Characterization of bacterial intrinsic transcription terminators identified with TERMITe - a novel method for comprehensive analysis of Term-seq data

Abstract

In recent years, Term-seq became a standard experimental approach for high-throughput identification of 3′ ends of bacterial transcripts. It was widely adopted to study transcription termination events and 3′ maturation of bacterial RNAs. Despite widespread utilization, a universal bioinformatics toolkit for comprehensive analysis of Term-seq sequencing data is still lacking. Here, we describe TERMITe, a novel method for the identification of stable 3′ RNA ends based on bacterial Term-seq data. TERMITe works with data obtained from both currently available Term-seq protocols and provides robust identification of the 3′ RNA termini. Unique features of TERMITe include the calculation of the transcription termination efficiency using matched RNA-seq data and the comprehensive annotation of the identified 3′ RNA ends, allowing functional analysis of the results. We have applied TERMITe to the comparative analysis of experimentally validated intrinsic terminators spanning different species across the bacterial domain of life, revealing substantial differences in their sequence and secondary structure. We also provide a complete atlas of experimentally validated intrinsic transcription termination sites for 13 bacterial species: Escherichia coli, Bacillus subtilis, Listeria monocytogenes, Enterococcus faecalis, Synechocystis sp., Streptomyces clavuligerus, Streptomyces griseus, Streptomyces coelicolor, Streptomyces avermitilis, Streptomyces lividans, Streptomyces tsukubaensis, Streptomyces venezuelae, and Zymomonas mobilis.