Lee Seunga, Bae Soon Hyung, Jeon Yunji, Seo Pil Joon, Choi Yeonhee
Department of Biological Sciences, Seoul National University, Seoul, Korea.
Research Center for Plant Plasticity, Seoul National University, Seoul, Korea.
BMC Genomics. 2024 Dec 23;25(1):1234. doi: 10.1186/s12864-024-11144-x.
Plants possess a high potential for somatic cell reprogramming, enabling the transition from differentiated tissue to pluripotent callus, followed by the formation of de novo shoots during plant regeneration. Despite extensive studies on the molecular network and key genetic factors involved in this process, the underlying epigenetic landscape remains incompletely understood.
Here, we explored the dynamics of the methylome and transcriptome during the two-step plant regeneration process. During the leaf-to-callus transition in Arabidopsis Ler, CG methylation shifted across genic regions, exhibiting a similar number of differentially methylated regions (DMRs) for both hypo- and hypermethylation. Pericentromeric regions underwent substantial CG and extensive CHH hypomethylation, alongside some CHG hypermethylation. Upon shoot regeneration from callus, genic regions displayed extensive reconfiguration of CG methylation, while pericentromeric methylation levels highly increased across all cytosine contexts, coinciding with the activation of the RNA-directed DNA methylation (RdDM) pathway. However, mutation in DEMETER (DME) DNA demethylase gene resulted in significant genic CG redistribution and global non-CG hypomethylation in pericentromeric regions, particularly during shoot regeneration. This non-CG hypomethylation observed in dme-2 mutants was, at least partly, due to RdDM downregulation. The dme-2 mutants affected gene expression involved in pluripotency and shoot meristem development, resulting in enhanced shoot regeneration through a reprogrammed state established by pericentromeric hypomethylation compared to wild type.
Our study demonstrates epigenetic changes, accompanied by transcriptome alterations, during pluripotency acquisition (leaf-to-callus) and regeneration (callus-to-de novo shoot). Additionally, it highlights the functions of the DME demethylase, particularly its close association with the RdDM pathway, which underlies pericentromeric non-CG methylation maintenance. These results provide important insights into the epigenetic reconfiguration associated with cell identity transition during somatic cell reprogramming.
植物具有体细胞重编程的巨大潜力，能够从分化组织转变为多能愈伤组织，随后在植物再生过程中形成从头再生的芽。尽管对参与这一过程的分子网络和关键遗传因素进行了广泛研究，但潜在的表观遗传景观仍未完全了解。
在此，我们探索了两步植物再生过程中甲基化组和转录组的动态变化。在拟南芥Ler从叶片到愈伤组织的转变过程中，CG甲基化在基因区域发生变化，低甲基化和高甲基化的差异甲基化区域（DMR）数量相似。着丝粒周围区域经历了大量的CG甲基化和广泛的CHH低甲基化，同时伴有一些CHG高甲基化。从愈伤组织再生芽时，基因区域显示出CG甲基化的广泛重新配置，而着丝粒周围甲基化水平在所有胞嘧啶背景下均显著增加，这与RNA指导的DNA甲基化（RdDM）途径的激活相一致。然而，去甲基化酶（DEMETER，DME）基因的突变导致基因CG的显著重新分布以及着丝粒周围区域的整体非CG低甲基化，尤其是在芽再生期间。在dme - 2突变体中观察到的这种非CG低甲基化至少部分是由于RdDM下调所致。dme - 2突变体影响了与多能性和芽分生组织发育相关的基因表达，与野生型相比，通过着丝粒周围低甲基化建立的重编程状态导致芽再生增强。
我们的研究表明，在多能性获得（叶片到愈伤组织）和再生（愈伤组织到从头再生芽）过程中，伴随着转录组改变发生了表观遗传变化。此外，它突出了DME去甲基化酶的功能，特别是其与RdDM途径的紧密关联，这是着丝粒周围非CG甲基化维持的基础。这些结果为体细胞重编程过程中与细胞身份转变相关的表观遗传重配置提供了重要见解。
