Mono-, di-, and trimethylation of histone H3 lysine 4 (H3K4me1/2/3) are associated with transcription, yet it remains controversial whether H3K4me1/2/3 promote or result from transcription. Our previous characterizations of Arabidopsis H3K4 demethylases suggest roles for H3K4me1 in transcription. However, the control of H3K4me1 remains unexplored in Arabidopsis, in which no methyltransferase for H3K4me1 has been identified. Here, we identify three Arabidopsis methyltransferases that direct H3K4me1. Analyses of their genome-wide localization using ChIP-seq and machine learning reveal that one of the enzymes cooperates with the transcription machinery, while the other two are associated with specific histone modifications and DNA sequences. Importantly, these two types of localization patterns are also found for the other H3K4 methyltransferases in Arabidopsis and mice. These results suggest that H3K4me1/2/3 are established and maintained via interplay with transcription as well as inputs from other chromatin features, presumably enabling elaborate gene control.

组蛋白 H3 赖氨酸 4 (H3K4me1/2/3) 的单甲基化、二甲基化和三甲基化与转录有关，但 H3K4me1/2/3 是促进转录还是由转录产生仍存在争议。我们之前对拟南芥H3K4 去甲基化酶的表征表明 H3K4me1 在转录中的作用。然而，H3K4me1 的控制在拟南芥中仍未得到探索，其中未鉴定出 H3K4me1 的甲基转移酶。在这里，我们确定了三个拟南芥指导 H3K4me1 的甲基转移酶。使用 ChIP-seq 和机器学习对其全基因组定位的分析表明，其中一种酶与转录机制合作，而另外两种与特定的组蛋白修饰和 DNA 序列相关。重要的是，在拟南芥和小鼠中的其他 H3K4 甲基转移酶也发现了这两种类型的定位模式。这些结果表明，H3K4me1/2/3 是通过与转录的相互作用以及来自其他染色质特征的输入而建立和维持的，大概可以实现精细的基因控制。