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

Currently, no reference data sets for the archaeal organisms were available, the distribution of 3´ 424 untranslated regions (3´UTRs) in E. coli ONT data closely resembles the data from a previous Term-425 seq study 26 . Untranslated regions at the 3´end of an annotated transcript are longer and more 426 uniformly distributed in E. coli than in the two archaeal species (Fig. 2c) As observed for E. coli termination sequences, Cytosines are enriched over Guanosine adjacent to 451 the TTS in P. furiosus (Fig. 2e) . Termination motifs detected in the E. coli data set cover both 452 intrinsic (poly(U)) and Rho-dependent termination signatures (see Supplementary Fig. 7a ,b) 26 . We 453 classified the stem-loop forming motif as Rho-dependent signatures, as these were not enriched in 454 the poly(U) terminated genes. However, the stem-loops could potentially also represent 455 processing or pause sites. 456 457