Fig. 9: Conserved 3’ termini of regulatory elements and sRNAs in bacteria.
From: TRS: a method for determining transcript termini from RNAtag-seq sequencing data
Presented is the read coverage around conserved 3’ termini of a regulatory element and sRNAs in E. coli K-12 and four other bacteria: K. pneumoniae, S. enterica, ETEC, and S. flexneri. The 3’ terminus (marked by a diamond arrow) was determined by applying TRS to previously published RNAtag-seq data for the different bacteria11. a A premature 3’ terminus identified upstream to mgtA CDS. b The 3’ terminus matching the sRNA FtsO in E. coli K-127. c The 3’ terminus matching the sRNA AceK-int in E. coli K-12, encoded within the CDS of aceK7,16. Presented 3’ termini are based on data of growth conditions that showed the highest read coverage and exhibited the most consistent results across the different bacteria. The growth conditions per gene and bacterium are as follows: mgtA – S. enterica, K. pneumoniae, and S. flexneri (acidic stress), ETEC (nutritional downshift). FtsO – S. enterica, S. flexneri, and ETEC (control), K. pneumoniae (heat shock). aceK – S. enterica, K. pneumoniae, and ETEC (nutritional downshift), S. flexneri (acidic stress), EPEC (stationary phase), E. coli K-12 (exponential phase). The read coverages of K. pneumoniae, S. enterica and EPEC are based on paired-end sequencing, and for ETEC, S. flexneri, and E. coli K-12 on single-end sequencing.
