Cold-Dependent Expression and Alternative Splicing of Arabidopsis Long Non-coding RNAs

被引:49
作者
Calixto, Cristiane P. G. [1 ]
Tzioutziou, Nikoleta A. [1 ]
James, Allan B. [2 ]
Hornyik, Csaba [3 ]
Guo, Wenbin [1 ,4 ]
Zhang, Runxuan [4 ]
Nimmo, Hugh G. [2 ]
Brown, John W. S. [1 ,3 ]
机构
[1] Univ Dundee, Sch Life Sci, Plant Sci Div, Dundee, Scotland
[2] Univ Glasgow, Coll Med Vet & Life Sci, Inst Mol Cell & Syst Biol, Glasgow, Lanark, Scotland
[3] James Hutton Inst, Cell & Mol Sci, Dundee, Scotland
[4] James Hutton Inst, Informat & Computat Sci, Dundee, Scotland
来源
FRONTIERS IN PLANT SCIENCE | 2019年 / 10卷
基金
英国生物技术与生命科学研究理事会;
关键词
long non-coding RNA; primary microRNA; alternative splicing; diel time-course; high-resolution RNA-seq; cold transcriptome; GENOME-WIDE IDENTIFICATION; TRANS-ACTING SIRNAS; NONSENSE-MEDIATED DECAY; GENE-EXPRESSION; FUNCTIONAL PREDICTION; RESPONSIVE LNCRNAS; CIRCADIAN CLOCK; LOW-TEMPERATURE; ANTISENSE RNA; SALT STRESS;
D O I
10.3389/fpls.2019.00235
中图分类号
Q94 [植物学];
学科分类号
071001 ;
摘要
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.
引用
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页数:16
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