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- Title
Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis.
- Authors
Vandivier, Lee E.; Campos, Rafael; Kuksa, Pavel P.; Silverman, Ian M.; Wang, Li-San; Gregory, Brian D.
- Abstract
Posttranscriptional chemical modification of RNA bases is a widespread and physiologically relevant regulator of RNA maturation, stability, and function. While modifications are best characterized in short, noncoding RNAs such as tRNAs, growing evidence indicates that mRNAs and long noncoding RNAs (lncRNAs) are likewise modified. Here, we apply our high-throughput annotation of modified ribonucleotides (HAMR) pipeline to identify and classify modifications that affect Watson-Crick base pairing at three different levels of the Arabidopsis thaliana transcriptome (polyadenylated, small, and degrading RNAs). We find this type of modifications primarily within uncapped, degrading mRNAs and lncRNAs , suggesting they are the cause or consequence of RNA turnover. Additionally, modifications within stable mRNAs tend to occur in alternatively spliced introns, suggesting they regulate splicing. Furthermore, these modifications target mRNAs with coherent functions, including stress responses. Thus, our comprehensive analysis across multiple RNA classes yields insights into the functions of covalent RNA modifications in plant transcriptomes.
- Subjects
RNA splicing; TRANSFER RNA; RNA modification &; restriction; LINCRNA; BASE pairs; NON-coding RNA
- Publication
Plant Cell, 2015, Vol 27, Issue 11, p3024
- ISSN
1040-4651
- Publication type
Article
- DOI
10.1105/tpc.15.00591