In vivo footprinting of MHC class II genes: bare promoters in the bare lymphocyte syndrome.

Major histocompatibility complex (MHC) class II genes are coordinately regulated and show tissue-specific expression. With the use of in vivo footprinting, common promoter sites in these genes were found to be occupied only in cells that expressed the genes, in spite of the presence of the promoter binding proteins. In vivo analysis of mutant cell lines that exhibited coordinate loss of class II MHC expression, including several from individuals with bare lymphocyte syndrome, revealed two in vivo phenotypes. One suggests a defect in gene activation, whereas the other suggests a defect in promoter accessibility.