title: 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 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.
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 Cell and Molecular Biology Graduate Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104.
authors.forename: Lee E
authors.initials: LE
authors.lastname: Vandivier
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104.
authors.forename: Rafael
authors.identifier: http://orcid.org/0000-0002-1395-8571
authors.initials: R
authors.lastname: Campos
authors.affiliation: Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104 Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104.
authors.forename: Pavel P
authors.identifier: http://orcid.org/0000-0003-2248-6403
authors.initials: PP
authors.lastname: Kuksa
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 Cell and Molecular Biology Graduate Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104.
authors.forename: Ian M
authors.initials: IM
authors.lastname: Silverman
authors.affiliation: Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104 Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104.
authors.forename: Li-San
authors.initials: LS
authors.lastname: Wang
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104 Cell and Molecular Biology Graduate Program, University of Pennsylvania, Philadelphia, Pennsylvania 19104 bdgregor@sas.upenn.edu.
authors.forename: Brian D
authors.identifier: http://orcid.org/0000-0001-7532-0138
authors.initials: BD
authors.lastname: Gregory
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D020029:Base Pairing / Q000235:genetics; D057809:HEK293 Cells; D006367:HeLa Cells; D006801:Humans; D058977:Molecular Sequence Annotation; D012315:RNA Caps / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D012265:Ribonucleotides / Q000378:metabolism; D013312:Stress, Physiological / Q000235:genetics; D059467:Transcriptome / Q000235:genetics
chemical_list: D012315:RNA Caps; D012333:RNA, Messenger; D012265:Ribonucleotides