Extended Data Fig. 1: Setd2 deletion in male PGCs leads to hypogonadism in adults.

a, Schematic representation of the dynamics of DNA methylation (DNAme) during female (red) and male (blue) germline development. Developing germ cells analyzed in this study are shown in bold. Key events for germline development are also shown. Note that in both sexes, de novo DNAme occurs in non-dividing quiescent cells. PGC: primordial germ cell; SG: spermatogonium; E: embryonic day; P: postnatal day. b, Dynamics of Dnmt3l and Dnmt3a expression across key stages of male germ cell development. FPKM (fragments per kilobase of exon model per million reads mapped) values were extracted from RNA-seq data from a previous study³⁴. The window of de novo DNAme during prenatal male germline development is shaded in yellow. c, Breeding scheme to obtain germline-specific Setd2 knockout (KO) prospermatogonia (PSG) and sorting strategy for purification of PSG using OCT3/4-EGFP³⁶. Potential genotypes of embryos derived from this cross are indicated and a microscopy image of GFP expression in E16.5 testis is shown (scale bar, 500 μm). Note that OCT3/4-EGFP is expressed exclusively in PSG in the testis. Dead cells were excluded by gating out PI positive cells during FACS. Sorted PSG (3.9% of total testis cells) were processed as previously described for ULI-N-ChIP-seq³⁵ and PBAT^41,42. d, Gross morphology of 12-week-old testis isolated from WT control (left) or Setd2 KO mice (right). Image is representative of three litters. Scale bar, 5 mm. e, Hematoxylin and eosin (HE) staining of 12-week-old testis (top) and epididymis (bottom) isolated from WT control (left) or Setd2 KO mice (right). Histological analyses shown are representative of multiple imaged sections from a single experiment. Scale bar, 50 μm.