Class II genes of the human major histocompatibility complex. The DO beta gene is a divergent member of the class II beta gene family

Characterization of a non-classical MHC class II gene in the vulnerable Chinese egret (Egretta eulophotes)

Genes of the major histocompatibility complex (MHC) are valuable makers of adaptive genetic variation in evolutionary ecology research, yet the non-classical MHC genes remain largely unstudied in wild vertebrates. In this study, we have characterized the non-classical MHC class II gene, Egeu-DAB4, in the vulnerable Chinese egret (Ciconiiformes, Ardeidae, Egretta eulophotes). Gene expression analyses showed that Egeu-DAB4 gene had a restricted tissue expression pattern, being expressed in seven examined tissues including the liver, heart, kidney, esophagus, stomach, gallbladder, and intestine, but not in muscle. With respect to polymorphism, only one allele of exon 2 was obtained from Egeu-DAB4 using asymmetric PCR, indicating that Egeu-DAB4 is genetically monomorphic in exon 2. Comparative analyses showed that Egeu-DAB4 had an unusual sequence, with amino acid differences suggesting that its function may differ from those of classical MHC genes. Egeu-DAB4 gene was only found in 30.56-36.56 % of examined Chinese egret individuals. Phylogenetic analysis showed a closer relationship between Egeu-DAB4 and the DAB2 genes in nine other ardeid species. These new findings provide a foundation for further studies to clarify the immunogenetics of non-classical MHC class II gene in the vulnerable Chinese egret and other ciconiiform birds.

Mapping the HLA-DO/HLA-DM complex by FRET and mutagenesis

HLA-DO (DO) is a nonclassic class II heterodimer that inhibits the action of the class II peptide exchange catalyst, HLA-DM (DM), and influences DM localization within late endosomes and exosomes. In addition, DM acts as a chaperone for DO and is required for its egress from the endoplasmic reticulum (ER). These reciprocal functions are based on direct DO/DM binding, but the topology of DO/DM complexes is not known, in part, because of technical limitations stemming from DO instability. We generated two variants of recombinant soluble DO with increased stability [zippered DOαP11A (szDOv) and chimeric sDO-Fc] and confirmed their conformational integrity and ability to inhibit DM. Notably, we found that our constructs, as well as wild-type sDO, are inhibitory in the full pH range where DM is active (4.7 to ∼6.0). To probe the nature of DO/DM complexes, we used intermolecular fluorescence resonance energy transfer (FRET) and mutagenesis and identified a lateral surface spanning the α1 and α2 domains of szDO as the apparent binding site for sDM. We also analyzed several sDM mutants for binding to szDOv and susceptibility to DO inhibition. Results of these assays identified a region of DM important for interaction with DO. Collectively, our data define a putative binding surface and an overall orientation of the szDOv/sDM complex and have implications for the mechanism of DO inhibition of DM.

The bovine gene map

The present status of the bovine gene map as well as some of the methods and strategies important for future efforts in completing the gene map of cattle are reviewed.

Multiple expressed MHC class II loci in salmonids; details of one non-classical region in Atlantic salmon (Salmo salar)

Background

In teleosts, the Major Histocompatibility Complex (MHC) class I and class II molecules reside on different linkage groups as opposed to tetrapods and shark, where the class I and class II genes reside in one genomic region. Several teleost MHC class I regions have been sequenced and show varying number of class I genes. Salmonids have one major expressed MHC class I locus (UBA) in addition to varying numbers of non-classical genes. Two other more distant lineages are also identifyed denoted L and ZE. For class II, only one major expressed class II alpha (DAA) and beta (DAB) gene has been identified in salmonids so far.

Results

We sequenced a genomic region of 211 kb encompassing divergent MHC class II alpha (Sasa-DBA) and beta (Sasa-DBB) genes in addition to NRGN, TIPRL, TBCEL and TECTA. The region was not linked to the classical class II genes and had some synteny to genomic regions from other teleosts. Two additional divergent and expressed class II sequences denoted DCA and DDA were also identified in both salmon and trout. Expression patterns and lack of polymorphism make these genes non-classical class II analogues. Sasa-DBB, Sasa-DCA and Sasa-DDA had highest expression levels in liver, hindgut and spleen respectively, suggestive of distinctive functions in these tissues. Phylogenetic studies revealed more yet undescribed divergent expressed MHC class II molecules also in other teleosts.

Conclusion

We have characterised one genomic region containing expressed non-classical MHC class II genes in addition to four other genes not involved in immune function. Salmonids contain at least two expressed MHC class II beta genes and four expressed MHC class II alpha genes with properties suggestive of new functions for MHC class II in vertebrates. Collectively, our data suggest that the class II is worthy of more elaborate studies also in other teleost species.

Deletion polymorphisms in the promoter region of Fcgamma receptor IIB is not associated with antigen-specific IgG2a and IgG2b antibody responses in NC/Nga mice

Fcgamma receptor (R) IIB, a low-affinity FcR for IgG, inhibits B cell Ag R (BCR)-mediated activation when these two receptors are cross-linked by Ag and IgG-containing immune complexs (ICs). We found deletion polymorphisms in the promoter region of fcgr2b in NC/Nga mice, a model for human atopic dermatitis. NC/Nga mice produced significantly higher levels of ovalbumin (OVA)-specific IgG, IgG2a and IgG2b than did BALB/c mice. Analysis of (BALB/c x NC/Nga)F1 x BALB/c or (BALB/c x NC/Nga) F1 x NC/Nga backcross mice revealed that deletion polymorphisms of fcgr2b in NC/Nga mice does not directly regulate hyper OVA-specific IgG2a and IgG2b Ab responses.

Right place, right time, right peptide: DO keeps DM focused

Peptide loading of major histocompatibility class II molecules is catalyzed in late endosomal and lysosomal compartments of cells by the catalytic action of human leukocyte antigen (HLA)-DM (H-2M in mice). In B cells, dendritic cells and thymic epithelial cells, the peptide loading of class II molecules is modified by the expression of the non-classical class II molecule, HLA-DO (H-2O in mice). Collectively, studies to date support that DO/H-2O expression inhibits the presentation of antigens acquired by cells via fluid phase endocytosis. However, in B cells, the expression of H-2O promotes the presentation of antigens internalized by the B-cell receptor. In this review, we summarize the literature pertaining to DO assembly, transport, and function, with an emphasis on the function of DO/H-2O.

A point mutation in the groove of HLA-DO allows egress from the endoplasmic reticulum independent of HLA-DM

B lymphocytes express the nonclassical class II molecule HLA-DO, which modulates the peptide loading activity of HLA-DM in the endocytic pathway. Binding to HLA-DM is required for HLA-DO to egress from the endoplasmic reticulum (ER). To gain insights into the mode of action of DO and on the role of DM in ER release, we sought to identify DM-binding residues on DO. Our results show that DOalpha encompasses the binding site for HLA-DM. More specifically, mutation of residue DOalpha41 on an exposed lateral loop of the alpha1 domain affects the binding to DM, ER egress, and activity of DO. Using a series of chimeric DR/DO molecules, we confirmed the role of the alpha chain and established that a second DM-binding region is located C-terminal to the DOalpha80 residue, most probably in the alpha2 domain. Interestingly, after mutation of a buried proline (alpha11) on the floor of the putative peptide-binding groove, HLA-DO remained functional but became independent of HLA-DM for ER egress and intracellular trafficking. Collectively, these results suggest that the binding of HLA-DM to DOalpha allows the complex to egress from the ER by stabilizing intramolecular contacts between the N-terminal antiparallel beta-strands of the DOalphabeta heterodimer.

The S Box of Major Histocompatibility Complex Class II Promoters Is a Key Determinant for Recruitment of the Transcriptional Co-activator CIITA

Tightly regulated expression of major histocompatibility complex (MHC) class II genes is critical for the immune system. A conserved regulatory module consisting of four cis-acting elements, the W, X, X2 and Y boxes, controls transcription of MHC class II genes. The X, X2, and Y boxes are bound, respectively, by RFX, CREB, and NF-Y to form a MHC class II-specific enhanceosome complex. The latter constitutes a landing pad for recruitment of the transcriptional co-activator CIITA. In contrast to the well defined roles of the X, X2, and Y boxes, the role of the W region has remained controversial. In vitro binding studies have suggested that it might contain a second RFX-binding site. We demonstrate here by means of promoter pull-down assays that the most conserved subsequence within the W region, called the S box, is a critical determinant for tethering of CIITA to the enhanceosome complex. Binding of CIITA to the enhanceosome requires both integrity of the S box and a remarkably stringent spacing between the S and X boxes. Even a 1-2-base pair change in the native S-X distance is detrimental for CIITA recruitment and promoter function. In contrast to current models, binding of RFX to a putative duplicated binding site in the W box is thus not required for either CIITA recruitment or promoter activity. This paves the way for the identification of novel factors mediating the contribution of the S box to the activation of MHC class II promoters.

Polymorphism in the bovine BOLA-DRB3 upstream regulatory regions detected through PCR-SSCP and DNA sequencing

In the present work, we describe through polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and DNA sequencing the polymorphism within the URR-BoLA-DRB3 in 15 cattle breeds. In total, seven PCR-SSCP defined alleles were detected. The alignment of studied sequences showed six polymorphic sites (four transitions, one transversion and one deletion) in the interconsensus regions of the BoLA-DRB3 upstream regulatory region (URR), while the consensus boxes were invariant. Five out of six detected polymorphic sites were of one nucleotide substitution in the interconsensus regions. It is expected that these mutations do not affect significantly the level of expression. In contrast, the deletion observed in the sequence between CCAAT and TATA boxes could have some effect on affinity interactions between the promoter region and the transcription factors. The URR-BoLA-DRB3 DNA analyzed sequences showed moderate level of nucleotide diversity, high level of identity among them and were grouped in the same clade in the phylogenetic tree. In addition, the phylogenetic tree, the similarity analysis and the sequence structure confirmed that the fragment analyzed in this study corresponds to the URR-BoLA-DRB3. The functional role of the observed polymorphic sites among the regulatory motifs in bovine needs to be analyzed and confirmed by means of gene expression assays.

Tab2 is a novel conserved RNA binding protein required for translation of the chloroplast psaB mRNA

The chloroplast psaB mRNA encodes one of the reaction centre polypeptides of photosystem I. Protein pulse-labelling profiles indicate that the mutant strain of Chlamydomonas reinhardtii, F14, affected at the nuclear locus TAB2, is deficient in the translation of psaB mRNA and thus deficient in photosystem I activity. Genetic studies reveal that the target site for Tab2 is situated within the psaB 5'UTR. We have used genomic complementation to isolate the nuclear Tab2 gene. The deduced amino acid sequence of Tab2 (358 residues) displays 31-46% sequence identity with several orthologues found only in eukaryotic and prokaryotic organisms performing oxygenic photosynthesis. Directed mutagenesis indicates the importance of a highly conserved C-terminal tripeptide in Tab2 for normal psaB translation. The Tab2 protein is localized in the chloroplast stroma where it is associated with a high molecular mass protein complex containing the psaB mRNA. Gel mobility shift assays reveal a direct and specific interaction between Tab2 and the psaB 5'UTR. We propose that Tab2 plays a key role in the initial steps of PsaB translation and photosystem I assembly.

Major histocompatibility complex class II DOA sequences from three Antarctic seal species verify stabilizing selection on the DO locus

To provide additional support for the sequence conservation and hence the regulatory role of the MHC class II DOA locus, we obtained the nucleotide sequences of exon 2 and exon 3, along with the intervening intron, of the Ross seal, and sequences from the exon 2 region from the Weddell and leopard seals. These are the first reports of the sequences of this locus from a carnivore species. The results demonstrate strong conservation among mammals for the exon sequence and produce a gene genealogy that is consistent in topology with a species tree.

Class II transactivator-induced expression of HLA-DO(beta) in HeLa cells

HLA-DO is an intracellular nonclassical MHC class II molecule expressed in the endocytic pathway of B lymphocytes. It shapes the repertoire of peptides bound to classical class II molecules such as HLA-DR by regulating the activity of HLA-DM. Using a peptide corresponding to the cytoplasmic tail of HLA-DO(beta), we have developed a mouse monoclonal antibody, HKC5. Immunofluorescence microscopy revealed that HKC5 recognizes HLA-DO molecules present in the endoplasmic reticulum as well as those in vesicular compartments of the endocytic pathway. In addition, the antibody detects the isolated beta chain on Western blots. Using mutants of the DO(beta) cytoplasmic tail fused to a reporter molecule and expressed in epithelial cells, we showed by flow cytometry that the antibody epitope includes one or both of the leucine residues forming the lysosomal sorting signal. Finally, we have used HKC5 to evaluate the presence of the HLA-DO(beta) chain in HeLa cells expressing the class II transactivator protein CIITA. Our flow cytometry and confocal microscopy analyses showed a marked expression of DO(beta) suggesting that HLA-DO could accumulate under the influence of CIITA in non-B cells.

The HLA-DOB gene displays limited polymorphism with only one amino acid substitution

The HLA-DO molecule is a non-classical class II heterodimer composed of alpha and beta chains. We have previously recognized that all eight of the allelic variations of the HLA-DOA gene represent non-synonymous amino acid substitution. In the present study, to analyze genetic polymorphism and allelic variation of the HLA-DOB gene which may affect the efficiency of class II restricted antigen presentation thereby being involved in the susceptibility of HLA associated diseases, we conducted direct DNA sequencing of HLA-DOB in 36 HLA class II homozygous typing cells and identified six new allelic variations (DOB*0101101, *0101102, *01012, *01022, *0104101 and *0104102) including five single nucleotide polymorphisms with only one amino acid substitution. Furthermore, strong linkage disequilibrium was detected between DOB*01022 and DRB1*1502 only, with no linkage disequilibrium between the DOA and the DOB genes. The HLA-DOB gene has been identified in other mammals, and their nucleotide sequences are well conserved. These facts suggest that limited polymorphism in the DOB gene is profitable to execute their unique function as a co chaperone and so strong selective pressure is operating to prevent generic variation against the DOB molecule interacting with the DM molecule and thus maintaining the specified immunological function of regulating antigen presentation.

Cattle MHC genes DOA and DOB: sequence polymorphisms and assignments to the class IIb region

In a study of the genetic polymorphism of the second exons of the cattle DOA and DOB genes, two and four allelic variants were detected, respectively. In the predicted amino acid sequence, the DOA polymorphism corresponded to variation at the respective residue position, whereas the nucleotide substitutions in the DOB gene were non-informative. PCR-RFLP assays were developed for DOA and DOB typing, and both loci were genetically mapped to the BoLA class IIb region by linkage analysis in the International Bovine Reference Panel. The single nucleotide polymorphisms detected in the BoLA-DOA and -DOB genes enable these loci to be used as markers in genetic trait analyses.

Nonclassical MHC class II molecules

Major histocompatibility complex (MHC) class II molecules are cell surface proteins that present peptides to CD4(+) T cells. In addition to these wellcharacterized molecules, two other class II-like proteins are produced from the class II region of the MHC, HLA-DM (DM) and HLA-DO (DO) (called H2-M, or H2-DM and H2-O in the mouse). The function of DM is well established; it promotes peptide loading of class II molecules in the endosomal/lysosomal system by catalyzing the release of CLIP peptides (derived from the class II-associated invariant chain) in exchange for more stably binding peptides. While DM is present in all class II- expressing antigen presenting cells, DO is expressed mainly in B cells. In this cell type the majority of DM molecules are not present as free heterodimers but are instead associated with DO in tight heterotetrameric complexes. The association with DM is essential for the intracellular transport of DO, and the two molecules remain associated in the endosomal system. DO can clearly modify the peptide exchange activity of DM both in vitro and in vivo, but the physiological relevance of this interaction is still only partly understood.

The impact of the non-classical MHC proteins HLA-DM and HLA-DO on loading of MHC class II molecules

Peptide binding to classical major histocompatibility complex (MHC) class II molecules is known to be determined by the properties of the class II peptide binding groove but recently it turned out to be co-controlled by the activity of the non-classical MHC molecules HLA-DM and HLA-DO: HLA-DM functions as a mediator of peptide exchange. In addition, HLA-DM is a chaperone for MHC class II molecules in endosomal and lysosomal loading compartments because it stabilizes the empty MHC class II peptide binding groove and keeps it receptive for peptide loading until appropriate peptide ligands are captured. Since HLA-DM favors the generation of high-stability peptide-MHC class II complexes by releasing low-stability peptide ligands, DM activity affects the peptide repertoire presented on the cell surface of antigen-presenting cells. HLA-DO is expressed mainly in B cells and binds tightly to HLA-DM thereby modulating its activity. Together, HLA-DM and HLA-DO are critical factors in shaping the MHC class II-associated self or foreign peptide repertoire of antigen presenting cells and, hence, govern initiation or prevention of an immune response.

Limited polymorphism in the HLA-DOA gene

The HLA-DO molecule, a heterodimer consisting of two novel members of the class II gene family, DOA and DOB, has recently been suggested to function as an important modulator in the HLA class II restricted antigen presentation pathway by interaction with the HLA-DM molecule. In this study, we have analyzed genetic polymorphism and allelic variation of the HLA-DOA gene in 37 HLA class II homozygous typing cells using the direct DNA sequencing technique. As a result, we recognized at least eight allelic variations, DOA*01011, *0101201, *0101202, *0101203, *01013, *0101401, *0101402 and *01015. None of them, however, result in amino acid substitution. The HLA-DOA gene has been identified in other mammals as well, and the nucleotide sequences were well conserved among these species. These results suggest that the DOA molecule has undergone strong selective pressure to preserve functional structure and conformation required for interaction with the DM molecule, preventing non-synonymous amino acid substitution.

Gene conversion can create new MHC alleles

It is possible to measure gene conversion of MHC genes with the help of a semi-nested PCR assay. Several considerations are of utmost importance when such an assay is set up. Using this assay, we have found that gene conversion occurs in MHC class II genes in mouse sperm, but not in somatic cells tested. Although this gene conversion occurs in germline cells, it is already completed in spermatogonia, and consequently is mitotic event unlinked to meiosis. The frequency of gene conversion events in MHC class II genes varies strongly from one allele to another, with the highest detected frequencies as high as 1/40,000 for an individual heterozygous for both donor and acceptor sequences. Deletions or insertions in one gene relative to the other seem to lower the efficiency of gene conversion considerably. Stretches within MHC genes amenable to gene conversion are located in CpG clusters, whereas MHC genes not involved in gene conversion have background CpG levels. DNA damage, either chemical or radiation induced, increases the frequency of gene conversion of MHC class II genes in cultured cells of the fibroblastoid lineage. The effect of chemical DNA damage seems roughly dose dependent, whereas irradiation has a maximal effect at low doses.

The Invariant Chain Gene Intronic Enhancer Shows Homology to Class II Promoter Elements

Coordinate expression of MHC class II proteins and the class II-associated invariant chain (Ii) is important for proper MHC class II functioning in Ag processing and presentation. The coordinate regulation of these genes results, in part, from the sharing of transcriptional regulatory regions between MHC class II and Ii genes; the Ii has previously been shown to have an upstream enhancer closely related to the essential class II promoter elements. We report here the characterization of a second enhancer in the Ii gene, located within the first intron. This intronic enhancer is contained within a 155-bp region, enhances transcription from the Ii minimal promoter, and also contains elements that are homologous to class II promoter elements X1, X2, and Y boxes.

Retroelements in the human MHC class II region

Molecular genetic studies of the human major histocompatibility complex (MHC) have led to the identification of more than 200 genes. Besides the large number of genes in the MHC, densely clustered areas of retroelements have been identified. These include short and long interspersed elements (SINEs and LINEs), and human endogenous retroviruses (HERVs). The presence of retroelements in the MHC provides a clear example of how these elements affect the genome plasticity of the host. Comparative analyses of these retroelements have proven highly useful in evolutionary studies of the MHC. Recently, HERV-encoded superantigens have been implicated as candidate autoimmune genes in type I diabetes and multiple sclerosis. In addition, genetic analyses have revealed that autoimmune diseases show strong associations with MHC class II genes. The intriguing correlations between retroviral encoded antigens, MHC class II genes and the development of autoimmune disease merit intense future investigations of retroelements, in particular those endogenous retroviruses located in the MHC class II region proper.

Presence of retroelements reveal the evolutionary history of the human DR haplotypes

Comparison of intron sequences has been a successful tool for drawing major conclusions about the evolutionary relationship of DRB genes. This complex family of genes is discussed in this review as well as a proposed model for the evolution of HLA-DR haplotypes. The model is based both on phylogenetic analysis of intron sequences as well as presence of ERV9 LTR elements located at identical position in intron 5 of a number of DRB genes. According to this model, two main evolutionary branches of DR haplotypes exist. The DR53 haplotype represents one branch, and the second branch contains the DR51, DR52, DR1, and DR8 haplotypes. After the divergence of the DR53 haplotype, an ERV9 LTR element was inserted in a primordial gene. Consequently, all DRB1 genes as well as the DRB3 gene within haplotypes of the second branch, contain this LTR element. In addition, conserved regulatory sequence motifs are found present within these LTR elements that might regulate DRB gene expression. Novel haplotypes are generated by recombinations and the maintenance of the DR haplotype variation as well as the frequent genetic rearrangements observed might be evolutionary advantageous.

HLA-DRB intron 1 sequences: implications for the evolution of HLA-DRB genes and haplotypes

Human DRB genes encode beta chains of the major histocompatibility complex (MHC) class II molecules. Although nine DRB loci have been mapped to the short arm of chromosome 6, an individual chromosome contains only one to five loci and is classified into one of five major haplotypes. To elucidate the origin of human DRB loci and haplotypes, intron 1 sequences approximately 5000 bp in length were determined for three DRB1 alleles (DRB1*03, DRB1*04, and DRB1*15) and five DRB genes (DRB2, DRB3, DRB4, DRB5, and DRB7). The sequences were subjected to phylogenetic analyses together with previously determined intron 4 and 5 sequences. The sequences provided two sources of information: Nucleotide substitutions that could be used to construct phylogenetic trees and to estimate divergence times and a set of insertions (mostly Alu elements) that reveal the order of splitting of duplicated genes. The combined data indicate that the ancestor of the human DRB genes was HLA-DRB1*04-like and that the DRB2, DRB7, DRB5, and DRB3 genes arose from this ancestor by four rounds of duplication 58, 56, 53, and 36 million years (MY) ago, respectively. The DRB4 gene may have arisen 46 MY ago by a deletion from the DRB1 and DRB2 genes and the DRB6 gene is probably an allele at the DRB2 locus. During the course of its evolution, the DRB1*04 gene acquired an intron 1 segment (including two Alu elements) from a gene that became the ancestor of DRB1*03. The present-day HLA-DR haplotypes were derived from three principal ancestral haplotypes: DRB1-DRB2, DRB1-DRB5, and DRB1-DRB7.

Evolutionary relationship of HLA-DRB genes inferred from intron sequences

The major histocompatibility complex (Mhc) consists of class I and class II genes. In the human Mhc (HLA) class II genes, nine DRB loci have been identified. To elucidate the origin of these duplicated loci and allelic divergences at the most polymorphic DRB1 locus, introns 4 and 5 as well as the 3' untranslated region (altogether approximately 1,000 base pairs) of seven HLA-DRB loci, three HLA-DRB1 alleles, and nine nonhuman primate DRB genes were examined. It is shown that there were two major diversification events in HLA-DRB genes, each involving gene duplications and allelic divergences. Approximately 50 million years (my) ago, DRB1*04 and an ancestor of the DRB1*03 cluster (DRB1*03, DRB1*15, and DRB3) diverged from each other and DRB5, DRB7, DRB8, and an ancestor of the DRB2 cluster (DRB2, DRB4, and DRB6) arose by gene duplication. Later, about 25 my ago, DRB1*15 diverged from DRB1*03, and DRB3 was duplicated from DRB1*03. Then, some 20 my ago, the lineage leading to the DRB2 cluster produced two new loci, DRB4 and DRB6. The DRB1*03 and DRB1*04 allelic lineages are extraordinarily old and have persisted longer than some duplicated genes. The orthologous relationships of DRB genes between human and Old World monkeys are apparent, but those between Catarrhini and New World monkeys are equivocal because of a rather rapid expansion and contraction of primate DRB genes by duplication and deletion.

Dissection of positive regulatory elements in the upstream region of the HLA-DPB1 gene

We investigated the cis-acting sequences that function in the B-cell-specific expression of the HLA-DPB1 gene. Class II B major histocompatibility genes contain a conserved upstream sequence that is important in the expression of these genes. This region has been divided into three major elements, the W, X, and Y boxes. In this paper, we identified an additional positive regulatory element upstream from the DPB1 W box. Using 5' deletion mutants and a substitution mutant, we mapped a positive element, called the W' box, between -184 approximately -169 bp. Sequence comparison revealed that the W' box shares homology with the W box. Electrophoretic mobility shift assay confirmed that the W box binds proteins that also recognize the W' box. Furthermore, deletion and substitution mutants indicate that the W and W' boxes effectively enhance CAT activities only when the X and Y boxes exist.

Characterization of three separated exons in the HLA class II DR region of the human major histocompatibility complex

The human major histocompatibility complex, HLA, is a highly polymorphic gene region which includes the DRA and DRB genes. The number of DRB genes differs between haplotypes. The DR4 haplotype seems to be one of the most complex with five DRB loci, DRB1, DRB4, DRB7, DRB8, and DRB9, in addition to the single DRA locus. We determined the nucleotide sequences of three separated DRB exons located between the DRB4 locus and the DRA locus in the DR4 haplotype, two DRB signal-peptide exons (S1 and S3) and one DRB first-domain exon (locus designation DRB9). Sequence comparisons suggest the following order of events for the origin of these exons: DRB9 seems to be the oldest exon and has previously been detected in multiple HLA haplotypes. DRB9 is more divergent than the three other known DRB pseudogenes, all of which have been found in apes. This suggests that DRB9 arose prior to the hominoid divergence. An L1 repeat has been inserted 3' to DRB9. Subsequently, a LTR of the ERV9 retrovirus-like family was inserted into the L1 repeat. Such LTRs have recently been observed in some of the other DRB genes. The pseudogenes DRB7 and DRB8 (containing only exons 3-6) arose after DRB9. Finally, the separated signal peptide exons S1 and S3 were formed. The molecular characterization of these separated DRB exons and insertion elements further clarifies the complex evolutionary history of the HLA-DR region. These selectively neutral exons may serve as useful markers for tracing the phylogeny of HLA haplotypes.

A repressor controls the timing and spatial localisation of stalk cell-specific gene expression in Dictyostelium

The ecmA and ecmB genes of Dictyostelium encode related extracellular matrix proteins and both are induced by DIF, the stalk cell-specific morphogen. The ecmA gene is expressed throughout the prestalk region of the migrating slug but only later, at culmination, do the prestalk cells express the ecmB gene. Expression of the ecmB gene is induced at the entrance to the stalk tube and we have identified two, apparently redundant, promoter elements that control this process. They act as repressors, preventing transcription in the tip of the migrating slug and the apical papilla of the culminant. They have a semi-palindromic consensus sequence TTGnCAA, where n is in one case 2 and in the other 4 bp. Either element alone is able to repress ecmB promoter activity in prestalk cells. Introduction of a single repressor element into the promoter of the ecmA gene changes its expression pattern to resemble that of the ecmB gene. Mutant elements, where n is altered, cause repression during the slug stage but allow premature ecmB expression during culmination; suggesting that the effective strength of the inductive signal may increase during culmination. Inhibition of cAMP-dependent protein kinase (PKA) in prestalk cells blocks both stalk cell maturation and ecmB gene expression. We show that the block to gene expression correlates precisely with the presence of a functional repressor element and this is consistent with the notion that expression of the ecmB gene is controlled by a PKA-dependent release from transcriptional repression.

Polymorphism in the regulatory region of HLA-DRB genes correlating with haplotype evolution

Class II genes of the human major histocompatibility complex (MHC) are polymorphic. Allelic variation of the coding region of these genes is involved in the antigen presentation and is associated with susceptibility to certain autoimmune diseases. The DR region is unique among human class II regions in that multiple DRB genes are expressed. Differential expression of the different DRB loci has been demonstrated, and we sequenced the proximal promoter region of the HLA-DRB genes, known to be involved in the regulation of these genes. We found locus-specific and allele-specific nucleotide variations in their regulatory regions and we determined the relationship between the regulatory regions of HLA-DRB genes. This polymorphism found in the regulatory conserved boxes could be involved in the observed differential expression of DRB loci. In addition, we found a polymorphism between the regulatory regions of DRB1 alleles which might be involved in an allele-specific regulation and therefore could be considered as an additional factor in susceptibility to autoimmune diseases.

Current concepts in DRA gene regulation

The purpose of this review is to provide an interpretative view of work from our laboratory on the DRA gene, and incorporate it with work from other laboratories. Specially, we will deal with: (a) the functional roles of transcription factors in DRA gene regulation; (b) the mechanisms of DRA induction by cytokines; (c) the analysis of DRA gene control in primary untransformed cells, and (d) interactions among transcription factors critical for DRA gene expression.

Evolutionary relationships of the classes of major histocompatibility complex genes

A number of hypotheses have been proposed to account for the evolutionary origin of the classes of major histocompatibility complex (MHC) genes of vertebrates. According to one hypothesis the class II MHC evolved first, whereas another hypothesis holds that the class I MHC originated first as a result of a recombination between an immunoglobulin-like C-domain and the peptide-binding domain of an HSP70 heat-shock protein. A phylogenetic tree of C-domains from MHC and related molecules supports a relationship between the class II MHC alpha chain and beta 2-microglobulin and between the class II MHC beta-chain and the class I alpha chain. If this phylogeny is correct, the hypothesis that the class I MHC evolved by recombination with HSP70 is less parsimonious than the hypothesis that class II evolved first. Furthermore, when MHC peptide-binding domains are simultaneously aligned with HSP70 domains and with V-domains from members of the immunoglobulin superfamily, they are slightly more similar to the latter than to the former; and the class II alpha 1 and beta 1 domains show much greater similarity to each other than would be expected if they evolved from separate HSP70 domains. Thus, most evidence supports the hypothesis that the ancestral MHC molecule had a class II-like structure.

The HXY box regulatory element modulates expression of the murine IA antigen-associated invariant chain in L fibroblasts

The murine invariant chain (Ii) gene has been shown to be interferon-gamma (IFN-gamma)-inducible in a number of nonlymphoid cell types. In mouse L cells, steady-state levels of Ii mRNA are barely detectable in untreated cells but increase sharply upon IFN-gamma treatment. In IFN-gamma treated L cells, transcription starts 23, 28, 38, and 40 bases downstream of the TATA box. To identify cis-acting elements regulating expression of the Ii gene, reporter plasmids containing deletions of the Ii promoter have been constructed and transfected into mouse L cells. Deletion of the H box results in a 50-100% increase in basal expression. Deletion of both the H and X boxes increases basal expression by 200-300% above that seen in constructs containing all three elements. A 25% decrease in basal level expression is seen for constructs that lack the Y-box element when compared to constructs containing the Y-box element but not the H- and X-box elements. DNase I footprinting analysis demonstrates protection of the H, X, and Y boxes as well as a nonconserved region between the H and X boxes. Mobility-shift experiments detect a factor specifically interacting with the Y box. Although the H-, X-, and Y-box elements interact with nuclear protein and are regulatory elements in L cells, these elements do not appear to play a role in IFN-gamma induction suggesting that other regulatory mechanisms must account for IFN-gamma's induction of the Ii in L cells.

DNA sequence analysis of 66 kb of the human MHC class II region encoding a cluster of genes for antigen processing

The genomic sequence of a 66,109 bp long region within the human MHC has been determined by manual and automated DNA sequencing. From cDNA mapping and sequencing data it is known that this region contains a cluster of at least four genes that are believed to be involved in antigen processing. Here, we describe the genomic organization of these genes, which comprise two proteasome-related genes (LMP2 and LMP7), thought to be involved in the proteolytic degradation of cytoplasmic antigens and two ABC transporter genes (TAP1 and TAP2), thought to be involved in pumping of the degraded peptides across the endoplasmic reticulum membrane. Analysis of the sequence homology and the intron/exon structures of the corresponding genes suggests that one gene pair arose by duplication from the other. Comparison of the available sequence data from other organisms shows striking conservation (70 to 84%) of this gene cluster in human, mouse and rat. The presence of several potential interferon stimulated response elements (ISREs) is in agreement with the experimentally observed up-regulation of these genes with gamma-interferon.

MHC Class II Beta-Chain Expression in the Rainbow Trout

A cDNA clone corresponding to the MHC class II beta-chain of the rainbow trout (Oncorhynchus mykiss) has been isolated and used in restriction fragment length polymorphism (RFLP) studies in a family of full siblings of rainbow trout. A very simple RFLP pattern was detected, suggesting segregation of a homozygote AA genotype and a heterozygote AB genotype. The MHC class II beta-chain of the rainbow trout seems to be transcribed in the same type of cells as class II genes of higher vertebrates even though the cDNA clone recognizes atypical messenger sizes of 2.2 kb and 3.6 kb in the analysed family. Surprisingly the transcripts seem to be allele-specific for the assigned genotypes.

Molecular linkage of the HLA-DR, HLA-DQ, and HLA-DO genes in yeast artificial chromosomes

Eight major histocompatibility complex (MHC) class II loci and the newly defined Y3/Ring 4 locus were isolated in overlapping yeast artificial chromosome (YAC) clones defining a 420-kb segment of human chromosome 6p21.3. YAC B1D12 spanning 320 kb contained seven of these loci from HLA-DRA to HLA-DQB2. A 330-kb YAC, A148A7, spanned from the HLA-DQA1 locus through the Y3/Ring 4 locus and extended at least 130 kb centromeric of YAC B1D12. Southern blotting demonstrated that YAC B1D12 derived from the HLA-DR3 haplotype and that YAC A148A7 derived from the HLA-DR7 haplotype of the heterozygous library donor. A third 150-kb YAC, A95C5, lay within this contig and contained only the HLA-DRA locus. A fourth 300-kb YAC, A76F11, was isolated by chromosome walking from the telomeric end of YAC B1D12. Probes isolated from the ends of the YAC genomic inserts have been used to confirm overlaps between the clones. These analyses demonstrated that the centromeric end of YAC A76F11 used the same genomic EcoRI cloning site as the telomeric end of YAC A95C5. YAC B1D12 used an EcoRI site only 2.1 kb telomeric of the aforementioned EcoRI site. These data suggest that certain EcoRI sites are used preferentially during construction of the library. These YACs complete the linkage of the DR and DQ subregions of the HLA complex in cloned DNA and provide the substrate for precise analysis of this portion of the class II region.

A novel class II MHC molecule with unusual tissue distribution

The repertoire of mature class II-restricted T cells is generated through a complex process of selection whereby early T cells confront class II molecules in the thymus, especially on epithelial cells. Expression of class II molecules on such cells is prominent both in the cortex and in the medulla. We have identified a novel class II molecule, H-20, which is expressed only in epithelial cells of the thymic medulla and in B cells. The unusual tissue distribution and the nonpolymorphic nature of H-20 suggest that its function is different from that of classical class II molecules.

Sixty-five radiation hybrids for the short arm of human chromosome 6: their value as a mapping panel and as a source for rapid isolation of new probes using repeat element-mediated PCR

We have used an irradiation and fusion procedure to generate somatic cell hybrids that retain fragments of the short arm of human chromosome 6 (6p). To identify hybrids retaining human material, we performed repeat element-mediated PCR on crude lysates of cells from individual clones. Sixty-five hybrids were shown to contain human material and fifty of those contained one or more 6p-specific probes. Detailed characterization of these hybrids identified a subset that divides 6p into ten mapping intervals. Using repeat element-mediated PCR, we were able to isolate and map 61 new DNA fragments from specific regions of 6p. Fifteen of these fragments were used to screen for restriction fragment length polymorphisms (RFLPs), and nine identified RFLPs with one or more enzymes. The radiation hybrids described in this study provide a valuable resource for high-resolution mapping of 6p and for the rapid isolation of region-specific markers.

The structure of human MHC class II genes

The class II molecules of the human major histocompatibility complex bind intracellularly processed peptides and present them to T-helper cells. They therefore have a critical role in the initiation of the immune response. A salient feature of the class II molecules is their polymorphism. It has been shown that some autoimmune diseases are associated with certain class II alleles. This article reviews the basic structural features of class II molecules, and the genes encoding them as well as mechanisms governing the development of their extraordinary polymorphism.

Structure of class II genes in wild mouse Mus saxicola: functional and evolutionary implications

Class II beta genes have been characterized from Mus saxicola, a wild mouse which diverged five millions years ago from the house mouse. The nucleotide sequences of the exons 2 and 3 of E beta 1, A beta 2 and E beta 2 genes have been determined in order to define the molecular mechanisms of interspecies variability. The E beta 1 and A beta 1 (J. X. She, personal communication) genes from Mus saxicola display extensive sequence variability in exon 2 when compared to those of the house mouse, in association with the variability of residues probably involved in antigen binding. On the other hand, most putative T cell contact residues from the I-E beta chain, and to a lesser extent from the I-A beta chain, were found conserved in mice. T cell contact residues from Mus saxicola I-A beta and I-E beta chains are identical to those of the b and q, and of the k haplotypes of the house mouse, respectively. Comparisons performed with A beta 2 and E beta 2 genes revealed that both are highly conserved and, in contrast to A beta 1 and E beta 1 genes, that a strong selective pressure for conservation occurs in the A beta 2 second exon. The different aspects of A beta 2 and E beta 2 genes evolution may correlate with the original function of their products. Comparisons of the intervening sequences revealed that the repeated motifs of the hotspot region present in the E beta 1b gene are also conserved in Mus saxicola. Recombinations may have occurred, in some cases in association with chi-like sequences.

HLA class II genes: typing by DNA analysis

A detailed understanding of the structure and function of the human major histocompatibility complex (MHC) has ensued from studies by molecular biologist during the last decade. Virtually all of the HLA genes have now been cloned, and the nucleotide sequences of their different allelic forms have been determined. Typing for these HLA alleles is a fundamental prerequisite for tissue matching in allogeneic organ transplantation. Until very recently, typing procedures have been dominated by serological and cellular methods. The availability of cloned DNA from HLA genes has now permitted the technique of restriction fragment length polymorphism (RFLP) analysis to be applied, with remarkable success and advantage, to phenotyping of both HLA Class I and Class II determinants. For the HLA Class II genes DR and DQ, a simple two-stage RFLP analysis permits the accurate identification of all specificities defined by serology, and of many which are defined by cellular typing. At the present time, however, RFLP typing of HLA Class I genes is not as practicable or as informative as that for HLA Class II genes. The present clinical applications of HLA-DR and DQ RFLP typing are predominantly in phenotyping of living donors, including selection of HLA-matched volunteer bone marrow donors, in allograft survival studies, and in studies of HLA Class II-associated diseases. However, the time taken to perform RFLP analysis precludes its use for the typing of cadaveric kidney donors. Nucleotide sequence data for the alleles of HLA Class II genes have now permitted the development of allele-specific oligonucleotide (ASO) typing, a second category of DNA analysis. This has been greatly facilitated by the ability to amplify specific HLA Class II DNA 'target' sequences using the polymerase chain reaction (PCR) technique. The accuracy of DNA typing techniques should ensure that this methodology will eventually replace conventional HLA phenotyping.

Evidence for heterogeneity of the DPA and DPB alleles derived from a DRw11,DQw7,DPw4 cell line

We have previously reported the complete sequence of the cDNAs corresponding to the alleles at the polymorphic loci (DRB1, DRB3, DQA1, DQB1) of the DRw11(5) cell line Swei. We now report the nucleotide and derived amino acid sequence of the alleles at the remaining two polymorphic loci, DPA1 and DPB1, from Swei, which types as DPw4b. Comparison of the DPw4b alpha sequence with previous DP alpha sequences indicates that it is identical to the DP alpha chains of DPw4 and DPw2. However, the DPw4b alpha cDNA encodes a unique 3' untranslated region that corresponds to sequences contained within the last intron of the DP alpha genomic gene. These results indicate that alternative splicing occurs within the Swei DP alpha RNA. Comparison of the DPw4b beta sequence with previously reported DP beta sequences indicates that the first domain is identical to the sequence of the DP beta chain derived from the Burkhardt (Burk) cell line, but that the second domain differs by two amino acids. In addition, a single amino acid difference from DPw2 at position 69 in the first domain of the DPw4b beta chain suggests that this residue is important in determining DP specificity. Furthermore, comparison with other DP beta DNA sequences suggests that variable regions occur at positions 8-11, 55-57, and 84-87.