The expanding role of RNA modifications in plant RNA polymerase II transcripts: highlights and perspectives

Regulation of gene expression is a complicated process based on the coordination of many different pathways, including epigenetic control of chromatin state, transcription, RNA processing, export of mature transcripts to the cytoplasm, and their translation into proteins. In recent years, with the development of high-throughput sequencing techniques, the importance of RNA modifications in gene expression has added another layer to this regulatory landscape. To date, >150 different types of RNA modifications have been found. Most RNA modifications, such as N6-methyladenosine (m6A) and pseudouridine (Ψ), were initially identified in highly abundant structural RNAs, such as rRNAs, tRNAs, and small nuclear RNAs (snRNAs). Current methods provide the opportunity to identify new types of modifications and to precisely localize them not only in highly expressed RNAs but also in mRNA and small RNA molecules. The presence of modified nucleotides in protein-coding transcripts can affect their stability, localization, and further steps of pre-mRNA maturation. Finally, it may affect the quality and quantity of protein synthesis. In plants, the epitranscriptomic field is still narrow, but the number of reports is growing rapidly. This review presents highlights and perspectives of plant epitranscriptomic modifications, focusing on various aspects of modifications of RNA polymerase II transcripts and their influence on RNA fate.