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.09.22.461331
DO 10.1101/2021.09.22.461331
A1 Oguzhan Begik
A1 Huanle Liu
A1 Anna Delgado-Tejedor
A1 Cassandra Kontur
A1 Antonio J. Giraldez
A1 Jean-Denis Beaudoin
A1 John S. Mattick
A1 Eva Maria Novoa
YR 2021
UL http://biorxiv.org/content/early/2021/10/27/2021.09.22.461331.abstract
AB RNA polyadenylation plays a central role in RNA maturation, fate and stability. In response to developmental cues, polyA tail lengths can vary, affecting the translatability and stability of mRNAs. Here we develop Nano3P-seq, a novel method that relies on nanopore sequencing to simultaneously quantify RNA abundance, tail composition and tail length dynamics at per-read resolution. By employing a template switching-based sequencing protocol, Nano3P-seq can sequence any given RNA molecule from its 3’end, regardless of its polyadenylation status, without the need of PCR amplification or ligation of RNA adapters. We demonstrate that Nano3P-seq captures a wide diversity of RNA biotypes, providing quantitative estimates of RNA abundance and tail lengths in mRNAs, lncRNAs, sn/snoRNAs, scaRNAs and rRNAs. We find that, in addition to mRNAs and lncRNAs, polyA tails can be identified in 16S mitochondrial rRNA in both mouse and zebrafish. Moreover, we show that mRNA tail lengths are dynamically regulated during vertebrate embryogenesis at the isoform-specific level, correlating with mRNA decay. Overall, Nano3P-seq is a simple and robust method to accurately estimate transcript levels and tail lengths in full-length individual reads, with minimal library preparation biases, both in the coding and non-coding transcriptome.Competing Interest StatementThe authors have declared no competing interest.