Please use this identifier to cite or link to this item: https://hdl.handle.net/2440/107004
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Type: Journal article
Title: Rapid recovery gene downregulation during excess-light stress and recovery in Arabidopsis
Author: Crisp, P.
Ganguly, D.
Smith, A.
Murray, K.
Estavillo, G.
Searle, I.
Ford, E.
Bogdanović, O.
Lister, R.
Borevitz, J.
Eichten, S.
Pogson, B.
Citation: The Plant Cell, 2017; 29(8):1836-1863
Publisher: American Society of Plant Biologists
Issue Date: 2017
ISSN: 1040-4651
1532-298X
Statement of
Responsibility: 
Peter A. Crisp, Diep R. Ganguly, Aaron B. Smith, Kevin D. Murray, Gonzalo M. Estavillo, Iain Searle, Ethan Ford, Ozren Bogdanović, Ryan Lister, Justin O. Borevitz, Steven R. Eichten, and Barry J. Pogson
Abstract: Stress recovery may prove to be a promising approach to increase plant performance, and theoretically, mRNA instability may facilitate faster recovery. Transcriptome (RNA-seq, qPCR, sRNA-seq, PARE) and methylome profiling during repeated excess-light stress and recovery was performed at intervals as short as three minutes. We demonstrate that 87% of the stress-upregulated mRNAs analysed exhibit very rapid recovery. For instance, HSP101 abundance declined two-fold every 5.1 minutes. We term this phenomenon Rapid Recovery Gene Downregulation (RRGD), whereby mRNA abundance rapidly decreases promoting transcriptome resetting. Decay constants (k) were modelled using two strategies, linear and non-linear least squares regressions, with the latter accounting for both transcription and degradation. This revealed extremely short half-lives ranging from 2.7-60.0 minutes for 222 genes. Ribosome footprinting using degradome data demonstrated RRGD loci undergo co-translational decay and identified changes in the ribosome stalling index during stress and recovery. However, small RNAs and 5'-3' RNA decay were not essential for recovery of the transcripts examined, nor were any of the six excess light-associated methylome changes. We observed recovery-specific gene expression networks upon return to favorable conditions and six transcriptional memory types. In summary, rapid transcriptome resetting is reported in the context of active recovery and cellular memory.
Keywords: Arabidopsis
Arabidopsis Proteins
RNA, Small Interfering
RNA, Messenger
Gene Expression Profiling
Sequence Analysis, RNA
DNA Methylation
Protein Biosynthesis
Transcription, Genetic
Down-Regulation
Gene Expression Regulation, Plant
Gene Silencing
RNA Stability
Genes, Plant
Nonlinear Dynamics
Light
Half-Life
Time Factors
Stress, Physiological
Genetic Loci
Real-Time Polymerase Chain Reaction
Transcriptome
Description: Published on July 12, 2017
Rights: ©2017 American Society of Plant Biologists. All Rights Reserved. OPEN.
DOI: 10.1105/tpc.16.00828
Grant ID: http://purl.org/au-research/grants/arc/CE140100008
http://purl.org/au-research/grants/arc/DE150101206
http://purl.org/au-research/grants/arc/FT120100862
Appears in Collections:Aurora harvest 3
Genetics publications

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