The histone H3K4 demethylase JMJ16 represses leaf senescence in Arabidopsis. The histone H3K4 demethylase JMJ16 represses leaf senescence in Arabidopsis

Leaf senescence is governed by a complex regulatory network involving dynamic reprogramming of gene expression. Recent evidence indicates that trimethylation of histone H3 at lysine 4 (H3K4me3) alters gene expression during leaf senescence. However, it is largely unknown how histone modification is regulated in an age-dependent manner. We found that JMJ16, an Arabidopsis JmjC-domain containing protein, is a specific H3K4 demethylase that negatively regulates leaf senescence. The histone demethylase activity and the JmjN, JmjC, and FYR domains of JMJ16, but not the zf-C5HC2 domain, are essential for JMJ16 function in the regulation of leaf senescence. Genome-wide analysis revealed a widespread coordinated up-regulation of H3K4me3 and gene expression associated with leaf senescence in the loss-of-function jmj16 mutant compared with the wild type. Genetic analysis indicated that JMJ16 negatively regulates leaf senescence at least partly through repressing the expression of WRKY53 and SAG201, two known positive regulators of leaf senescence. Further analyses demonstrated that JMJ16 associates with WRKY53 and SAG201, and represses precocious expression of WRKY53 and SAG201 in mature leaves by reducing H3K4me3 levels at these loci. Moreover, association of JMJ16 on WRKY53 and SAG201 loci increased at mature stage but decreased at later stage, suggesting that the age-dependent dynamic chromatin association of JMJ16 is required for precise transcriptional activation of SAGs during leaf senescence. Thus, JMJ16 is an important regulator of leaf senescence that demethylates H3K4 at senescence-associated genes in an age-dependent manner. Overall design: Examination of the difference of transcriptomes, H3K4me3 modifications and JMJ16 binding in Col and jmj16 KO Arabidopsis.

叶片衰老由复杂的调控网络所支配，该网络涵盖基因表达的动态重编程过程。近期研究证据表明，组蛋白H3第4位赖氨酸三甲基化（H3K4me3）可在叶片衰老过程中改变基因表达模式。然而，组蛋白修饰如何以年龄依赖的方式被调控，在很大程度上仍未明确。本研究发现，拟南芥中含JmjC结构域的蛋白JMJ16是一种特异性H3K4去甲基化酶，可负向调控叶片衰老。JMJ16的组蛋白去甲基化酶活性，以及其JmjN、JmjC与FYR结构域（而非zf-C5HC2结构域），是其调控叶片衰老功能所必需的。全基因组分析显示，与野生型拟南芥相比，功能缺失型jmj16突变体中，与叶片衰老相关的H3K4me3修饰与基因表达呈现广泛的协同上调现象。遗传分析表明，JMJ16至少部分通过抑制WRKY53与SAG201这两个已知的叶片衰老正向调控因子的表达，来负向调控叶片衰老。进一步分析证实，JMJ16可结合至WRKY53与SAG201的基因座，并通过降低这些位点的H3K4me3修饰水平，抑制成熟叶片中WRKY53与SAG201的过早表达。此外，JMJ16在WRKY53与SAG201基因座上的结合丰度在成熟阶段升高，而在衰老后期降低，这表明JMJ16以年龄依赖的方式动态结合染色质，这对于叶片衰老过程中衰老相关基因（SAGs）的精准转录调控是必需的。综上，JMJ16是叶片衰老的重要调控因子，可通过年龄依赖的方式对衰老相关基因位点的H3K4进行去甲基化修饰。实验整体设计：检测哥伦比亚野生型（Col）与jmj16基因敲除（KO）拟南芥的转录组、H3K4me3修饰组以及JMJ16结合谱的差异。