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

Abstract

Ciita was discovered for its role in regulating transcription of major histocompatibility complex class II (MHCII) genes. Subsequently, CIITA was predicted to control many other genes based on reporter and ChIP-seq analysis but few such predictions have been verified in vivo using Ciita−/− mice. Testing these predictions for classical dendritic cells (cDCs) has been particularly difficult, since Ciita−/− mice lack MHCII expression required to identify cDCs. However, recent identification of the cDC-specific transcription factor Zbtb46 allows identification of cDCs independently of MHCII expression. We crossed Zbtb46gfp mice onto the Ciita−/− background and found that all cDC lineages developed in vivo in the absence of Ciita. We then compared the complete transcriptional profile of wild-type and Ciita−/− cDCs to define the physiological footprint of CIITA for both immature and activated cDCs. We find that CIITA exerts a highly restricted control over only the MHCII, H2-DO and H2-DM genes, in DC1 and DC2 cDC subsets, but not over other proposed targets, including Ii. These findings emphasize the caveats needed in interpreting transcription factor binding sites identified by in vitro reporter analysis, or by ChIP-seq, which may not necessarily indicate their functional activity in vivo.

Progenitor-derived human endothelial cells evade alloimmunity by CRISPR/Cas9-mediated complete ablation of MHC expression

“…Differential gene expression analysis revealed 57 significantly differentially expressed genes (FDR-adjusted P < 0.05) with a fold change of 4 or higher when comparing β 2 -microglobulin null , CIITA null , and dually ablated β 2 -microglobulin null +CIITA null ECs with the control ECs (AAVS1) ( Tables 1 and 2). As expected, loss of known CIITA-regulated genes were significantly underrepresented in cells ablated of CIITA (Fisher's exact test P < 0.0001) when compared with the AAVS1-targeted EC control (23). Only 1 gene, encoding the elastin microfibril interface-locate protein 1 (EMILIN1), was significantly downregulated in β 2 -microglobulin null ECs compared with the AAVS1-targeted EC control.…”

High Amount of Transcription Factor IRF8 Engages AP1-IRF Composite Elements in Enhancers to Direct Type 1 Conventional Dendritic Cell Identity

“…Dual germline deletion of Irf4 and Irf8 deletes both CD4 + and CD8 + cDCs, currently identified as cDC2s and cDC1s, respectively, in the spleen (Tamura et al, 2005), although it is possible that only these splenic cDC markers, but not the entire lineage, are affected. In fact, this is the case for Ciita -/mice, which have been reported to lack all cDCs, but instead only lose expression of MHC class II (MHCII), used to identify the cDC lineage (Anderson et al, 2017).…”

NLRC5 promotes transcription of BTN3A1-3 genes and Vγ9Vδ2 T cell-mediated killing

“…These two NLRs, CIITA and NLRC5, are recruited to their respective target gene promoter by a multiprotein complex known as “enhanceosome” ( Ludigs et al., 2015 ; Meissner et al., 2012a ; Neerincx et al., 2012 ). This complex assembles on the promoter sequence called “SXY” module, which is composed of four individual elements (S, X 1 , X 2 , and Y) oriented and spaced in a specific manner ( Anderson et al., 2017 ; Ludigs et al., 2015 ; Masternak et al., 2003 ; Meissner et al., 2012b ; Neerincx et al., 2012 ( Krawczyk et al., 2004 )). Although we still do not know which factor recognizes the S-box, the X 1 -box is bound by the regulatory factor X (RFX) complex, the X 2 -box by cAMP-responsive element binding protein (CREB)/activating transcription factor (ATF) family members, and the Y-box by the nuclear transcription factor Y (NFY)-complex ( Chelbi et al., 2017 ).…”