Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis

Plant Cell. 2015 Nov;27(11):3024-37. doi: 10.1105/tpc.15.00591. Epub 2015 Nov 11.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing / genetics*
  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Base Pairing / genetics
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • Molecular Sequence Annotation
  • RNA Caps / metabolism*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Reproducibility of Results
  • Ribonucleotides / metabolism
  • Stress, Physiological / genetics
  • Transcriptome / genetics


  • RNA Caps
  • RNA, Messenger
  • Ribonucleotides