Methylation of histone 3 lysine 36 (H3K36me) has emerged as an essential epigenetic component for the faithful regulation of gene expression. Despite its importance in development and disease, how the molecular agents collectively shape the H3K36me landscape is unclear. We use mouse mesenchymal stem cells to perturb the H3K36me methyltransferases (K36MTs) and infer the activities of the five most prominent enzymes: SETD2, NSD1, NSD2, NSD3, and ASH1L. We find that H3K36me2 is the most abundant of the three methylation states and is predominantly deposited at intergenic regions by NSD1, and partly by NSD2. In contrast, H3K36me1/3 are most abundant within exons and are positively correlated with gene expression. We demonstrate that while SETD2 deposits most H3K36me3, it may also deposit H3K36me2 within transcribed genes. Additionally, loss of SETD2 results in an increase of exonic H3K36me1, suggesting other (K36MTs) prime gene bodies with lower methylation states ahead of transcription. While NSD1/2 establish broad intergenic H3K36me2 domains, NSD3 deposits H3K36me2 peaks on active promoters and enhancers. Meanwhile, the activity of ASH1L is restricted to the regulatory elements of developmentally relevant genes, and our analyses implicate PBX2 as a potential recruitment factor. Within genes, SETD2 primarily deposits H3K36me3, while the other K36MTs deposit H3K36me1/2 independently of SETD2 activity. For the deposition of H3K36me1/2, we find a hierarchy of K36MT activities where NSD1 > NSD2 > NSD3 > ASH1L. While NSD1 and NSD2 are responsible for most genome-wide propagation of H3K36me2, the activities of NSD3 and ASH1L are confined to active regulatory elements.

中文翻译：

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SETD2、NSD1、NSD2、NSD3 和 ASH1L 的系统扰动揭示了它们对 H3K36 甲基化的不同贡献


组蛋白 3 赖氨酸 36 （H3K36me） 的甲基化已成为忠实调控基因表达的重要表观遗传成分。尽管它在发育和疾病中很重要，但分子制剂如何共同塑造 H3K36me 景观尚不清楚。我们使用小鼠间充质干细胞扰乱 H3K36me 甲基转移酶 （K36MT） 并推断五种最突出的酶的活性：SETD2、NSD1、NSD2、NSD3 和 ASH1L。我们发现 H3K36me2 是三种甲基化状态中最丰富的，主要由 NSD1 沉积在基因间区域，部分由 NSD2 沉积。相比之下，H3K36me1/3 在外显子中最丰富，并且与基因表达呈正相关。我们证明，虽然 SETD2 沉积了大部分 H3K36me3，但它也可能将 H3K36me2 沉积在转录基因中。此外，SETD2 的缺失导致外显子 H3K36me1 的增加，表明其他 （K36MT） 引物基因体在转录前具有较低的甲基化状态。NSD1/2 建立了广泛的基因间 H3K36me2 结构域，而 NSD3 在活性启动子和增强子上沉积 H3K36me2 峰。同时，ASH1L 的活性仅限于发育相关基因的调节元件，我们的分析表明 PBX2 是一个潜在的募集因子。在基因中，SETD2 主要沉积 H3K36me3，而其他 K36MT 沉积 H3K36me1/2，独立于 SETD2 活性。对于 H3K36me1/2 的沉积，我们发现 K36MT 活性的层次结构，其中 NSD1 > NSD2 > NSD3 > ASH1L。虽然 NSD1 和 NSD2 负责 H3K36me2 的大部分全基因组传播，但 NSD3 和 ASH1L 的活性仅限于活性调节元件。