RNA-seq analysis to study the effect of CRISPR/dCas9-mediated counter-silencing of the Lsr2-like xenogeneic silencer protein CgpS from C. glutamicum
In this study, we performed RNA-seq analysis to study the effect of CRISPR/dCas9-mediated counter-silencing of the Lsr2-like xenogeneic silencer protein CgpS from C. glutamicum ATCC 13032. Therefore, we studied the genome-wide transcriptome profile of C. glutamicum wild-type cells co-expressing dcas9 and one sgRNA (sgRNA-CS1 or -CS3). Both sgRNAs were designed to guide dCas9 to the CgpS target promoter Pcg1974 from the CGP3 prophage region. The homologous region on the coding strand of sgRNA-CS1 overlapped with the putative CgpS binding motif as well as with the dominant transcriptional start site. In contrast, sgRNA-CS3 bound the template strand in the region of maximal CgpS binding coverage.