Fingerprints of modified RNA bases from deep sequencing profiles

Posttranscriptional modifications of RNA bases are found not only in many noncoding RNAs but also have recently been identified in coding (messenger) RNAs as well. They require complex and laborious methods to locate, and many still lack methods for localized detection. Here Stanford University researchers test the ability of next-generation sequencing (NGS) to detect and distinguish between ten modified bases in synthetic RNAs. They compare ultra-deep sequencing patterns of modified bases, including miscoding, insertions and deletions (indels), and truncations, to unmodified bases in the same contexts. The data show widely varied responses to modification, ranging from no response, to high levels of mutations, insertions, deletions, and truncations. The patterns are distinct for several of the modifications, and suggest the future use of ultra-deep sequencing as a fingerprinting strategy for locating and identifying modifications in cellular RNAs.

Structures of canonical (shaded) and modified RNA bases in this study (modifications highlighted in red). MMLV reverse transcriptase (PDB: 4mh8), from which Super Script IV was derived, is shown at right.