Julius-von-Sachs-Institute, Department of Molecular Plant Physiology and Biophysics, University of Wuerzburg, Wuerzburg, Germany.
PLoS Genet. 2013;9(2):e1003267. doi: 10.1371/journal.pgen.1003267. Epub 2013 Feb 7.
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.
根癌是在毒性根瘤农杆菌菌株的 T-DNA 整合到植物基因组后形成的。T-DNA 编码的癌基因的表达引发转化植物细胞的增殖和分化。根癌的发生伴随着转录、代谢物水平和生理过程的全局变化。根瘤中高水平的脱落酸 (ABA) 调节干旱胁迫响应基因的表达并介导干旱胁迫适应，这对于类似野生型的肿瘤生长是必不可少的。已经提出了表观遗传过程（如 DNA 甲基化）对根癌发育的影响；然而，尚未对此进行全面研究。在这项研究中，拟南芥根瘤的甲基化模式在全基因组和单个基因水平上进行了分析。亚硫酸氢盐测序分析表明，根瘤中的癌基因 Ipt、IaaH 和 IaaM 未甲基化。然而，这些癌基因容易受到 siRNA 介导的甲基化的影响，这会抑制它们的表达，从而抑制根瘤的生长。用免疫沉淀获得的甲基化 DNA 杂交的基因组芯片显示，根瘤的基因组呈全局超甲基化，而启动子则呈低甲基化。非 CG 甲基化减少的突变体比野生型对照形成更大的肿瘤，表明超甲基化抑制植物肿瘤生长。根瘤和起源于其的茎组织的差异甲基化模式与转录变化相关。已知受 ABA 转录抑制并在根瘤中甲基化的基因在拟南芥用 ABA 处理后，其启动子被甲基化。这表明根瘤中高水平的 ABA 可能介导 DNA 甲基化并调节参与干旱胁迫保护的基因的表达。总之，我们的研究提供了证据表明，表观遗传过程调节基因表达、生理过程和根瘤肿瘤的发生。
