During meiotic prophase in male mammals, the X and Y chromosomes are incorporated in the XY body. This heterochromatic body is transcriptionally silenced and marked by increased ubiquitination of histone H2A. This led us to investigate the relationship between histone H2A ubiquitination and chromatin silencing in more detail. First, we found that ubiquitinated H2A also marks the silenced X chromosome of the Barr body in female somatic cells. Next, we studied a possible relationship between H2A ubiquitination, chromatin silencing, and unpaired chromatin in meiotic prophase. The mouse models used carry an unpaired autosomal region in male meiosis or unpaired X and Y chromosomes in female meiosis. We show that ubiquitinated histone H2A is associated with transcriptional silencing of large chromatin regions. This silencing in mammalian meiotic prophase cells concerns unpaired chromatin regions and resembles a phenomenon described for the fungus Neurospora crassa and named meiotic silencing by unpaired DNA.Chromatin remodeling is at the basis of control of cellspecific gene expression, cell determination, and differentiation. The nucleosome units of chromatin consist of two each of the histones H2A, H2B, H3, and H4. The N-terminal ends of these core histones extend from the nucleosome and can undergo posttranslational covalent modifications, such as methylation, acetylation, phosphorylation, and ADP-ribosylation of specific amino acid residues. Together, these modifications constitute the so-called histone code (45). Interaction of other nuclear proteins with chromatin is dependent on the histone code at specific chromatin regions and determines local chromatin structure, which can be open or closed. A remarkable component of the histone code is ubiquitination of C-terminal lysine residues of histones H2A and H2B. Ubiquitin, a protein of 7 kDa, can be attached to lysine residues of a specific protein substrate through the action of a multienzyme complex containing ubiquitin-activating (E1), ubiquitin-conjugating (E2), and ubiquitin ligase (E3) enzymes. Polyubiquitination can target proteins for degradation by the proteasome (34, 35). Monoubiquitination of histones, however, is a stable modification that does not decrease the half-life of the target histone (56).In the yeast Saccharomyces cerevisiae, histone H2A ubiquitination is not required for cell growth or sporulation (47), but histone H2B ubiquitination is an essential mechanism involved in sporulation (37). Most importantly, it has been shown that ubiquitination of H2B by the ubiquitin-conjugating enzyme RAD6, interacting with the ubiquitin ligase BRE1, is a prerequisite for dimethylation of histone H3 at lysine residues 4 and 79 (5,12,37,46). This mechanism is thought to be associated with potentiation of gene activation. It is not known whether this "trans-histone" mechanism is conserved between yeast and mammals. RAD6 shows marked evolutionary conservation. The two mammalian homologs of yeast RAD6, Hr6a/Ube2a and Hr6b/Ube2b, both show approximately 70% amino...