5-azacytidine induces transcriptome changes in Escherichia coli via DNA methylation-dependent and DNA methylation-independent mechanisms

BMC Microbiology

Research Article

Kevin T. Militello¹  Robert D. Simon¹  Justine C. Lazatin¹  Anthony DiNatale¹  Stacy M. Hennick¹  Sarah Cantatore¹  Alexandra H. Mandarano² 

[1] State University of New York at Geneseo, ISC 357, 1 College Circle, 14454, Geneseo, NY, USA;State University of New York at Geneseo, ISC 357, 1 College Circle, 14454, Geneseo, NY, USA;Cornell University, 14853, Ithaca, NY, USA;

关键词: Stationary phase;    5-azacytidine;    DNA methylation inhibitor;    DNA methylation;    5-methylcytosine;    Dcm;    RpoS;    Escherichia coli;    Sodium bisulfite sequencing;    DNA microarray;   

DOI  :  10.1186/s12866-016-0741-4

 received in 2015-10-14, accepted in 2016-06-14,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundEscherichia 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.ResultsTo identify genes that are controlled by 5-methylcytosine in E. 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 and dcm knockout strain via reverse transcription quantitative PCR.ConclusionsOur 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.

【 授权许可】

CC BY   
© The Author(s). 2016