Anderson Sarah N, Zynda Gregory J, Song Jawon, Han Zhaoxue, Vaughn Matthew W, Li Qing, Springer Nathan M
Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108.
Texas Advanced Computing Center, University of Texas, Austin, TX 78758.
G3 (Bethesda). 2018 May 31;8(6):1921-1932. doi: 10.1534/g3.118.200284.
DNA methylation is a chromatin modification that can provide epigenetic regulation of gene and transposon expression. Plants utilize several pathways to establish and maintain DNA methylation in specific sequence contexts. The chromomethylase (CMT) genes maintain CHG (where H = A, C or T) methylation. The RNA-directed DNA methylation (RdDM) pathway is important for CHH methylation. Transcriptome analysis was performed in a collection of lines carrying mutant alleles for CMT or RdDM-associated genes. While the majority of the transcriptome was not affected, we identified sets of genes and transposon families sensitive to context-specific decreases in DNA methylation in mutant lines. Many of the genes that are up-regulated in CMT mutant lines have high levels of CHG methylation, while genes that are differentially expressed in RdDM mutants are enriched for having nearby mCHH islands, implicating context-specific DNA methylation in the regulation of expression for a small number of genes. Many genes regulated by CMTs exhibit natural variation for DNA methylation and transcript abundance in a panel of diverse inbred lines. Transposon families with differential expression in the mutant genotypes show few defining features, though several families up-regulated in RdDM mutants show enriched expression in endosperm tissue, highlighting the potential importance for this pathway during reproduction. Taken together, our findings suggest that while the number of genes and transposon families whose expression is reproducibly affected by mild perturbations in context-specific methylation is small, there are distinct patterns for loci impacted by RdDM and CMT mutants.
DNA甲基化是一种染色质修饰，可对基因和转座子表达进行表观遗传调控。植物利用多种途径在特定序列背景下建立和维持DNA甲基化。染色体甲基转移酶（CMT）基因维持CHG（其中H = A、C或T）甲基化。RNA介导的DNA甲基化（RdDM）途径对CHH甲基化很重要。对一组携带CMT或RdDM相关基因突变等位基因的株系进行了转录组分析。虽然转录组的大部分未受影响，但我们鉴定出了对突变株系中DNA甲基化背景特异性降低敏感的基因和转座子家族。许多在CMT突变株系中上调的基因具有高水平的CHG甲基化，而在RdDM突变体中差异表达的基因附近富含甲基化的CHH岛（mCHH islands），这表明背景特异性DNA甲基化参与了少数基因的表达调控。许多受CMT调控的基因在一组不同近交系中表现出DNA甲基化和转录丰度的自然变异。在突变基因型中差异表达的转座子家族几乎没有明确的特征，不过在RdDM突变体中上调的几个家族在胚乳组织中表达富集，这突出了该途径在繁殖过程中的潜在重要性。综上所述，我们的研究结果表明，虽然其表达受到背景特异性甲基化轻微扰动可重复影响的基因和转座子家族数量较少，但受RdDM和CMT突变体影响的基因座存在明显模式。
