Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m 6 A modification

Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. We adapted nanopore direct RNA sequencing to examine RNA from a wild-type accession of the model plant and a mutant defective in mRNA methylation (m A). Here we show that m A c...

Full description

Saved in:
Bibliographic Details
Published ineLife Vol. 9
Main Authors Parker, Matthew T, Knop, Katarzyna, Sherwood, Anna V, Schurch, Nicholas J, Mackinnon, Katarzyna, Gould, Peter D, Hall, Anthony Jw, Barton, Geoffrey J, Simpson, Gordon G
Format Journal Article
LanguageEnglish
Published England 14.01.2020
Subjects
Adenosine - analogs & derivatives
Adenosine - metabolism
Arabidopsis - genetics
Arabidopsis - metabolism
Gene Expression Profiling
Methylation
Nanopores
Poly A - genetics
Poly A - metabolism
RNA Caps
RNA Processing, Post-Transcriptional
RNA Splicing
RNA, Messenger - chemistry
RNA, Messenger - genetics
RNA, Messenger - metabolism
RNA, Plant - chemistry
RNA, Plant - genetics
RNA, Plant - metabolism
RNA, Untranslated - chemistry
RNA, Untranslated - genetics
Sequence Analysis, RNA
computational biology
polyadenylation
systems biology
RNA
nanopore
A. thaliana
chromosomes
epitranscriptome
gene expression
Online AccessGet full text

Cover

More Information
Summary:Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification. We adapted nanopore direct RNA sequencing to examine RNA from a wild-type accession of the model plant and a mutant defective in mRNA methylation (m A). Here we show that m A can be mapped in full-length mRNAs transcriptome-wide and reveal the combinatorial diversity of cap-associated transcription start sites, splicing events, poly(A) site choice and poly(A) tail length. Loss of m A from 3' untranslated regions is associated with decreased relative transcript abundance and defective RNA 3' end formation. A functional consequence of disrupted m A is a lengthening of the circadian period. We conclude that nanopore direct RNA sequencing can reveal the complexity of mRNA processing and modification in full-length single molecule reads. These findings can refine Arabidopsis genome annotation. Further, applying this approach to less well-studied species could transform our understanding of what their genomes encode.
ISSN:2050-084X