Cold-dependent expression and alternative splicing of Arabidopsis long non-coding RNAs

Calixto, C. P.G., Tzioutziou, N. A., James, A. B. , Hornyik, C., Guo, W., Zhang, R., Nimmo, H. G. and Brown, J. W.S. (2019) Cold-dependent expression and alternative splicing of Arabidopsis long non-coding RNAs. Frontiers in Plant Science, 10, 235. (doi: 10.3389/fpls.2019.00235) (PMID:30891054) (PMCID:PMC6413719)

[img]
Preview
Text
190176.pdf - Published Version
Available under License Creative Commons Attribution.

2MB

Abstract

Plants re-program their gene expression when responding to changing environmental conditions. Besides differential gene expression, extensive alternative splicing (AS) of pre-mRNAs and changes in expression of long non-coding RNAs (lncRNAs) are associated with stress responses. RNA-sequencing of a diel time-series of the initial response of Arabidopsis thaliana rosettes to low temperature showed massive and rapid waves of both transcriptional and AS activity in protein-coding genes. We exploited the high diversity of transcript isoforms in AtRTD2 to examine regulation and post-transcriptional regulation of lncRNA gene expression in response to cold stress. We identified 135 lncRNA genes with cold-dependent differential expression (DE) and/or differential alternative splicing (DAS) of lncRNAs including natural antisense RNAs, sORF lncRNAs, and precursors of microRNAs (miRNAs) and trans-acting small-interfering RNAs (tasiRNAs). The high resolution (HR) of the time-series allowed the dynamics of changes in transcription and AS to be determined and identified early and adaptive transcriptional and AS changes in the cold response. Some lncRNA genes were regulated only at the level of AS and using plants grown at different temperatures and a HR time-course of the first 3 h of temperature reduction, we demonstrated that the AS of some lncRNAs is highly sensitive to small temperature changes suggesting tight regulation of expression. In particular, a splicing event in TAS1a which removed an intron that contained the miR173 processing and phased siRNAs generation sites was differentially alternatively spliced in response to cold. The cold-induced reduction of the spliced form of TAS1a and of the tasiRNAs suggests that splicing may enhance production of the siRNAs. Our results identify candidate lncRNAs that may contribute to the regulation of expression that determines the physiological processes essential for acclimation and freezing tolerance.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Nimmo, Professor Hugh and James, Dr Allan
Authors: Calixto, C. P.G., Tzioutziou, N. A., James, A. B., Hornyik, C., Guo, W., Zhang, R., Nimmo, H. G., and Brown, J. W.S.
College/School:College of Medical Veterinary and Life Sciences > School of Molecular Biosciences
Journal Name:Frontiers in Plant Science
Publisher:Frontiers Media
ISSN:1664-462X
ISSN (Online):1664-462X
Copyright Holders:Copyright © 2019 Calixto, Tzioutziou, James, Hornyik, Guo, Zhang, Nimmo and Brown
First Published:First published in Frontiers in Plant Science 10: 235
Publisher Policy:Reproduced under a Creative Commons License

University Staff: Request a correction | Enlighten Editors: Update this record

Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
607041Mechanisms and function of alternative splicing in the plant circadian clockHugh NimmoBiotechnology and Biological Sciences Research Council (BBSRC)BB/K006835/1RI MOLECULAR CELL & SYSTEMS BIOLOGY