Crown gall tumors develop after integration of the T-DNA of virulent 
Agrobacterium tumefaciens strains into the plant genome. Expression of the 
T-DNA-encoded oncogenes triggers proliferation and differentiation of 
transformed plant cells. Crown gall development is known to be accompanied by 
global changes in transcription, metabolite levels, and physiological processes. 
High levels of abscisic acid (ABA) in crown galls regulate expression of drought 
stress responsive genes and mediate drought stress acclimation, which is 
essential for wild-type-like tumor growth. An impact of epigenetic processes 
such as DNA methylation on crown gall development has been suggested; however, 
it has not yet been investigated comprehensively. In this study, the methylation 
pattern of Arabidopsis thaliana crown galls was analyzed on a genome-wide scale 
as well as at the single gene level. Bisulfite sequencing analysis revealed that 
the oncogenes Ipt, IaaH, and IaaM were unmethylated in crown galls. 
Nevertheless, the oncogenes were susceptible to siRNA-mediated methylation, 
which inhibited their expression and subsequently crown gall growth. Genome 
arrays, hybridized with methylated DNA obtained by immunoprecipitation, revealed 
a globally hypermethylated crown gall genome, while promoters were rather 
hypomethylated. Mutants with reduced non-CG methylation developed larger tumors 
than the wild-type controls, indicating that hypermethylation inhibits plant 
tumor growth. The differential methylation pattern of crown galls and the stem 
tissue from which they originate correlated with transcriptional changes. Genes 
known to be transcriptionally inhibited by ABA and methylated in crown galls 
became promoter methylated upon treatment of A. thaliana with ABA. This suggests 
that the high ABA levels in crown galls may mediate DNA methylation and regulate 
expression of genes involved in drought stress protection. In summary, our 
studies provide evidence that epigenetic processes regulate gene expression, 
physiological processes, and the development of crown gall tumors.