Sequence-specific interactions of nuclear factors with conserved sequences of human class II major histocompatibility complex genes.

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Abstract
All class II major histocompatibility complex genes contain two highly conserved sequences, termed X and Y, within the promoter region(s), which may have a role in regulation of expression. To study trans-acting factors that interact with these sequences, sequence-specific DNA binding activity has been examined by the gel electrophoresis retardation assay using the HLA-DQ2.beta. gene 5'' flanking DNA and nuclear extracts derived from various cell types. Several specific protein-binding activities were found using a 45-base-pair (bp) HinfI/Sau961 (-142 to -98 bp) and a 38-bp Sau96I/Sau96I (-97 to -60 bp) fragments, which include conserved sequence X (-113 to -100 bp) and conserved sequence Y (-80 to -71 bp), respectively. Competition experiments, methylation interference analysis, and DNase I footprinting demonstrated that distinct proteins in a nuclear extract of Raji cells (a human B lymphoma line) bind to sequence X, to sequence Y, and to DNA 5'' of the X sequence (termed sequence W). The factor binding site in the W sequence is also found to be conserved among .beta.-chain genes and is suggested to be a .gamma.-interferon control region.