NLRC5 Exclusively Transactivates MHC Class I and Related Genes through a Distinctive SXY Module

Abstract

MHC class II (MHCII) genes are transactivated by the NOD-like receptor (NLR) family member CIITA, which is recruited to SXY enhancers of MHCII promoters via a DNA-binding “enhanceosome” complex. NLRC5, another NLR protein, was recently found to control transcription of MHC class I (MHCI) genes. However, detailed understanding of NLRC5’s target gene specificity and mechanism of action remained lacking. We performed ChIP-sequencing experiments to gain comprehensive information on NLRC5-regulated genes. In addition to classical MHCI genes, we exclusively identified novel targets encoding non-classical MHCI molecules having important functions in immunity and tolerance. ChIP-sequencing performed with Rfx5−/− cells, which lack the pivotal enhanceosome factor RFX5, demonstrated its strict requirement for NLRC5 recruitment. Accordingly, Rfx5-knockout mice phenocopy Nlrc5 deficiency with respect to defective MHCI expression. Analysis of B cell lines lacking RFX5, RFXAP, or RFXANK further corroborated the importance of the enhanceosome for MHCI expression. Although recruited by common DNA-binding factors, CIITA and NLRC5 exhibit non-redundant functions, shown here using double-deficient Nlrc5−/−CIIta−/− mice. These paradoxical findings were resolved by using a “de novo” motif-discovery approach showing that the SXY consensus sequence occupied by NLRC5 in vivo diverges significantly from that occupied by CIITA. These sequence differences were sufficient to determine preferential occupation and transactivation by NLRC5 or CIITA, respectively, and the S box was found to be the essential feature conferring NLRC5 specificity. These results broaden our knowledge on the transcriptional activities of NLRC5 and CIITA, revealing their dependence on shared enhanceosome factors but their recruitment to distinct enhancer motifs in vivo. Furthermore, we demonstrated selectivity of NLRC5 for genes encoding MHCI or related proteins, rendering it an attractive target for therapeutic intervention. NLRC5 and CIITA thus emerge as paradigms for a novel class of transcriptional regulators dedicated for transactivating extremely few, phylogenetically related genes.

NLRC5/MHC class I transactivator is a target for immune evasion in cancer

“…Transcriptional regulation of MHC class I genes remained largely undefined until the recent discovery of CITA (MHC class I transactivator), known as NLRC5 [NODlike receptor (NLR) family, caspase recruitment (CARD) domain containing 5] (11,12). NLRC5 is an IFN-γ-inducible nuclear protein (13)(14)(15) that specifically associates with and activates promoters of MHC class I genes by generating a CITA enhanceosome complex with other transcription factors (14,16,17). A striking feature of CITA/NLRC5 is that it does not solely induce MHC class I genes but also activates other critical genes involved in the MHC class I antigen-presentation pathway, including the immunoproteasome component LMP2 (PSMB9), peptide transporter TAP1, and B2M (14,17), thus regulating most of the key components in the MHC class I antigen-presentation machinery.…”

“…NLRC5 is an IFN-γ-inducible nuclear protein (13)(14)(15) that specifically associates with and activates promoters of MHC class I genes by generating a CITA enhanceosome complex with other transcription factors (14,16,17). A striking feature of CITA/NLRC5 is that it does not solely induce MHC class I genes but also activates other critical genes involved in the MHC class I antigen-presentation pathway, including the immunoproteasome component LMP2 (PSMB9), peptide transporter TAP1, and B2M (14,17), thus regulating most of the key components in the MHC class I antigen-presentation machinery. Nlrc5-deficient mice exhibit impaired constitutive and inducible expression of MHC class I genes in vivo (18)(19)(20)(21)(22).…”

T Cell Priming by Activated Nlrc5-Deficient Dendritic Cells Is Unaffected despite Partially Reduced MHC Class I Levels

“…These include an IFNresponsive element, NF-kB binding sites, and a highly conserved regulatory motif known as SXY module, which is proximal to the transcription start site (1). Recent studies led to the discovery of NOD-like receptor (NLR) caspase recruitment domaincontaining protein 5 (NLRC5) as the transcriptional regulator occupying the SXY sequence (2)(3)(4)(5)(6)(7)(8). NLRC5 does not directly bind the DNA, but it is recruited by the enhanceosome, a DNAbinding complex assembling on the SXY module (2)(3)(4)(5)(6).…”

“…Recent studies led to the discovery of NOD-like receptor (NLR) caspase recruitment domaincontaining protein 5 (NLRC5) as the transcriptional regulator occupying the SXY sequence (2)(3)(4)(5)(6)(7)(8). NLRC5 does not directly bind the DNA, but it is recruited by the enhanceosome, a DNAbinding complex assembling on the SXY module (2)(3)(4)(5)(6). By analogy with CIITA, a thoroughly studied NLR family member that acts as a transcriptional regulator of MHC class II genes, NLRC5 recruits in turn chromatin remodeling and transcription factors, thus orchestrating the transactivation of MHCI genes (9).…”

The Minor MHC Class I Gene UDA of Ducks Is Regulated by Let-7 MicroRNA

“…1). The regulation of MHC class I genes is mediated by a number of cis-acting regulatory sites, including the W/S, X1 and X2, and Y sites by RFX, CREB/ATF and NF-Y (37,38), and transactivator NLRC5 (39), and inducible enhancer A bound by NF-kB (40) and an IFN-stimulated response element (ISRE) bound by IFN regulatory factors (41). As we previously showed, UAA*03 and UDA promoters contain all the canonical MHC class I cis-regulatory elements, UBA has a deletion in the X1 box, whereas UCA lacks the NF-kB binding site (16).…”