Trophoblasts lack expression of all classical 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. Murine B-cells CH27 were stably transfected with TncRNA and analyzed for MHC class II and CIITA expression by FACS and Northern blots. Functional assessment of CIITA promoter III (pIII) was performed by transient transfection of promoter-reporter constructs. Methylation of pIII was assessed by Southern blots and FACS. TncRNA suppressed constitutive I-Ak and CIITA expression in murine B-cells CH27. The mechanism involves inhibition of CIITA pIII activity. The mechanism does not involve methylation of the promoter.