The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis [ncRNA-seq]

DNA methylation alters the epigenetic landscape of the genome, plays critical roles in regulating gene expression, and ensures transposon silencing. As evidenced by the numerous defects associated with aberrant DNA methylation landscapes, establishing proper tissue-specific methylation patterns is critical. Yet, how such differences arise remains a largely open question in both plants and animals. Here we demonstrate that four CLASSY proteins (CLSY1-4), which are differentially expressed during plant development, play major roles in controlling tissue-specific DNA methylation patterns. Depending on the tissue, the genetic requirements for specific CLSYs differ significantly and on a global scale, certain clsy mutants are sufficient to largely shift the epigenetic landscape between tissues. Together, these findings not only reveal substantial epigenetic diversity between tissues, but assign these changes to specific CLSY proteins, revealing how locus-specific targeting combined with tissue-specific expression enables the CLSYs to generate epigenetic diversity during plant development. Overall design: smRNA-seq libraries were sequenced.

DNA甲基化（DNA methylation）可改变基因组的表观遗传景观，在调控基因表达中发挥关键作用，并维持转座子（transposon）的沉默。诸多与异常DNA甲基化图谱相关的发育缺陷均证实，建立正确的组织特异性甲基化模式至关重要。然而，此类组织特异性甲基化差异的产生机制在动植物中仍是一个尚未完全解决的开放科学问题。本研究证实，在植物发育过程中差异表达的四种CLASSY蛋白（CLSY1-4），在调控组织特异性DNA甲基化模式中发挥核心作用。不同组织对特定CLSY蛋白的遗传需求存在显著差异；且在全基因组层面上，特定clsy突变体足以在组织间大幅重塑表观遗传景观。综上，本研究结果不仅揭示了组织间显著的表观遗传多样性，还将这些表观遗传变化归因于特定的CLSY蛋白，并阐明了位点特异性靶向与组织特异性表达相结合的CLSY蛋白，如何在植物发育过程中产生表观遗传多样性。实验整体设计：对smRNA-seq（小分子RNA测序）文库进行了测序。