Based on the formation of the XY body at pachytene and expression studies of a few X-linked genes, the X and Y chromosomes seem to undergo transcriptional inactivation during mammalian spermatogenesis. However, the extent and the mechanism of X and Y inactivation are not known. Here, we show that both the X and Y chromosomes undergo sequential changes in their histone modifications beginning at the pachytene stage of meiosis. These changes usually are associated with transcriptional inactivation in somatic cells, and they coincide with the exclusion of the phosphorylated (active) form of RNA polymerase II from the XY body. Both sex chromosomes undergo extensive deacetylation at histones H3 and H4 and (di)methylation of lysine (K)9 on histone H3; however, there are no changes in H3-K4 methylation. These changes persist even when the XY body disappears in late pachytene, and the X and Y chromosomes segregate from one another after the first meiotic division. By the spermatid stage, histone modifications of the X and Y chromosomes revert to those of active chromatin and RNA polymerase II reengages with both chromosomes. Our observations indicate that X and Y inactivation is extensive and persists even when the X and Y chromosomes are separated in secondary spermatocytes. These findings provide insights into epigenetic programming and chromatin dynamics in the male germ line.epigenetic ͉ meiosis ͉ X inactivation ͉ chromatin ͉ methylation T he process of spermatogenesis in mammals consists of the sequential stages shown in Fig. 1, starting with diploid spermatogonia and ending in haploid sperm. At the pachytene stage ( Fig. 1), when the pairing of the homologous autosomal chromosomes occurs, the X and Y chromosomes pair only at their pseudoautosomal regions and form the sex, or XY, body (1-6). In cytological preparations, the sex body is heteropycnotic, staining more intensely than the autosomes (7). Previous studies demonstrated that several genes on the X chromosome are subject to transcriptional repression during meiosis, beginning at pachytene with reactivation by the spermatid stage (8, 9). Furthermore, RNA polymerase II has been shown to be excluded from the XY body at pachytene (10, 11). However, the mechanism and even the extent of X and Y inactivation (XYi) during spermatogenesis are not known.Unlike the inactive X in female somatic cells, the promoters of housekeeping genes on the X chromosome remain unmethylated throughout spermatogenesis in both humans and mice (8,12). Xist, the X-inactive-specific transcript gene associated with X inactivation (Xi) in female cells, is transiently transcribed in the mouse testes at pachytene and repressed again in spermatids (13,14). However, Xist transcription is not essential, given that male mice with an ablated Xist gene have normal spermatogenesis (15) and XY bodies (9, 16). Thus, the mechanisms of Xi in female somatic cells and XYi during spermatogenesis appear to have fundamental differences.Recent evidence that the XY body at pachytene is enriched for histone H3-l...