title: 5-azacytidine induces transcriptome changes in Escherichia coli via DNA methylation-dependent and DNA methylation-independent mechanisms.
abstract: 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.
  
  
  
  To 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.
  
  
  
  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.
authors.affiliation: State University of New York at Geneseo, ISC 357, 1 College Circle, Geneseo, NY, 14454, USA. militello@geneseo.edu.
authors.forename: Kevin T
authors.initials: KT
authors.lastname: Militello
authors.affiliation: State University of New York at Geneseo, ISC 357, 1 College Circle, Geneseo, NY, 14454, USA.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Simon
authors.affiliation: State University of New York at Geneseo, ISC 357, 1 College Circle, Geneseo, NY, 14454, USA.|Cornell University, Ithaca, NY, 14853, USA.
authors.forename: Alexandra H
authors.initials: AH
authors.lastname: Mandarano
authors.affiliation: State University of New York at Geneseo, ISC 357, 1 College Circle, Geneseo, NY, 14454, USA.
authors.forename: Anthony
authors.initials: A
authors.lastname: DiNatale
authors.affiliation: State University of New York at Geneseo, ISC 357, 1 College Circle, Geneseo, NY, 14454, USA.
authors.forename: Stacy M
authors.initials: SM
authors.lastname: Hennick
authors.affiliation: State University of New York at Geneseo, ISC 357, 1 College Circle, Geneseo, NY, 14454, USA.
authors.forename: Justine C
authors.initials: JC
authors.lastname: Lazatin
authors.affiliation: State University of New York at Geneseo, ISC 357, 1 College Circle, Geneseo, NY, 14454, USA.
authors.forename: Sarah
authors.initials: S
authors.lastname: Cantatore
mesh_terms: D044503:5-Methylcytosine / Q000378:metabolism / Q000502:physiology; D001374:Azacitidine / Q000037:antagonists & inhibitors*; D001483:Base Sequence; D018929:Cell Culture Techniques; D003596:Cytosine; D019175:DNA Methylation / Q000187:drug effects*; D004269:DNA, Bacterial; D048168:Escherichia coli K12 / Q000187:drug effects* / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects*; D055786:Gene Knockout Techniques; D005798:Genes, Bacterial; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D012329:RNA, Bacterial / Q000302:isolation & purification; D017421:Sequence Analysis; D059467:Transcriptome / Q000187:drug effects*; D015854:Up-Regulation
chemical_list: D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D012329:RNA, Bacterial; D044503:5-Methylcytosine; D003596:Cytosine; D001374:Azacitidine
keywords: 5-azacytidine; 5-methylcytosine; DNA methylation; DNA methylation inhibitor; DNA microarray; Dcm; Escherichia coli; RpoS; Sodium bisulfite sequencing; Stationary phase