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Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome

View ORCID ProfileMatthew T. Parker, Katarzyna Knop, Anna V. Sherwood, View ORCID ProfileNicholas J. Schurch, Katarzyna Mackinnon, Peter D. Gould, Anthony Hall, Geoffrey J. Barton, View ORCID ProfileGordon G. Simpson
doi: https://doi.org/10.1101/706002
Matthew T. Parker
1School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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Katarzyna Knop
1School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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Anna V. Sherwood
1School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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Nicholas J. Schurch
1School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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  • ORCID record for Nicholas J. Schurch
Katarzyna Mackinnon
1School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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Peter D. Gould
2Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
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Anthony Hall
3Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
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Geoffrey J. Barton
1School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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  • For correspondence: g.g.simpson@dundee.ac.uk g.j.barton@dundee.ac.uk
Gordon G. Simpson
1School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
4James Hutton Institute, Invergowrie, DD2 5DA, UK
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  • ORCID record for Gordon G. Simpson
  • For correspondence: g.g.simpson@dundee.ac.uk g.j.barton@dundee.ac.uk
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Abstract

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 Arabidopsis thaliana and a mutant defective in mRNA methylation (m6A). Here we show that m6A 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 m6A from 3’ untranslated regions is associated with decreased relative transcript abundance and defective RNA 3′ end formation. A functional consequence of disrupted m6A 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.

Footnotes

  • ‡ Biomathematics and Statistics Scotland, The James Hutton Institute, Aberdeen, AB15 8QH, UK

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Posted July 17, 2019.
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Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome
Matthew T. Parker, Katarzyna Knop, Anna V. Sherwood, Nicholas J. Schurch, Katarzyna Mackinnon, Peter D. Gould, Anthony Hall, Geoffrey J. Barton, Gordon G. Simpson
bioRxiv 706002; doi: https://doi.org/10.1101/706002
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Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome
Matthew T. Parker, Katarzyna Knop, Anna V. Sherwood, Nicholas J. Schurch, Katarzyna Mackinnon, Peter D. Gould, Anthony Hall, Geoffrey J. Barton, Gordon G. Simpson
bioRxiv 706002; doi: https://doi.org/10.1101/706002

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