Epitranscriptome Analysis: Pinpointing Locations of RNA Modifications - Biocompare

With over 150 known RNA modifications and an increased understanding that these modifications can serve as post-transcriptional regulators, knowing what methods work for epitranscriptome analysis is becoming more important. In a Biocompare article, Caitlin Smith, Ph.D., highlights several ways to study RNA modifications with regional and single-nucleotide resolution. The article includes comments from NEB Associate Director of Research Erbay Yigit, Ph.D. on two methods. For the complete list, refer to Biocompare's full article.

Binding and sequencing methods depend on the modification type and RNA class

Yigit highlights that no one method can map every RNA modification reliably, as there are so many types of modifications. He says that the right method will depend on the type of RNA modification and the class of RNA. Additionally, modifications that are more commonly studied have more detection methods available.

Mass spectrometry is the gold standard

For typical mass spectrometry (LC-MS/MS), RNA is digested into single nucleosides, providing accurate modification levels without modification locations. However, Yigit notes that RNA can be digested into longer fragments to allow for modifications to be mapped to specific locations. The large input RNA amounts needed for LC-MS/MS prevents mass spectrometry from becoming an everyday technique.

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