Nanopore direct RNA sequencing maps the complexity of arabidopsis mRNA processing and m6A modification

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Nanopore direct RNA sequencing maps the complexity of arabidopsis mRNA processing and m6A modification. / Parker, Matthew T.; Knop, Katarzyna; Sherwood, Anna V.; Schurch, Nicholas J.; Mackinnon, Katarzyna; Gould, Peter D.; Hall, Anthony J.W.; Barton, Geoffrey J.; Simpson, Gordon G.

In: eLife, Vol. 9, e49658, 2020.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Parker, MT, Knop, K, Sherwood, AV, Schurch, NJ, Mackinnon, K, Gould, PD, Hall, AJW, Barton, GJ & Simpson, GG 2020, 'Nanopore direct RNA sequencing maps the complexity of arabidopsis mRNA processing and m6A modification', eLife, vol. 9, e49658. https://doi.org/10.7554/eLife.49658

APA

Parker, M. T., Knop, K., Sherwood, A. V., Schurch, N. J., Mackinnon, K., Gould, P. D., Hall, A. J. W., Barton, G. J., & Simpson, G. G. (2020). Nanopore direct RNA sequencing maps the complexity of arabidopsis mRNA processing and m6A modification. eLife, 9, [e49658]. https://doi.org/10.7554/eLife.49658

Vancouver

Parker MT, Knop K, Sherwood AV, Schurch NJ, Mackinnon K, Gould PD et al. Nanopore direct RNA sequencing maps the complexity of arabidopsis mRNA processing and m6A modification. eLife. 2020;9. e49658. https://doi.org/10.7554/eLife.49658

Author

Parker, Matthew T. ; Knop, Katarzyna ; Sherwood, Anna V. ; Schurch, Nicholas J. ; Mackinnon, Katarzyna ; Gould, Peter D. ; Hall, Anthony J.W. ; Barton, Geoffrey J. ; Simpson, Gordon G. / Nanopore direct RNA sequencing maps the complexity of arabidopsis mRNA processing and m6A modification. In: eLife. 2020 ; Vol. 9.

Bibtex

@article{cd6dd849dc2e44fb980db9781c6e7cda,
title = "Nanopore direct RNA sequencing maps the complexity of arabidopsis mRNA processing and m6A modification",
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{\textquoteright} untranslated regions is associated with decreased relative transcript abundance and defective RNA 30 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.",
author = "Parker, {Matthew T.} and Katarzyna Knop and Sherwood, {Anna V.} and Schurch, {Nicholas J.} and Katarzyna Mackinnon and Gould, {Peter D.} and Hall, {Anthony J.W.} and Barton, {Geoffrey J.} and Simpson, {Gordon G.}",
note = "Publisher Copyright: {\textcopyright} Copyright Parker et al. T.",
year = "2020",
doi = "10.7554/eLife.49658",
language = "English",
volume = "9",
journal = "eLife",
issn = "2050-084X",
publisher = "eLife Sciences Publications Ltd.",

}

RIS

TY - JOUR

T1 - Nanopore direct RNA sequencing maps the complexity of arabidopsis mRNA processing and m6A modification

AU - Parker, Matthew T.

AU - Knop, Katarzyna

AU - Sherwood, Anna V.

AU - Schurch, Nicholas J.

AU - Mackinnon, Katarzyna

AU - Gould, Peter D.

AU - Hall, Anthony J.W.

AU - Barton, Geoffrey J.

AU - Simpson, Gordon G.

N1 - Publisher Copyright: © Copyright Parker et al. T.

PY - 2020

Y1 - 2020

N2 - 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 30 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.

AB - 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 30 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.

U2 - 10.7554/eLife.49658

DO - 10.7554/eLife.49658

M3 - Journal article

C2 - 31931956

AN - SCOPUS:85077786155

VL - 9

JO - eLife

JF - eLife

SN - 2050-084X

M1 - e49658

ER -

ID: 272025647