JARID1 is the largest ARID subfamily. It contains four highly homologous members. RBP2 (JARID1A) can enhance nuclear hormone receptor transactivation in reporter assays (26). PLU-1 is highly expressed in breast cancers, and in reporter assays has transcriptional repressor properties (27). SMCX (JARID1C) and SMCY (JARID1D) are thought to be regulators of minor histocompatability antigen (28,29). The four JARID1 proteins share 83% amino acid identity within the ARID and are highly related across their full sequences. This subfamily, in common with JARID2, contains highly conserved JmJN and JmJC domains. The proposed nomenclature reflects these relationships. The function of JmJN and JmJC domains is not yet clear, but they exist in proteins other than ARID family members (30,31). Two representatives of the JARID1 subfamily were chosen for analysis. A second subfamily member was included for two reasons. First, amino acid identity between PLU-1 (JARID1B) and the other three members of this subfamily varies more than is typical within subfamilies in the Loop 2 and Helix 5 region of the ARID sequence (see Figure 1). PLU-1 has a histidine within the Helix 5
