CTCF Controls Expression and Chromatin Architecture of the Human Major Histocompatibility Complex Class II Locus

Abstract

The major histocompatibility complex class II (MHC-II) locus includes a dense cluster of genes that function to initiate immune responses. Expression of insulator CCCTC binding factor (CTCF) was found to be required for expression of all MHC class II genes associated with antigen presentation. Ten CTCF sites that divide the MHC-II locus into apparent evolutionary domains were identified. To define the role of CTCF in mediating regulation of the MHC II genes, chromatin conformation capture assays, which provide an architectural assessment of a locus, were conducted across the MHC-II region. Depending on whether MHC-II genes and the class II transactivator (CIITA) were being expressed, two CTCF-dependent chromatin architectural states, each with multiple configurations and interactions, were observed. These states included the ability to express MHC-II gene promoter regions to interact with nearby CTCF sites and CTCF sites to interact with each other. Thus, CTCF organizes the MHC-II locus into a novel basal architecture of interacting foci and loop structures that rearranges in the presence of CIITA. Disruption of the rearranged states eradicated expression, suggesting that the formation of these structures is key to coregulation of MHC-II genes and the locus.Spanning nearly 700 kb of the short arm of chromosome 6 at 6p21.31, the major histocompatibility complex class II (MHC-II) locus contains a dense cluster of highly polymorphic genes that encode the alpha and beta chains of the classical MHC-II heterodimeric molecules (reviewed in references 8, 21, and 59). Three MHC-II isotypes, HLA-DR, -DQ, and -DP, can be formed, and they present antigenic peptides to CD4 T lymphocytes in order to initiate, control, and/or maintain adaptive immune responses (20). This antigen presentation process is aided by two MHC-II region-encoded molecules, HLA-DM and HLA-DO, which are also alpha/beta heterodimers with sequence and structural homology with MHC-II proteins (55, 64). The locus includes several MHC-II homologous pseudogenes that represent defunct duplications of ancient MHC-II genes (29). Also within the locus are five genes that do not bear structural homology to MHC-II proteins, the TAP1 and TAP2 genes involved in peptide transport for MHC-I antigen presentation, the proteasome 20s core beta subunit genes PSMB8 and PSMB9, and the bromodomain and extra terminal domain transcriptional regulator gene BRD2 (25,38,67).MHC-II genes are expressed in B lymphocytes, macrophages, and dendritic cells and certain cells within the thymus. Gamma interferon (IFN-␥) is a potent inducer of MHC-II gene expression in most cell types (12). The transcription factors RFX (regulatory factor X), CREB (cyclic AMP [cAMP] response element binding protein), and NF-Y (nuclear factor Y) are constitutively and ubiquitously expressed and bind to highly conserved MHC-II gene-and related gene promoterproximal sequences termed the X1, X2, and Y boxes (9, 51, 59). CIITA (class II transactivator) interacts with the X-Y box-bound factors and mediates the i...

The DNA-binding factor Ctcf critically controls gene expression in macrophages

“…30,39 In line with this, we found specific reduction of MHC class II expression on Kupffer cells in the liver in LysM-Cre Ctcf f/f mice. Since the number of Kupffer cells in the liver was not affected, our findings corroborate the 40 Overexpression of c-Myc may result in enhanced proliferation but may also induce apoptosis.…”

“…30 Despite significant deletion of Ctcf (Figure 1), flow-cytometric analyses of peritoneal or splenic macrophages did not show evidence for reduced surface MHC class II expression in LysM-Cre Ctcf f/f mice, compared with wild-type littermates (Figure 2a). In contrast, flow cytometric and histological analysis of the liver of LysM-Cre Ctcf f/f mice demonstrated substantial reduction of MHC class II expression (Figure 2a and b).…”

CTCF: the protein, the binding partners, the binding sites and their chromatin loops

“…At the major histocompatibility complex class II (MHCII) locus, CTCF and cohesin binding to, and looping between, upstream sequences precedes transcriptional activation. Upon binding of the MHCII trans-activator CIITA to the promoter sequences, loops are induced between them and the various CTCF sites, resulting in increased expression of MHCII genes [64,65].…”

The intellectual disability of trisomy 21: differences in gene expression in a case series of patients with lower and higher IQ

“…Interestingly, the intergenic region between HLA-DQA1 and HLA-DRB1, is characterized by the presence of a CTCF-binding CCCTC sequence, XL9, of high histone acetylation and of particular importance for the control of the expression of both HLA genes and for the chromatin architecture of the MHC class II locus. [18][19][20][21] The fact that CTCF expression is increased and transcription of HLA DQA1 and HLA DRB1 is decreased in the IQ À group could be in favor to a repressor role for CTCF. On the other hand, the RFX1 gene, coding for a protein that binds to the X-boxes of MHC class II genes and which is essential in their expression, shows a three-fold decreased level of expression in the IQÀ group in comparison to the IQ þ group.…”

“…Furthermore, it was found recently that cohesin and CTCF-binding sites have a high degree of overlap, and interacts with each other. 20,[22][23][24] Moreover, often cohesin and CTCF have been found to colocalize at several thousand sites in non-repetitive sequences in the human genome. 22,24,25 In addition to the regulation of gene expression, cohesin has also other important functions: it forms a huge tripartite ring, mediates the sister chromatid cohesion, and facilitates the repair of damaged DNA.…”