II senses mA and inosine sites and enables targeted nanopore direct RNA-sequencing.

Nanopore direct RNA-sequencing is the first commercialized method to sequence native RNA directly, thus preserving RNA modifications. With the current technology, sequencing is initiated from the 3'end. While for relatively short polyadenylated RNAs, full coverage is obtained, the 5'end of many long RNAs is not sufficiently covered resulting in a substantial 3'bias. We aimed to cleave such RNAs in a sequence-specific manner in order to generate new unique 3'ends that can be targeted by custom adapters. We identified the DNA endonuclease II as a candidate enzyme. II was originally described to cleave double-stranded DNA at GGWCC sites, where W is an A or T. Here, we show that II cleaves also long RNAs in GGACC contexts, if hybridized to a complementary DNA oligo. Furthermore, we provide evidence that II cleavage of RNA is modification sensitive and does not cleave RNA with mA or inosine in the central position. We propose II as "methylation sensor" for the DRACH recognition motif GGACC of the mA writer complex. Finally, we show that II cleavage products are accessible to targeted Nanopore direct RNA-sequencing.