Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada.
McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada.
Genome Biol. 2024 Oct 10;25(1):263. doi: 10.1186/s13059-024-03415-3.
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.
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组成部分。尽管它在发育和疾病中很重要，但分子试剂如何共同塑造 H3K36me 景观尚不清楚。
我们使用小鼠间充质干细胞来扰乱 H3K36me 甲基转移酶（K36MTs），并推断出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，部分由 NSD2 沉积。相比之下，H3K36me1/3 在exon 中最丰富，与基因表达呈正相关。我们证明，虽然 SETD2 沉积了大多数 H3K36me3，但它也可能在转录基因内沉积 H3K36me2。此外，SETD2 的缺失会导致exon 中 H3K36me1 的增加，这表明其他（K36MTs）在转录前用较低的甲基化状态对基因体进行预修饰。虽然 NSD1/2 建立广泛的基因间 H3K36me2 域，但 NSD3 在活跃的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控元件，我们的分析表明 PBX2 可能是一个潜在的募集因子。
在基因内，SETD2 主要沉积 H3K36me3，而其他 K36MTs 在不依赖 SETD2 活性的情况下沉积 H3K36me1/2。对于 H3K36me1/2 的沉积，我们发现 K36MT 活性存在一个层次结构，其中 NSD1>NSD2>NSD3>ASH1L。虽然 NSD1 和 NSD2 负责 H3K36me2 在全基因组上的广泛传播，但 NSD3 和 ASH1L 的活性仅限于活跃的调控元件。
