Genome-wide CIITA-binding profile identifies sequence preferences that dictate function versus recruitment

Abstract

The class II transactivator (CIITA) is essential for the expression of major histocompatibility complex class II (MHC-II) genes; however, the role of CIITA in gene regulation outside of MHC-II biology is not fully understood. To comprehensively map CIITA-bound loci, ChIP-seq was performed in the human B lymphoblastoma cell line Raji. CIITA bound 480 sites, and was significantly enriched at active promoters and enhancers. The complexity of CIITA transcriptional regulation of target genes was analyzed using a combination of CIITA-null cells, including a novel cell line created using CRISPR/Cas9 tools. MHC-II genes and a few novel genes were regulated by CIITA; however, most other genes demonstrated either diminished or no changes in the absence of CIITA. Nearly all CIITA-bound sites were within regions containing accessible chromatin, and CIITA's presence at these sites was associated with increased histone H3K27 acetylation, suggesting that CIITA's role at these non-regulated loci may be to poise the region for subsequent regulation. Computational genome-wide modeling of the CIITA bound XY box motifs provided constraints for sequences associated with CIITA-mediated gene regulation versus binding. These data therefore define the CIITA regulome in B cells and establish sequence specificities that predict activity for an essential regulator of the adaptive immune response.

Revisiting the specificity of the MHC class II transactivator CIITA in classical murine dendritic cells in vivo

“…In contrast to studies based on reporter or ChIP‐seq analysis, our results imply a highly restricted transcriptional footprint for CIITA for cDCs in vivo. Studies using cell lines found that CIITA could activate promoters of genes that are highly expressed in cDCs, such the Ii (CD74) , consistent with reports that CIITA binds to the Ii locus . By contrast, we find no regulation of Ii by CIITA in cDCs in vivo.…”

“…The SXY module was identified at the promoter of numerous genes in the MHC locus and was thus thought to restrict the activity of CIITA to this region of the genome . Subsequently, whole‐genome sequencing and ChIP‐seq in CIITA‐deficient B cell lines have revealed SXY modules and CIITA binding sites across the genome, expanding the putative genomic footprint of CIITA . Bioinformatic analyses and in‐vitro promoter assays have identified genes with proximal CIITA‐binding sites that are putatively regulated by CIITA and that are predicted to have functions related to antigen processing and presentation .…”

DNA methylation and mRNA expression of HLA‐DQA1 alleles in type 1 diabetes mellitus

“…Inhibition of methyltransferases restored binding of both factors and led to high HLA-DQA1 and DQB1 expression. 27,28 These results suggest an importance of the promoter proximal regions of these genes and their methylation status. However, this observation was made in the cell lines derived from acute lymphocytic leukaemia, where different types of regulation can be involved.…”

“…showed that two important transcription factors that help to form enhanceosome, RFX and CIITA, did not bind to the hypermethylated promoter proximal regions of HLA‐DQA1 and DQB1 genes. Inhibition of methyltransferases restored binding of both factors and led to high HLA‐DQA1 and DQB1 expression . These results suggest an importance of the promoter proximal regions of these genes and their methylation status.…”

Avaliação do fator CIITA como potencial adjuvante molecular para vacinas e imunoterapias

“…Whatever this additional domain confers different functions to the isoform I is still not clear. The isoform III is the best characterized among the three isoforms 2 , since it was the first discovered and has been used in diverse studies involving protein knockout or overexpression to investigate the CIITA regulation, activities and also its applicability in immunotherapies [25][26][27][28][29][30][31][32][33][34] .…”