Class II transactivator promoter activity is suppressed through regulation by a trophoblast noncoding RNA1

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Abstract
Trophoblasts lack expression of all classic major histocompatibility complex (MHC) antigens. Determination of the mechanism involved could provide insight into selective gene suppression and allograft tolerance. Suppression of class II expression in trophoblasts is secondary to dominant negative trans-acting factors that suppress class II transactivator (CIITA) transcription. We recently described a trophoblast-derived noncoding RNA (TncRNA) that suppresses class II expression. We examined the effects of TncRNA on the CIITA promoter, CIITA, and MHC class II expression. HeLa clones stably transfected with TncRNA were analyzed for MHC class II and CIITA expression by fluorescence-activated cell sorting, Northern blots, and quantitative polymerase chain reaction. Activity and functional dissection of CIITA promoter IV (pIV) was assessed by transient co-transfection of promoter-reporter constructs. Methylation of pIV was assessed by Southern blots, fluorescence-activated cell sorting, and quantitative polymerase chain reaction. TncRNA suppressed interferon-gamma-induced human leukocyte antigen-DR and CIITA expression in HeLa cells. The mechanism involves inhibition of CIITA pIV through a defined inhibitory domain on the promoter. The mechanism does not involve methylation of the promoter. A novel method of CIITA suppression is described where a noncoding RNA selectively mediates the suppression of CIITA pIV possibly by complementary RNA-DNA binding to an inhibitory domain on the promoter. Selective suppression of MHC class II could have important implications in allograft tolerance and in developing class II-deficient cells or tissues for the purpose of transplantation or drug delivery systems.