Date of this Version
The Plant Cell
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.
Copyright American Society of Plant Biologists. Reproduced with permission.
Vandivier, L. E., Campos, R., Kuksa, P. P., Silverman, I. M., Wang, L., & Gregory, B. D. (2015). Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidposis. The Plant Cell, 27 (11), 3024-3037. http://dx.doi.org/10.1105/tpc.15.00591
Additional FilesSupplemental_Data_Chemical modifications mark alternatively spliced.pdf (8616 kB)
Supplemental_File_1_Chemical modifications mark alternatively spliced.csv (107 kB)
Supplemental_File_2_Chemical modifications mark alternatively spliced.csv (182 kB)
Date Posted: 14 July 2017
This document has been peer reviewed.