Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria (Ju et al., Nat Microbiol 2019)
Full-length RNA profiling of bacterial transcriptomes by SEnd-seq. A sample data track of the log-phase E. coli transcriptome showing the comparison between standard RNA-seq and SEnd-seq. Dashed lines highlight the sharp boundaries of transcripts delineated by SEnd-seq, which are obscured in standard RNA-seq.
The ability to determine full-length nucleotide composition of individual RNA molecules is essential for understanding the architecture and function of a transcriptome. Commonly used short-read RNA-seq methods require fragmentation of RNA, which decouples the 5’ end of an RNA molecule from its 3’ end. We have developed SEnd-seq (simultaneous 5′- and 3′-end RNA sequencing) that simultaneously maps transcript start and end sites with single-nucleotide resolution. We apply this method to characterize the Escherichia coli transcriptome and find the pervasive occurrence of overlapping bidirectional terminators located between opposing gene pairs or between a gene and an opposing non-coding RNA. We further show that convergent transcription is the main driver for efficient bidirectional termination. This finding suggests an underappreciated role of RNA polymerase collisions in transcriptional regulation and showcases SEnd-seq as a valuable tool for discovering new biology.