6.1.6 is one of several immunoselected mutants from EBV-transformed human B cell lines that have undergone coordinate loss of expression of all their HLA class II genes. Similar defects have been found in cells from some patients with class II immunodeficiencies. Previous studies have suggested that the defects in 6.1.6 and in the other class II regulatory mutants are in transactive factors required for class II transcription. The defective factors, however, have not been identified. Here we present two lines of evidence that serve to localize the site of action of the factor that is defective in 6.1.6. First, transfected indicator genes linked to HLA DRA promoter fragments that include the conserved X box region are transiently expressed at greatly reduced levels in 6.1.6, compared with the progenitor cell line T5-1. Second, a DNA-protein complex, termed X-A, formed by nuclear extracts from T5-1 with DRA sequences containing the X box and a few bases 5' and 3' to it, is missing with extracts from 6.1.6. Extracts from some but not all patients with class II-negative immunodeficiency also fail to form X-A, whereas extracts from class II-negative mutants derived from the Burkitt's line Raji do form an apparently normal X-A complex. The X-A complex contains proteins of approximately 22, 32, 82, and 92 kDa that can be cross-linked to a 5-bromodeoxyuridine-substituted X box probe by UV light. A defect in an X box-binding protein, or in a factor required for its binding, is a likely cause for the loss of transcription of the class II genes in 6.1.6.

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