Nanopore-based native RNA sequencing provides insights into prokaryotic transcription, operon structures, rRNA maturation and modifications

Felix Grünberger; Robert Knüppel; Michael Jüttner; Martin Fenk; Andreas Borst; Robert Reichelt; Winfried Hausner; Jörg Soppa; Sebastien Ferreira-Cerca; Dina Grohmann

Next, we applied the described de novo and sample-compare model to the full 16S rRNA of all three 600 organisms and compared the results to positions known from literature 48,49 . Applying a probability 601 threshold of 0.5, we found that 60% (de novo) and 1.89% (sample-compare, 28 bases) of the bases 602 in the 16S rRNA are modified in H. volcanii (Fig. 6e) , which emphasizes the better performance of 603 the sample-compare model by the vastly reduced number of false-positivly detected RNA 604 modifications. 10 of the 28 predicted bases (please note that approximately five bases contribute 605 to the signal in the nanopore and that a base single modification therefore influences the current 606 signal at the surrounding bases as well) can be assigned to known base modifications at positions 607 910, 1430 and 1450/1451 49 . Using the same threshold for E. coli (de novo: 50.5%, sample-compare: 608 the author/funder. All rights reserved. No reuse allowed without permission.