RNA-sequencing based analysis of Listeria monocytogenes 10403S::?BCHL Prha-sigH and ?BCHL Prha

In this study, RNA-seq was used to compare the transcriptomes of Listeria monocytogenes 10403S::?BCHL Prha-sigH and ?BCHL Prha. RNA-seq was performed on ?BCHL Prha-sigH and ?BCHL Prha RNA samples representing three independent biological replicates at log phase in Brain Heart Infusion (BHI) broth under rhamnose induction. Indexed and purified cDNA libraries (6 libraries including 3 replicates for 2 strains) were loaded together onto an independent flow cell without any other samples; sequencing was carried out by running Hiseq 2500 (single-end, 150-bp per read). Reads alignment was carried out using the Burrows-Wheeler Aligner (BWA). Differential expression of genes in different strains was statistically assessed using the BaySeq method. To identify sigH-dependent promoters, a new method of moving sliding windows of 50 nt along the whole genome was used to compare the normalized RNA-seq coverage (NRC) between the two strains. Using the standard whole gene differential expression analysis, significant upregulation of 5 genes in 4 operons was found in the sigH overexpressing strain. While with the sliding windiow analysis, 2 additional sH-dependent promoters were identified. Our results show that three sH-dependent transcritption units that encode competence proteins, including the comEABC , comGABCDEFG and coiA. Overall design: Transcriptome profiles of L. monocytogenes 10403S::?BCHL Prha-sigH and ?BCHL Prha were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500.