As researchers open up to the reality of RNA modification, an expanded epitranscriptomics toolbox takes shape.
THE RNA CODE COMES INTO FOCUSBY K E L LY R A E C H I I n 2004, oncologist Gideon Rechavi at Tel Aviv University in Israel and his colleagues compared all the human genomic DNA sequences then available with their corresponding messenger RNAs -the molecules that carry the information needed to make a protein from a gene. They were looking for signs that one of the nucleotide building blocks in the RNA sequence, called adenosine (A), had changed to another building block called inosine (I). This ' A-to-I editing' can alter a protein's coding sequence, and, in humans, is crucial for keeping the innate immune response in check. "It sounds simple, but in real life it was really complicated," Rechavi recalls. "Several groups had tried it before and failed" because sequencing mistakes and single-nucleotide mutations had made the data noisy. But using a new bioinformatics approach, his team uncovered thousands of sites in the transcriptome -the complete set of mRNAs found in an organism or cell population -and later studies upped the number into the millions 1 . Inosine is something of a special case: researchers can readily detect this chink in the armour by comparing DNA and RNA sequences. But at least one-quarter of our mRNAs harbour chemical tags -decorations to the A, C, G and U nucleotides -that are invisible to today's sequencing technologies. (Similar chemical tags, called epigenetic markers, are also found on DNA.) Researchers aren't sure what these chemical changes in RNA do, but they're trying to find out.A wave of studies over the past five yearsmany of which focus on a specific RNA mark called N 6 -methyladenosine (m 6 A) -have mapped these alterations across transcriptomes and demonstrated their importance to health and disease. But the problem is vast: these marks coat not only mRNA but other RNA transcripts as well, and they cut across TECHNOLOGY FEATURE © 2 0 1 7 M a c m i l l a n P u b l i s h e r s L i m i t e d , p a r t o f S p r i n g e r N a t u r e . A l l r i g h t s r e s e r v e d .