Access Type

Open Access Thesis

Date of Award

January 2013

Degree Type


Degree Name




First Advisor

Andrew Feig


Bacterial small RNAs and the RNA chaperone Hfq play crucial roles in post-transcriptional gene regulation, often as parts of stress-response pathways, but little is known about their roles in regulation of gene transcription. A recent report showed that changes in methylation patterns caused by DNA cytosine methyltransferase (Dcm) were linked to gene regulation occurring during the transition to stationary phase. Here, we show that Dcm involves in the stress responses under nutrient starvation and cold stress. Dcm and Hfq together mediate gene expression under cold stress. Hfq promotes Dcm-catalyzed cytosine methylation at specific sites near the rpoS promoter, which is consistent with the genome-wide analysis and linking known stress response pathways to altered methylation. Overexpressing DsrA, an sRNA induced at low temperature to regulate genes required for cold adaptation, stimulates this DNA methylation behavior, showing that the regulation is sRNA-dependent. This represents the first example of an RNA-directed DNA methylation mechanism in bacteria responsible for modulating gene expression.