Major alleles of CDCA7a shape CG-methylation in Arabidopsis thaliana

DNA methylation is a key epigenetic mark that impacts gene expression and represses transposable elements (TEs) in eukaryotes. Numerous examples of cis-elements targeted by DNA methylation, particularly at CG sites (mCG), have been reported to be under selective pressure in animals and plants. By contrast, there is limited knowledge of trans-regulators of mCG leading to adaptation. Here, using genome-wide association studies, we identify CELL DIVISION CYCLE-ASSOCIATED PROTEIN 7 ALPHA (CDCA7a) as a trans-regulator of mCG in natural populations of Arabidopsis thaliana. CDCA7a and its paralog, CDCA7ß, directly bind to the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1), which facilitates access of methyltransferases to DNA. CDCA7a/ß selectively regulates mCG and minimally impacts other DDM1-dependent processes such as non-CG methylation and histone variant deposition. We identify the cis-regulatory sequence modulating CDCA7a expression in natural populations and determining the degree of mCG and TE silencing. The geographic distribution of CDCA7a alleles suggests that new alleles have repeatedly expanded to novel ecological niches, indicating a potential role in local adaptation. Altogether, our findings provide new insight into how changes in global DNA methylation levels through transcriptional regulation of the epigenetic machinery have the capacity to facilitate local adaptation. Overall design: Whole genome bisulfite sequencing of cdca7a-2, smp2, and AT4G37130 mutants.

DNA甲基化（DNA methylation）是真核生物中关键的表观遗传标记，可调控基因表达并抑制转座因子（transposable elements, TEs）的活性。已有诸多研究报道，DNA甲基化靶向的顺式作用元件（cis-elements）——尤其是CG位点（mCG）——在动植物中处于选择压力之下。与之相对，人们对介导适应性形成的mCG反式调控因子（trans-regulators）的认知仍较为有限。本研究通过全基因组关联研究（genome-wide association studies），在拟南芥（Arabidopsis thaliana）的自然种群中鉴定出细胞分裂周期相关蛋白7α（CELL DIVISION CYCLE-ASSOCIATED PROTEIN 7 ALPHA, CDCA7a）作为mCG的反式调控因子。CDCA7a及其旁系同源基因CDCA7β可直接结合染色质重塑因子DNA甲基化减少1（DECREASE IN DNA METHYLATION 1, DDM1），进而协助DNA甲基转移酶接触DNA底物。CDCA7a/β仅选择性调控mCG水平，对其他依赖DDM1的生物学过程（如非CG甲基化与组蛋白变体沉积）影响微弱。本研究还鉴定出自然种群中调控CDCA7a表达、并决定mCG水平与转座因子沉默程度的顺式调控序列。CDCA7a等位基因的地理分布特征显示，新等位基因曾反复扩张至全新的生态位，提示其在局部适应性中发挥潜在作用。综上，本研究揭示了通过表观遗传机制的转录调控改变全局DNA甲基化水平，进而促进局部适应性的全新机制。实验设计概述：对cdca7a-2、smp2及AT4G37130突变体开展全基因组亚硫酸氢盐测序。