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 (m6 A), 5-methylcytosine (m5 C), 
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.