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Published on: May 14, 2020
Changes in mRNA Degradation Efficiencies under Varying Conditions Are Regulated by Multiple Determinants in
Daishin Ueno1, Maki Mikami1, Shotaro Yamasaki1
1Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, 630-0192 Japan.
Abstract:
Multiple mechanisms are involved in gene expression, with mRNA degradation being critical for the control of mRNA accumulation. In plants, although some trans-acting factors and motif sequences have been identified in deadenylation-dependent mRNA degradation, endonucleolytic cleavage-dependent mRNA degradation has not been studied in detail. Previously, we developed truncated RNA-end sequencing (TREseq) in Arabidopsis thaliana and detected G-rich sequence motifs around 5' degradation intermediates. However, it remained to be elucidated whether degradation efficiencies of 5' degradation intermediates in A. thaliana vary among growth conditions and developmental stages. To address this issue, we conducted TREseq of cultured cells under heat stress and at three developmental stages (seedlings, expanding leaves and expanded leaves) and compared 5' degradation intermediates data among the samples. Although some 5' degradation intermediates had almost identical degradation efficiencies, others differed among conditions. We focused on the genes and sites whose degradation efficiencies differed. Changes in degradation efficiencies at the gene and site levels revealed an effect on mRNA accumulation in all comparisons. These changes in degradation efficiencies involved multiple determinants, including mRNA length and translation efficiency. These results suggest that several determinants govern the efficiency of mRNA degradation in plants, helping the organism to adapt to varying conditions by controlling mRNA accumulation.
Insights
Plant mRNA degradation efficiency varies with growth conditions and developmental stages, impacting gene expression control. This study reveals multiple factors influencing mRNA decay, aiding plant adaptation.
Area of Science:
- Plant molecular biology
- Gene expression regulation
- RNA biology
Background:
- mRNA degradation is crucial for controlling gene expression in plants.
- While deadenylation-dependent pathways are known, endonucleolytic cleavage-dependent mRNA degradation requires further investigation.
- Previous work identified G-rich motifs near 5' degradation intermediates using TREseq in Arabidopsis thaliana.
Purpose of the Study:
- To investigate variations in 5' degradation intermediate degradation efficiencies in Arabidopsis thaliana under different growth conditions and developmental stages.
- To identify specific genes and cleavage sites where degradation efficiencies change.
- To understand the impact of these changes on overall mRNA accumulation and plant adaptation.
Main Methods:
- Utilized truncated RNA-end sequencing (TREseq) on cultured Arabidopsis thaliana cells.
- Applied TREseq under heat stress conditions.
- Analyzed TREseq data from three distinct developmental stages: seedlings, expanding leaves, and expanded leaves.
Main Results:
- Degradation efficiencies of 5' mRNA degradation intermediates showed variability across different conditions and developmental stages.
- Specific genes and cleavage sites exhibited altered degradation efficiencies.
- Changes in degradation efficiency directly influenced mRNA accumulation levels.
- mRNA length and translation efficiency were identified as key determinants affecting degradation efficiency.
Conclusions:
- Plant mRNA degradation efficiency is dynamically regulated by multiple determinants, including mRNA length and translation efficiency.
- These regulatory mechanisms allow plants to adapt to environmental stresses and developmental changes by controlling mRNA accumulation.
- Endonucleolytic cleavage-dependent mRNA degradation plays a significant role in plant gene expression plasticity.
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