We studied the enrichment and distribution of the histone variant mH2A1 in the 
condensed inactive X (Xi) chromosome. By using highly specific antibodies 
against mH2A1 and stable HEK 293 cell lines expressing either green fluorescent 
protein (GFP)-mH2A1 or GFP-H2A, we found that the Xi chromosome contains 
approximately 1.5-fold more mH2A1 than the autosomes. To determine the in vivo 
distribution of mH2A1 along the X chromosome, we used a native chromatin 
immunoprecipitation-on-chip technique. DNA isolated from 
mH2A1-immunoprecipitated nucleosomes from either male or female mouse liver were 
hybridized to tiling microarrays covering 5 kb around most promoters or the 
entire X chromosome. The data show that mH2A1 is uniformly distributed across 
the entire Xi chromosome. Interestingly, a stronger mH2A1 enrichment along the 
pseudoautosomal X chromosome region was observed in both sexes. Our results 
indicate a potential role for macroH2A in large-scale chromosome structure and 
genome stability.