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Translational landscape of protein-coding and non-protein-coding RNAs upon light exposure in Arabidopsis

Translational landscape of protein-coding and non-protein-coding RNAs upon light exposure in... Abstract Light is one of the most essential environmental clues for plant growth and morphogenesis. Exposure to blue monochromatic light from darkness is a turning point for plant biological activity and as a result dramatic changes in gene expression occur. To understand the translational impacts of blue light, we have performed ribosome profiling analysis and called translated ORFs de novo within not only mRNAs but also non-coding RNAs. Translation efficiency of 3,823 protein-coding ORFs, such as nuclear chloroplast-related genes, was up-regulated by blue light exposure. Moreover, the translational activation of the microRNA biogenesis-related genes, DCL1 and HYL1, was induced by blue light. Considering the 3-nt codon periodicity of ribosome footprints, a few hundred short ORFs (sORFs) lying on non-coding RNAs (ncRNAs) and upstream ORFs (uORFs) on mRNAs were found that had differential translation status between blue light and dark. uORFs are known to have a negative effect on expression of the main ORFs (mORFs) on the same mRNAs. Our analysis suggests that translation of uORFs is likely to be more stimulated than that of the corresponding mORFs, and uORF-mediated translational repression of the mORFs in five genes was induced by blue light exposure. With data-based annotation of the ORFs, our analysis provides insights into the translatome in response to environmental changes, such as those involving light. This content is only available as a PDF. Author notes Yukio Kurihara, Yuko Makita; these authors contributed equally. © The Author(s) 2019. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model) http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Plant and Cell Physiology Oxford University Press

Translational landscape of protein-coding and non-protein-coding RNAs upon light exposure in Arabidopsis

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References (73)

Publisher
Oxford University Press
Copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com
ISSN
0032-0781
eISSN
1471-9053
DOI
10.1093/pcp/pcz219
Publisher site
See Article on Publisher Site

Abstract

Abstract Light is one of the most essential environmental clues for plant growth and morphogenesis. Exposure to blue monochromatic light from darkness is a turning point for plant biological activity and as a result dramatic changes in gene expression occur. To understand the translational impacts of blue light, we have performed ribosome profiling analysis and called translated ORFs de novo within not only mRNAs but also non-coding RNAs. Translation efficiency of 3,823 protein-coding ORFs, such as nuclear chloroplast-related genes, was up-regulated by blue light exposure. Moreover, the translational activation of the microRNA biogenesis-related genes, DCL1 and HYL1, was induced by blue light. Considering the 3-nt codon periodicity of ribosome footprints, a few hundred short ORFs (sORFs) lying on non-coding RNAs (ncRNAs) and upstream ORFs (uORFs) on mRNAs were found that had differential translation status between blue light and dark. uORFs are known to have a negative effect on expression of the main ORFs (mORFs) on the same mRNAs. Our analysis suggests that translation of uORFs is likely to be more stimulated than that of the corresponding mORFs, and uORF-mediated translational repression of the mORFs in five genes was induced by blue light exposure. With data-based annotation of the ORFs, our analysis provides insights into the translatome in response to environmental changes, such as those involving light. This content is only available as a PDF. Author notes Yukio Kurihara, Yuko Makita; these authors contributed equally. © The Author(s) 2019. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Journal

Plant and Cell PhysiologyOxford University Press

Published: Mar 1, 2020

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