In animals, H3K4me2 and H3K4me3 are enriched at the transcription start site (TSS) and function as epigenetic marks that regulate gene transcription, but their functions in plants have not been fully characterized. We used chromatin immunoprecipitation sequencing to analyze the rice genome-wide changes to H3K4me1/H3K4me2/H3K4me3 following the loss of an H3K4-specific methyltransferase, SDG701. The knockdown of SDG701 resulted in a global decrease in H3K4me2/H3K4me3 levels throughout the rice genome. An RNA-sequencing analysis revealed that many genes related to diverse developmental processes were misregulated in the SDG701 knockdown mutant. In rice, H3K4me3 and H3K36me3 are positively correlated with gene transcription; however, surprisingly, the H3K4me2 level was negatively associated with gene transcription levels. Furthermore, the H3K4me3 level at the TSS region decreased significantly in the genes that exhibited down-regulated expression in the SDG701 knockdown mutant. In contrast, the genes with up-regulated expression in the mutant were associated with a considerable decrease in H3K4me2 levels over the gene body region. A comparison of the genome-wide distributions of H3K4me2 in eukaryotes indicated that the H3K4me2 level is not correlated with the gene transcription level in yeast, but is positively and negatively correlated with gene expression in animals and plants, respectively. Our results uncovered H3K4me2 as a novel repressive mark in plants.

中文翻译：

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H3K4me2 在植物中充当抑制性表观遗传标记。


在动物中，H3K4me2 和 H3K4me3 在转录起始位点 (TSS) 富集，并作为调节基因转录的表观遗传标记发挥作用，但它们在植物中的功能尚未完全表征。我们使用染色质免疫沉淀测序来分析 H3K4 特异性甲基转移酶 SDG701 丢失后 H3K4me1/H3K4me2/H3K4me3 的水稻全基因组变化。 SDG701 的敲除导致整个水稻基因组中 H3K4me2/H3K4me3 水平的整体下降。 RNA测序分析显示，SDG701敲低突变体中许多与不同发育过程相关的基因被错误调节。在水稻中，H3K4me3和H3K36me3与基因转录呈正相关；然而，令人惊讶的是，H3K4me2 水平与基因转录水平呈负相关。此外，在SDG701敲低突变体中表达下调的基因中，TSS区域的H3K4me3水平显着降低。相反，突变体中表达上调的基因与基因体区域 H3K4me2 水平的显着降低相关。真核生物中H3K4me2全基因组分布的比较表明，H3K4me2水平与酵母中的基因转录水平不相关，但与动物和植物中的基因表达分别呈正相关和负相关。我们的结果发现 H3K4me2 是植物中的一种新型抑制标记。