The effects of chromatin on MHC class II gene regulation

Major histocompatibility complex class II (MHC-II) molecules function by presenting exogenously derived antigenic peptides to CD4+ T lymphocytes. The presentation of these antigens is critical in the development, proliferation, and differentiation of antigen specific CD4 T cells during adaptive immune responses. Expression of MHC-II genes is largely dependent on the transcription factor, class II transactivator (CIITA). CIITA functions as the master regulator of MHC class II genes by mediating both their constitutive and inducible expression. It induces transcription of MHC class II genes via interactions with the assembled factors RFX, NF-Y, and CREB at a conserved upstream regulatory region composed of the W/Z, X, and Y box. CIITA has also been shown to interact with histone acetylation (HAT) proteins such as CBP/p300, suggesting that the recruitment of CBP/p300 by CIITA may serve to modify histones and hence open chromatin at the MHC-II promoter.; A sequence analysis of the Human MHC locus has revealed nine sequences homologous to the canonical X box regulatory elements of MHC-II genes. These sequences were found within the HLA-DR sub-region and were termed X box-like sequences (XL) 1-9. A detailed analysis of XL boxes 1-9, using CIITA-positive and -negative B cell lines, has revealed that XL boxes 4,7, and 8 bound the MHC class II-specific transcription factors RFX and CIITA and were transcriptionally active. The histone code associated with active XL boxes and that of the HLA-DRA X box were identified and found to be consistent. A physical interaction between XL box 4 and the HLA-DRA promoter was observed in a chromatin-looping assay. Another XL box (XL9), located between HLA-DRB1 and HLA-DQA1 genes, displayed high levels of histone acetylation but lacked CIITA and RFX binding. We found that sequences just downstream of this XL box specifically bind CTCF both in vivo and in vitro. Moreover, the CTCF binding portion can function as an efficient enhancer-blocking element that is associated with the nuclear matrix. Therefore, these data provide evidence that certain XL box sequences contribute to chromatin accessibility of the HLA-DR region and supports the involvement of these XL sequences in the regulation of MHC-II genes.