NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing

While de novo DNA methylation (DNAme) in mammalian germ cells is dependent upon DNMT3A and DNMT3L, oocytes and spermatozoa show distinct patterns of DNAme. In mouse oocytes, de novo DNAme requires the lysine methyltransferase (KMTase) SETD2, which deposits H3K36me3. Surprisingly, we show here that SETD2 is dispensable for de novo DNAme in the male germline. Rather, the KMTase NSD1, which broadly deposits H3K36me2 in euchromatic regions, plays a critical role in de novo DNAme in prospermatogonia, including of imprinted genes. However, males deficient in germline NSD1 show a more severe defect in spermatogenesis than Dnmt3l-/- males. Furthermore, unlike DNMT3L, NSD1 safeguards a subset of genes against H3K27me3-associated transcriptional silencing. In contrast, H3K36me2 plays only a minor role in de novo DNAme during oogenesis and females with NSD1 deficient oocytes are fertile. Thus, the sexually dimorphic pattern of DNAme in mature mouse gametes is driven by distinct profiles of H3K36 methylation. ChIP-seq from control and Setd2 KO, Nsd1 KO or Dnmt3l KO prospermaogonia at E16.5 and P0. WGBS (PBAT) in control and Setd2 KO or Nsd1 KO prospermaogonia at E16.5 and P0. RNA-seq from control and Nsd1 KO or Dnmt3l KO prospermatogonia at E16.5 and P0.哺乳动物生殖细胞中的从头DNA甲基化（de novo DNA methylation, DNAme）依赖于DNMT3A与DNMT3L，但卵母细胞与精子展现出截然不同的DNA甲基化模式。在小鼠卵母细胞中，从头DNA甲基化需要赖氨酸甲基转移酶（lysine methyltransferase, KMTase）SETD2，该酶可催化沉积组蛋白H3第36位赖氨酸三甲基化（H3K36me3）。令人意外的是，本研究证实SETD2对于雄性生殖系的从头DNA甲基化并非必需。与之相反，在常染色质区域广泛沉积组蛋白H3第36位赖氨酸二甲基化（H3K36me2）的赖氨酸甲基转移酶NSD1，在前精原细胞的从头DNA甲基化过程中发挥关键作用，这一调控过程涵盖印记基因的甲基化修饰。然而，生殖系NSD1缺陷的雄性个体，其精子发生缺陷程度较Dnmt3l^-/-雄性更为严重。此外，与DNMT3L不同，NSD1可保护特定基因免受组蛋白H3第27位赖氨酸三甲基化（H3K27me3）介导的转录沉默。与之形成对比的是，H3K36me2在卵子发生的从头DNA甲基化过程中仅发挥微弱作用，且NSD1缺陷卵母细胞的雌性个体仍可正常生育。综上，成熟小鼠配子中DNA甲基化的性别二态性模式，由不同的H3K36甲基化谱所驱动。本数据集包含以下三类高通量测序数据：1. 对照、Setd2基因敲除（Setd2 KO）、Nsd1基因敲除（Nsd1 KO）或Dnmt3l基因敲除（Dnmt3l KO）的胚胎第16.5天（E16.5）及出生后0天（P0）前精原细胞的染色质免疫共沉淀测序（ChIP-seq）数据；2. 对照、Setd2 KO或Nsd1 KO的胚胎第16.5天及出生后0天前精原细胞的PBAT法全基因组亚硫酸氢盐测序（WGBS (PBAT)）数据；3. 对照、Nsd1 KO或Dnmt3l KO的胚胎第16.5天及出生后0天前精原细胞的RNA测序（RNA-seq）数据。