Identification of class II transcriptional activator-induced genes by representational difference analysis: Discoordinate regulation of the DN alpha/DO beta heterodimer

Class II transcriptional activator (CIITA) is a master regulator of MHC cla ss II genes, including DR, DP, and DQ, and MHC class II-associated genes DM and invariant chain. To determine the repertoire of genes that is regulate d by CIITA and to identify uncharacterized CIITA-inducible genes, we used r epresentational difference analysis. Representational difference analysis s creens for differentially expressed transcripts, All CIITA-induced genes we re MHC class II related. We have identified the alpha subunit, DN alpha, of the class II processing factor DO as an additional CIITA-inducible gene. N orthern analysis confirmed that DN alpha is induced by IFN-gamma in 2fTGH f ibrosarcoma cells, and CIITA is necessary for high-level expression in B ce lls. The beta subunit, DO beta, is not inducible in fibrosarcoma cells by I FN-gamma or exogenous CIITA expression. Moreover, in contrast to other clas s II genes, DO beta expression remains high in the absence of CIITA in B ce lls. The promoters for DN alpha and DO beta contain the highly conserved WX Y motifs, and, like other class II genes, expression of both DN alpha and D O beta requires RFX. These findings demonstrate that both DN alpha and DO b eta are regulated by RFX, However, DN alpha is defined for the first time a s a CIITA-inducible gene, and DO beta as a MHC class II gene whose expressi on is independent of CIITA.