MACROH2As are core histones that have a unique hybrid structure consisting of an amino-terminal domain that closely resembles a full-length histone H2A followed by a large nonhistone region. The human MACROH2A1 gene, on chromosome 5, encodes two MACROH2A subtypes, MACROH2A1.1 and MACROH-2A1.2, produced by alternate splicing. Here we report the identification of MACROH2A2, a new MACROH2A subtype encoded by a separate gene on human chromosome 10, MACROH2A2. The amino acid sequence of human MACROH2A2 is 68% identical to human MACROH2A1.2. We show by immunofluorescence on mouse tissue sections that MACROH2A2, like MACROH2A1.2, is concentrated in the inactive X chromosome. However, MACROH2A2 has a very different pattern of expression in the cell types present in the liver and kidney. When MACROH2A2 and MACROH2A1.2 are present in the same nucleus, they have a similar, though nonidentical, pattern of localization, with both subtypes present in the inactive X chromosome. Our results suggest a developmental role for MACROH2A subtypes.The MACROH2A core histones were first observed as two 42-kDa proteins that remained associated with rat liver mononucleosomes in 0.5 M NaCl (1). The sequences of cDNAs that encode these proteins revealed that they have a unique hybrid structure consisting of an amino-terminal domain that closely resembles a full-length histone H2A followed by a large nonhistone domain. MACROH2As are released from the nucleosome core at the same salt concentration as conventional H2As and appear to be released as a heterodimer with H2B (1). This indicates that the H2A region of MACROH2A replaces conventional H2A in the nucleosome core. It was estimated that 1 in 30 nucleosomes in rat liver would contain MACROH2A, assuming one MACROH2A per nucleosome (1). The H2A region (amino acids 1-122) is followed by a short linker region (10 amino acids) and then a region that is rich in basic amino acids (28 amino acids) (see Fig. 1). This basic region resembles basic tails present in other histones and most likely binds DNA.The nonhistone region of MACROH2As is a feature not found in other known core histones. It constitutes 57% of the protein and contains a putative leucine zipper motif consisting of four heptad repeats (1). The majority of the nonhistone region appears to have evolved from a gene of unknown function that originated prior to the appearance of eukaryotes (2). Among the sequences that are similar to the nonhistone region is a conserved domain present in proteins involved in the replication of RNA viruses (2).We identified two distinct MACROH2A cDNA sequences (1) and used specific antibodies to assign these sequences to the two MACROH2A proteins that were resolved by electrophoresis (3). We named these subtypes MACROH2A1.1 and MACROH2A1.2. The nucleotide sequences of cDNAs that encode MACROH2A1.1 and MACROH2A1.2 differed only in a single internal segment that encodes part of the nonhistone region (1, 3), and these subtypes are formed by alternate splicing of a single gene, macroH2A1, on mouse chromosome 1...