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

The copyright holder for this preprint (which was not peer-reviewed) is . https://doi.org/10.1101/2019.12.18.880849 doi: bioRxiv preprint Detection and confirmation of rRNA processing in E. coli 491 Next, we aimed to analyse the multi-step rRNA processing pathway which is the major RNA 492 maturation pathway in any prokaryotic cell. We first focus on the E. coli data set as the processing 493 of bacterial rRNAs is well characterized 64-66 . Ribosomal RNA in E. coli is transcribed from 7 494 independent rDNA operons, containing the mature rRNAs (16S, 23S and 5S rRNAs) and some 495 tRNAs which are intersped by RNA spacers elements 67 . In agreement with a previous study, 496 transcription of rrnC from two promoters (transcription start sites at -293 and -175) was detected 497 accurately (Fig. 4a,b) 68 . 498