5-azacytidine induces transcriptome changes in Escherichia coli via DNA methylation-dependent and DNA methylation-independent mechanisms. Issue 1 (December 2016)

• Record Type: Journal Article
• Authors: Militello, Kevin; Simon, Robert; Mandarano, Alexandra; DiNatale, Anthony; Hennick, Stacy; Lazatin, Justine; Cantatore, Sarah
• Is Part Of: BMC microbiology. Volume 16:Issue 1(2016)
• Page Start: 1
• Page End: 12
• Publication Date: 2016-12
• Subjects: Stationary phase -- 5-azacytidine -- DNA methylation inhibitor -- DNA methylation -- 5-methylcytosine -- Dcm -- RpoS -- Escherichia coli -- Sodium bisulfite sequencing -- DNA microarray; Microbiology -- Periodicals; 579.05
• DOI: 10.1186/s12866-016-0741-4
• Languages: English
• ISSNs: 1471-2180

Abstract

Abstract Background Escherichia coli K-12 strains contain DNA cytosine methyltransferase (Dcm), which generates 5-methylcytosine at 5′CCWGG3′ sites. Although the role of 5-methylcytosine in eukaryotic gene expression is relatively well described, the role of 5-methylcytosine in bacterial gene expression is largely unknown. Results To identify genes that are controlled by 5-methylcytosine inE. coli, we compared the transcriptomes of cells grown in the absence and presence of the DNA methylation inhibitor 5-azacytidine. We observed expression changes for 63 genes. The majority of the gene expression changes occurred at early stationary phase and were up-regulations. To identify gene expression changes due to a loss of DNA methylation, we compared the expression of selected genes in a wild-type anddcm knockout strain via reverse transcription quantitative PCR. Conclusions Our data indicate that 5-azacytidine can influence gene expression by at least two distinct mechanisms: DNA methylation loss and a mechanism that is independent of DNA methylation loss. In addition, we have identified new targets of 5-methylcytosine-mediated regulation of gene expression. In summary, our data indicate that 5-azacytidine impacts the composition of the bacterial transcriptome, and the primary effect is increased gene expression at early stationary phase.