Based on studies of animals and yeasts, methylation of histone H3 lysine 4 (H3K4me1/2/3, for mono-, di-, and tri-methylation, respectively) is regarded as the key epigenetic modification of transcriptionally active genes. In plants, however, H3K4me2 correlates negatively with transcription, and the regulatory mechanisms of this counterintuitive H3K4me2 distribution in plants remain largely unexplored. A previous genetic screen for factors regulating plant regeneration identified Arabidopsis LYSINE-SPECIFIC DEMETHYLASE 1-LIKE 3 (LDL3), which is a major H3K4me2 demethylase. Here, we show that LDL3-mediated H3K4me2 demethylation depends on the transcription elongation factor Paf1C and phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (RNAPII). In addition, LDL3 binds to phosphorylated RNAPII. These results suggest that LDL3 is recruited to transcribed genes by binding to elongating RNAPII and demethylates H3K4me2 cotranscriptionally. Importantly, the negative correlation between H3K4me2 and transcription is significantly attenuated in the ldl3 mutant, demonstrating the genome-wide impacts of the transcription-driven LDL3 pathway to control H3K4me2 in plants. Our findings implicate H3K4me2 demethylation in plants as chromatin records of transcriptional activity, which ensures robust gene control.

中文翻译：

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共转录去甲基化导致拟南芥活性基因 H3K4me2 整体丢失

基于对动物和酵母的研究，组蛋白 H3 赖氨酸 4（H3K4me1/2/3，分别表示单甲基化、二甲基化和三甲基化）的甲基化被认为是转录活性基因的关键表观遗传修饰。然而，在植物中，H3K4me2 与转录呈负相关，并且植物中这种违反直觉的 H3K4me2 分布的调节机制在很大程度上仍未被探索。之前对植物再生调节因子的遗传筛选发现了拟南芥赖氨酸特异性脱甲基酶 1-LIKE 3 (LDL3)，它是一种主要的 H3K4me2 脱甲基酶。在这里，我们表明 LDL3 介导的 H3K4me2 去甲基化取决于转录延伸因子 Paf1C 和 RNA 聚合酶 II (RNAPII) 的 C 端结构域 (CTD) 的磷酸化。此外，LDL3 还与磷酸化的 RNAPII 结合。这些结果表明，LDL3 通过与延伸的 RNAPII 结合并共转录使 H3K4me2 去甲基化而被募集到转录基因中。重要的是，H3K4me2 与转录之间的负相关性在ldl3突变体中显着减弱，这证明了转录驱动的 LDL3 途径在植物中控制 H3K4me2 的全基因组影响。我们的研究结果表明植物中 H3K4me2 去甲基化作为转录活性的染色质记录，这确保了强大的基因控制。