Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis
Year: 2015
Type: article
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.
Source: The Plant Cell
DOI: 10.1105/tpc.15.00591
Institution: University of Pennsylvania
Language: English
Topic: RNA modifications and cancer
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $4,934
Awards: Global Analysis of RNA-protein Interactions in Plants, Training Program in Cell and Molecular Biology, Structural, Functional, and Evolutionary Analysis of Long Non-coding RNAs in Control of Stress Response and the Epigenome in Diverse Plant Species, CAREER: Global Analysis of RNA-dependent RNA Polymerase Function, Predoctoral Training Program in Genetics, Computational genome-wide RNA profiling using next-generation sequencing
OpenAlex ID: W2177207484