In plants, cytosine DNA methylation (mC) is largely associated with transcriptional repression of transposable elements, but it can also be found in the body of expressed genes, referred to as gene body methylation (gbM). gbM is correlated with ubiquitously expressed genes; however, its function, or absence thereof, is highly debated. The different outputs that mC can have raise questions as to how it is interpreted—or read—differently in these sequence and genomic contexts. To screen for potential mC-binding proteins, we performed an unbiased DNA affinity pull-down assay combined with quantitative mass spectrometry using methylated DNA probes for each DNA sequence context. All mC readers known to date preferentially bind to the methylated probes, along with a range of new mC-binding protein candidates. Functional characterization of these mC readers, focused on the MBD and SUVH families, was undertaken by ChIP-seq mapping of genome-wide binding sites, their protein interactors, and the impact of high-order mutations on transcriptomic and epigenomic profiles. Together, these results highlight specific context preferences for these proteins, and in particular the ability of MBD2 to bind predominantly to gbM. This comprehensive analysis of Arabidopsis mC readers emphasizes the complexity and interconnectivity between DNA methylation and chromatin remodeling processes in plants.

中文翻译：

---

拟南芥 DNA 甲基化读取蛋白的表征


在植物中，胞嘧啶 DNA 甲基化 （mC） 在很大程度上与转座因子的转录抑制有关，但它也可以在表达基因的体内发现，称为基因体甲基化 （gbM）。gbM 与普遍表达的基因相关;然而，它的功能或不存在存在很大争议。mC 可能具有的不同输出引发了关于在这些序列和基因组环境中如何以不同的方式解释或读取的问题。为了筛选潜在的 mC 结合蛋白，我们对每个 DNA 序列环境使用甲基化 DNA 探针进行了无偏倚的 DNA 亲和沉降测定结合定量质谱测定。迄今为止已知的所有 mC 读取器优先与甲基化探针以及一系列新的 mC 结合候选蛋白结合。这些 mC 阅读器的功能表征侧重于 MBD 和 SUVH 家族，通过对全基因组结合位点、它们的蛋白质相互作用物以及高阶突变对转录组和表观基因组谱的影响进行 ChIP-seq 定位。总之，这些结果突出了这些蛋白质的特定环境偏好，特别是 MBD2 主要与 gbM 结合的能力。这种对拟南芥 mC 读数仪的全面分析强调了植物中 DNA 甲基化和染色质重塑过程之间的复杂性和相互关联性。