Document Type
Technical Report
Date of this Version
10-2016
Publication Source
The Plant Cell
Volume
28
Issue
10
Start Page
2385
Last Page
2397
DOI
10.1105/tpc.16.00456
Abstract
RNA turnover is necessary for controlling proper mRNA levels posttranscriptionally. In general, RNA degradation is via exoribonucleases that degrade RNA either from the 5′ end to the 3′ end, such as XRN4, or in the opposite direction by the multisubunit exosome complex. Here, we use genome-wide mapping of uncapped and cleaved transcripts to reveal the global landscape of cotranslational mRNA decay in the Arabidopsis thaliana transcriptome. We found that this process leaves a clear three nucleotide periodicity in open reading frames. This pattern of cotranslational degradation is especially evident near the ends of open reading frames, where we observe accumulation of cleavage events focused 16 to 17 nucleotides upstream of the stop codon because of ribosomal pausing during translation termination. Following treatment of Arabidopsis plants with the translation inhibitor cycloheximide, cleavage events accumulate 13 to 14 nucleotides upstream of the start codon where initiating ribosomes have been stalled with these sequences in their P site. Further analysis in xrn4 mutant plants indicates that cotranslational RNA decay is XRN4 dependent. Additionally, studies in plants lacking CAP BINDING PROTEIN80/ABA HYPERSENSITIVE1, the largest subunit of the nuclear mRNA cap binding complex, reveal a role for this protein in cotranslational decay. In total, our results demonstrate the global prevalence and features of cotranslational RNA decay in a plant transcriptome.
Copyright/Permission Statement
Copyright American Society of Plant Biologists. Reproduced with permission.
Recommended Citation
Yu, X., Willmann, M. R., Anderson, S. J., & Gregory, B. D. (2016). Genome-Wide Mapping of Uncapped and Cleaved Transcripts Reveals a Role for the Nuclear mRNA Cap-Binding Complex in Cotranslational RNA Decay in Arabidopsis. The Plant Cell, 28 (10), 2385-2397. http://dx.doi.org/10.1105/tpc.16.00456
Additional Files
Supplemental_Data_Genome-wide mapping of uncapped and cleaved transcripts.pdf (2804 kB)Supplemental_Data_Set_1_Genome-wide mapping of uncapped and cleaved transcripts.xlsx (40 kB)
Supplemental_Data_Set_2_Genome-wide mapping of uncapped and cleaved transcripts.xlsx (17 kB)
Supplemental_Data_Set_3_Genome-wide mapping of uncapped and cleaved transcripts.xlsx (79 kB)
Included in
Biology Commons, Genetics and Genomics Commons, Nucleic Acids, Nucleotides, and Nucleosides Commons
Date Posted: 14 July 2017
This document has been peer reviewed.