Discovering and Mapping the Modified Nucleotides That Comprise the Epitranscriptome of mRNA

An important mechanism of gene expression regulation is the regulated modification of nucleotides in messenger RNA (mRNA). These modified nucleotides affect mRNA translation, stability, splicing, and other processes. A cluster of nucleotide modifications is found adjacent to the mRNA cap structure and another set can be found internally within transcripts. The most prominent modifications are methylations of adenosine to form either N 6 -methyladenosine (m 6 A), an internal modified nucleotide, or N 6 ,2 -O-dimethyladenosine (m 6 Am), which is found exclusively at the first templated nucleotide of certain mRNAs. In addition, other rare modified nucleotides have been identified and together these form the epitranscriptomic code of mRNA. In the case of some modified nucleotides, the presence, location, or abundance is a subject of debate. Here, we review the methods that enable the discovery of modified nucleotides and how these approaches can be used to map epitranscriptomic modifications in mRNA. Outline 1 Introduction 2 The history of the detection of methylated nucleotides in mRNA 3 Advantages and challenges of biochemical methods 4 Next-generation sequencing-based technologies for mapping internal nucleotide modifications 5 Mapping the cap epitranscriptome 6 Concluding remarks and further directions