Characterization of the cDNA Encoding a Protein Binding to the Major Histocompatibility Complex Class II Y Box

The expression of HLA class II genes is regulated by a series of cis-acting elements and trans-acting factors. Several cis-acting elements have been identified and have been termed the Z box, X box, Y box, octamer, and ``TATA'' box. The Y box contains an inverted CCAAT box. By probing a phage λ gt11 library with double-stranded oligonucleotides, we have directly isolated a cDNA encoding a Y box-binding protein designated YB-1. YB-1 binding has an absolute requirement for the CCAAT box and relative specificity for the Y box. It has a Mr of 35,414, contains 18% basic residues, and contains putative nuclear localization signals. An inverse correlation of YB-1 and HLA-DR β chain mRNA levels suggests that YB-1 is a negative regulatory factor.