title: Deciphering the epitranscriptome: A green perspective.
abstract: The advent of high-throughput sequencing technologies coupled with new detection methods of RNA modifications has enabled investigation of a new layer of gene regulation - the epitranscriptome. With over 100 known RNA modifications, understanding the repertoire of RNA modifications is a huge undertaking. This review summarizes what is known about RNA modifications with an emphasis on discoveries in plants. RNA ribose modifications, base methylations and pseudouridylation are required for normal development in Arabidopsis, as mutations in the enzymes modifying them have diverse effects on plant development and stress responses. These modifications can regulate RNA structure, turnover and translation. Transfer RNA and ribosomal RNA modifications have been mapped extensively and their functions investigated in many organisms, including plants. Recent work exploring the locations, functions and targeting of N6-methyladenosine (m6A), 5-methylcytosine (m5C), pseudouridine (Ψ), and additional modifications in mRNAs and ncRNAs are highlighted, as well as those previously known on tRNAs and rRNAs. Many questions remain as to the exact mechanisms of targeting and functions of specific modified sites and whether these modifications have distinct functions in the different classes of RNAs.
authors.affiliation: School of Biological Sciences, The University of Adelaide, South Australia,, 5005, Australia.|School of Agriculture, Food and Wine, The Waite Research Institute, The University of Adelaide, South Australia,, 5005, Australia.
authors.forename: Alice
authors.initials: A
authors.lastname: Burgess
authors.affiliation: School of Biological Sciences, The University of Adelaide, South Australia,, 5005, Australia.|School of Agriculture, Food and Wine, The Waite Research Institute, The University of Adelaide, South Australia,, 5005, Australia.
authors.forename: Rakesh
authors.initials: R
authors.lastname: David
authors.affiliation: School of Biological Sciences, The University of Adelaide, South Australia,, 5005, Australia. iain.searle@adelaide.edu.au.|School of Agriculture, Food and Wine, The Waite Research Institute, The University of Adelaide, South Australia,, 5005, Australia. iain.searle@adelaide.edu.au.|The University of Adelaide and Shanghai Jiao Tong University Joint International Centre for Agriculture and Health, Joint International Research Laboratory of Metabolic & Developmental Sciences, Adelaide, Australia. iain.searle@adelaide.edu.au.
authors.forename: Iain Robert
authors.initials: IR
authors.lastname: Searle
mesh_terms: D044503:5-Methylcytosine / Q000378:metabolism; D000241:Adenosine / Q000031:analogs & derivatives / Q000378:metabolism; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing; D011560:Pseudouridine / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*
chemical_list: D011560:Pseudouridine; D044503:5-Methylcytosine; C010223:N-methyladenosine; D000241:Adenosine
keywords: Arabidopsis; N6-methyladenosine (m6A); Pseudouridine (Ψ); RNA 5-methylcytosine (m5C); RNA modifications; epitranscriptome