Cis-element dependence and occupancy of the human invariant chain promoter in CIITA-dependent and -independent transcription

Abstract

The major histocompatibility complex (MHC)-associated invariant chain (Ii) associates with the class II α/β heterodimer during its biosynthesis, inhibiting association of endogenous peptides with the peptide-binding cleft. It is therefore not surprising that there are significant similarities in regulatory mechanisms controlling the expression of the structural class II MHC and Ii genes. One important similarity is that both classes of genes can be expressed via CIITA-dependent or -independent mechanisms. In this report, we have dissected CIITA-dependent and -independent transcription of the Ii gene using an isogenic B-LCL cell pair (Jijoye and clone-13) which do or do not express the class II MHC transactivator (CIITA), respectively. Experiments using mutant or deletion constructs of the Ii gene promoter indicate that while both the X-box and Ii-κB1 elements are critical for CIITA-dependent transcription in B lymphocytes, the Ii-κB1 element is of greater importance for CIITA-independent Ii gene transcription, with the X-box playing a secondary role. Despite these clear differences in cis-element dependence of CIITA-dependent and -independent Ii transcription, there are only subtle differences in the occupancy of these elements in vivo as assessed by genomic footprinting. These differences are restricted to occupancy of the X-box and Y-box, with which the RF-X and NF-Y complexes interact in Ii-positive cells. This difference in the occupancy of the X-box and Y-box in this cell pair indicates that while protein/protein interactions between CIITA and promoter-bound factors stabilize promoter occupancy, these interactions are not absolutely required for occupancy and transcription of the invariant chain gene.