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Genome-wide characterization of differential transcript usage in Arabidopsis thaliana

Dries Vaneechoutte UGent, April R Estrada, Ying-Chen Lin, Ann E Loraine and Klaas Vandepoele UGent (2017) PLANT JOURNAL. 92(6). p.1218-1231
abstract
Alternative splicing and the usage of alternate transcription start- or stop sites allows a single gene to produce multiple transcript isoforms. Most plant genes express certain isoforms at a significantly higher level than others, but under specific conditions this expression dominance can change, resulting in a different set of dominant isoforms. These events of differential transcript usage (DTU) have been observed for thousands of Arabidopsis thaliana, Zea mays and Vitis vinifera genes, and have been linked to development and stress response. However, neither the characteristics of these genes, nor the implications of DTU on their protein coding sequences or functions, are currently well understood. Here we present a dataset of isoform dominance and DTU for all genes in the AtRTD2 reference transcriptome based on a protocol that was benchmarked on simulated data and validated through comparison with a published reverse transciptase-polymerase chain reaction panel. We report DTU events for 8148 genes across 206 public RNA-Seq samples, and find that protein sequences are affected in 22% of the cases. The observed DTU events show high consistency across replicates, and reveal reproducible patterns in response to treatment and development. We also demonstrate that genes with different evolutionary ages, expression breadths and functions show large differences in the frequency at which they undergo DTU, and in the effect that these events have on their protein sequences. Finally, we showcase how the generated dataset can be used to explore DTU events for genes of interest or to find genes with specific DTU in samples of interest.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
ALTERNATIVE SPLICING LANDSCAPE, NONSENSE-MEDIATED DECAY, RNA-SEQ, 3-KETOACYL-COA THIOLASES, GENE-EXPRESSION, REVEALS, STRESS, PLANTS, QUANTIFICATION, COMPLEXITY, differential transcript usage, alternative splicing, Arabidopsis thaliana, RNA-Seq, transcriptomics
journal title
PLANT JOURNAL
Plant J.
volume
92
issue
6
pages
1218 - 1231
Web of Science type
Article
Web of Science id
000418227300019
ISSN
0960-7412
1365-313X
DOI
10.1111/tpj.13746
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
8545427
handle
http://hdl.handle.net/1854/LU-8545427
date created
2018-01-18 13:32:26
date last changed
2018-02-13 10:39:37
@article{8545427,
  abstract     = {Alternative splicing and the usage of alternate transcription start- or stop sites allows a single gene to produce multiple transcript isoforms. Most plant genes express certain isoforms at a significantly higher level than others, but under specific conditions this expression dominance can change, resulting in a different set of dominant isoforms. These events of differential transcript usage (DTU) have been observed for thousands of Arabidopsis thaliana, Zea mays and Vitis vinifera genes, and have been linked to development and stress response. However, neither the characteristics of these genes, nor the implications of DTU on their protein coding sequences or functions, are currently well understood. Here we present a dataset of isoform dominance and DTU for all genes in the AtRTD2 reference transcriptome based on a protocol that was benchmarked on simulated data and validated through comparison with a published reverse transciptase-polymerase chain reaction panel. We report DTU events for 8148 genes across 206 public RNA-Seq samples, and find that protein sequences are affected in 22\% of the cases. The observed DTU events show high consistency across replicates, and reveal reproducible patterns in response to treatment and development. We also demonstrate that genes with different evolutionary ages, expression breadths and functions show large differences in the frequency at which they undergo DTU, and in the effect that these events have on their protein sequences. Finally, we showcase how the generated dataset can be used to explore DTU events for genes of interest or to find genes with specific DTU in samples of interest.},
  author       = {Vaneechoutte, Dries and Estrada, April R and Lin, Ying-Chen and Loraine, Ann E and Vandepoele, Klaas},
  issn         = {0960-7412},
  journal      = {PLANT JOURNAL},
  keyword      = {ALTERNATIVE SPLICING LANDSCAPE,NONSENSE-MEDIATED DECAY,RNA-SEQ,3-KETOACYL-COA THIOLASES,GENE-EXPRESSION,REVEALS,STRESS,PLANTS,QUANTIFICATION,COMPLEXITY,differential transcript usage,alternative splicing,Arabidopsis thaliana,RNA-Seq,transcriptomics},
  language     = {eng},
  number       = {6},
  pages        = {1218--1231},
  title        = {Genome-wide characterization of differential transcript usage in Arabidopsis thaliana},
  url          = {http://dx.doi.org/10.1111/tpj.13746},
  volume       = {92},
  year         = {2017},
}

Chicago
Vaneechoutte, Dries, April R Estrada, Ying-Chen Lin, Ann E Loraine, and Klaas Vandepoele. 2017. “Genome-wide Characterization of Differential Transcript Usage in Arabidopsis Thaliana.” Plant Journal 92 (6): 1218–1231.
APA
Vaneechoutte, D., Estrada, A. R., Lin, Y.-C., Loraine, A. E., & Vandepoele, K. (2017). Genome-wide characterization of differential transcript usage in Arabidopsis thaliana. PLANT JOURNAL, 92(6), 1218–1231.
Vancouver
1.
Vaneechoutte D, Estrada AR, Lin Y-C, Loraine AE, Vandepoele K. Genome-wide characterization of differential transcript usage in Arabidopsis thaliana. PLANT JOURNAL. 2017;92(6):1218–31.
MLA
Vaneechoutte, Dries, April R Estrada, Ying-Chen Lin, et al. “Genome-wide Characterization of Differential Transcript Usage in Arabidopsis Thaliana.” PLANT JOURNAL 92.6 (2017): 1218–1231. Print.