Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis

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 highthroughput annotation of modified ribonucleotides (HAMR) pipeline to identify and classify modifications that affect WatsonCrick 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.

Polysomes, Stress Granules, and Processing Bodies: A Dynamic Triumvirate Controlling Cytoplasmic mRNA Fate and Function

“…We also did not consider nuclear mechanisms of transcript turnover that can involve CBP80 . Nor did we consider N 6 -methyladenosine and other modifications of specific nucleotides (the epitranscriptome; Luo et al, 2014;Vandivier et al, 2015;Zuber et al, 2016;David et al, 2017), which may influence RNA-protein interactions and, hence, the nuclear or cytoplasmic fates of individual transcripts. The wealth of new discoveries of the dynamic cytoplasmic mRNP triumvirate has unearthed new challenging questions (see Outstanding Questions) that may provide insights relevant to other eukaryotes or of value to crop improvement.…”

POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins

“…Most previous studies have focused on cis -regulation, the epigenome, the transcriptome, and the proteome, leaving post-transcriptional regulation not fully explored and connected with existing knowledge. Although RNA splicing has been well-studied, other post-regulatory signatures, such as RNA modification and RNA editing, have not been profiled until recently (3–5). Furthermore, most studies of genomic variants (e.g.…”

“…Clicking on the genomic positions will direct the user to the UCSC Genome Browser, which will display any associated binding sites and regulatory events (4). In ‘Structure’ visualization mode, we provide RNA structural profiling data (5) and predicted RNA secondary structures based on these data (6). In ‘RBP’ search mode, we provide the sequence motifs (7) and structural preferences (8) of the RBP.…”

METTL2 forms a complex with the DALRD3 anticodon-domain binding protein to catalyze formation of 3-methylcytosine in specific arginine tRNA isoacceptors

“…In addition, human METTL2A and METTL2B are required for m3C formation in the arginine tRNA isoacceptors, tRNA-Arg-CCU and Arg-UCU. The presence of m3C in tRNA-Arg-CCU and Arg-UCU has been detected in multiple mammalian species but not in yeast or plants (Arimbasseri et al, 2016b;Baum and Beier, 1998;Clark et al, 2016;Keith, 1984;Vandivier et al, 2015), suggesting that METTL2A/B-catalyzed modification of arginine tRNAs evolved within the animal kingdom. However, the molecular mechanism by which METTL2A and 2B recognizes only a subset of arginine tRNA substrates as well as the biological roles of m3C modification in mammals are unknown.…”