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

MinKNOW and the run can be canceled allowing the loading of a new library (see Supplementary 379 Nanopore native RNA-seq data must be corrected by 12 nucleotides (Fig. 2b ). It has been observed 405 previously that about 12 nt are missing at the 5'-end of the sequenced RNAs. This observation can 406 be explained by a lack of control of the RNA translocation speed after the motor protein falls off 407 the 5´ end of the RNA (see Supplementary Figure 6a ) 56,57 . Promoter analysis confirmed the 408 presence of well-known sequence motifs of bacterial and archaeal promoters 27,31,58 . This includes 409 the TATA-box and B-recognition element (BRE) characteristic for archaeal promoters and the -10 410 element in bacterial promoters (Fig. 2d) . The -35 element in E. coli has been previously shown to 411 be less enriched compared to the -10 site 5 , which might explain why this element cannot be 412 detected in the Nanopore data set. To analyse TSSs in more detail, we compared the 5´ UTR lengths 413 for all genes with predicted TSS in ONT and Illumina data sets (see Supplementary Figure 6b ,c,d). 414