MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China.
Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA.
Plant Cell. 2021 Aug 13;33(7):2183-2196. doi: 10.1093/plcell/koab098.
DNA methylation plays vital roles in repressing transposable element activity and regulating gene expression. The chromatin-remodeling factor Decrease in DNA methylation 1 (DDM1) is crucial for maintaining DNA methylation across diverse plant species, and is required for RNA-directed DNA methylation (RdDM) to maintain mCHH islands in maize (Zea mays). However, the mechanisms by which DDM1 is involved in RdDM are not well understood. In this work, we used chromatin immunoprecipitation coupled with high-throughput sequencing to ascertain the genome-wide occupancy of ZmDDM1 in the maize genome. The results revealed that ZmDDM1 recognized an 8-bp-long GC-rich degenerate DNA sequence motif, which is enriched in transcription start sites and other euchromatic regions. Meanwhile, 24-nucleotide siRNAs and CHH methylation were delineated at the edge of ZmDDM1-occupied sites. ZmDDM1 co-purified with Argonaute 4 (ZmAGO4) proteins, providing further evidence that ZmDDM1 is a component of RdDM complexes in planta. Consistent with this, the vast majority of ZmDDM1-targeted regions co-localized with ZmAGO4-bound genomic sites. Overall, our results suggest a model that ZmDDM1 may be recruited to euchromatic regions via recognition of a GC-rich motif, thereby remodeling chromatin to provide access for RdDM activities in maize.
DNA 甲基化在抑制转座元件活性和调节基因表达方面发挥着重要作用。染色质重塑因子 Decrease in DNA methylation 1（DDM1）对于维持不同植物物种的 DNA 甲基化至关重要，并且对于 RNA 指导的 DNA 甲基化（RdDM）维持玉米（Zea mays）中的 mCHH 岛也是必需的。然而，DDM1 参与 RdDM 的机制尚不清楚。在这项工作中，我们使用染色质免疫沉淀结合高通量测序来确定 ZmDDM1 在玉米基因组中的全基因组占据情况。结果表明，ZmDDM1 识别富含 GC 的 8 个碱基长的简并 DNA 序列基序，该基序在转录起始位点和其他常染色质区域富集。同时，24 个核苷酸的 siRNA 和 CHH 甲基化在 ZmDDM1 占据的位点边缘被划定。ZmDDM1 与 Argonaute 4（ZmAGO4）蛋白共沉淀，进一步证明 ZmDDM1 是植物中 RdDM 复合物的一个组成部分。与此一致，绝大多数 ZmDDM1 靶向区域与 ZmAGO4 结合的基因组位点共定位。总的来说，我们的结果表明，ZmDDM1 可能通过识别富含 GC 的基序被招募到常染色质区域，从而重塑染色质，为玉米中的 RdDM 活性提供途径。
