Exon-intron organization and complete nucleotide sequence of a human major histocompatibility antigen DC beta gene

Allelic sequence variation of the HLA-DQ loci: relationship to serology and to insulin-dependent diabetes susceptibility

Analysis of sequence variation in the polymorphic second exon of the major histocompatibility complex genes HLA-DQ alpha and -DQ beta has revealed 8 allelic variants at the alpha locus and 13 variants at the beta locus. Correlation of sequence variation with serologic typing suggests that the DQw2, DQw3, and DQ(blank) types are determined by the DQ beta subunit, while the DQw1 specificity is determined by DQ alpha. The nature of the amino acid at position 57 in the DQ beta subunit is correlated with susceptibility to insulin-dependent diabetes mellitus. This region of the DQ beta chain contains shared peptides with Epstein-Barr virus and rubella virus.

Generation of rabbit antipeptide antibodies to HLA-class II antigens by the use of synthetic peptides

A group of eight synthetic peptides, corresponding in sequence to selected regions of HLA-DQ histocompatibility antigens, was used for rabbit immunization to examine their antigenicity and for localizing exposed regions in the native glycoproteins. Those antibodies were then tested in their ability to recognize the HLA-DQ alloantigens. Seven peptides elicited rabbit antibodies, four of which reacted with human glycoproteins prepared from chronic lymphocytic leukaemia cells. The results indicate that sequence stretches 63 to 79 and probably 82 to 93 of the beta chain correspond to exposed regions in DQw1, DQw2 and DQw3 molecules. However, the specificity of those antipeptide antibodies was low, due to extensive crossreactions with amino acid sequencies of high homology occurring in DQ alloantigens.

MHC class II sequences of an HLA-DR2 narcoleptic

Narcolepsy has a 98% association with the DR2-Dw2/DQw1 haplotype. To establish if a disease-specific allele is present in narcolepsy, a cDNA library was made from a B-cell line from a DR2,4/DQw1,3 narcoleptic. Clones encoding the two expressed DR2 beta chains, along with DQw1 alpha and beta chains, were isolated and completely sequenced. The coding regions of these four genes were similar to published nucleotide and protein sequences from corresponding healthy controls, with some minor exceptions. The 3' untranslated region of one of the DR2 beta genes in the narcoleptic was extended by 42 bp. Complete sequences were not available for DQw1.2 alpha or beta from healthy individuals, but first domain nucleotide sequences showed only a single nonproductive difference in DQ alpha. Partial protein sequences of both DQ alpha and beta from published data were identical. Although the effects of minor differences cannot be ruled out completely, it is concluded that there are probably no narcolepsy-specific DR beta or DQ alpha/beta sequences, and that the alleles found in narcolepsy are representative of those found in the healthy population.

An HLA-D region restriction fragment associated with refractory Behçet's disease

We examined the association between HLA-DQ and refractory Behçet's disease at the genomic DNA level. Using a restriction endonuclease Taq I and a DQ beta cDNA probe, we identified the 1.9 kb DQ beta restriction endonuclease fragment tightly associated with refractory Behçet's disease. This observation indicates that genomic HLA-DQ variations affect the development of refractory Behçet's disease.

HLA-DQw3.1 and DQw3.2 associated exon polymorphisms detected by oligonucleotide probes

HLA class II polymorphisms have been analyzed on the genomic level by two oligonucleotide probes corresponding to the DNA sequence coding for the amino acids 23-30 in the first domain of the beta chain of DQw3.1 and DQw3.2. Specific hybridization to single endonuclease fragments of DNA from some HLA homozygous cells was detected. Here we report the distribution of these DNA exon sequences among different DQ alleles, and demonstrate that the probes may be used to type for DQw3.1 and DQw3.2 respectively.

Use of synthetic oligonucleotides for genomic DNA dot hybridization to split the DQw3 haplotype

Comparison of two different HLA-DQ beta gene sequences from two DR4 individuals, probably corresponding to DQw3.2 (DQR4) and DQw3.1 (DQR5) specificities, has shown several nucleotide variations. Eight oligonucleotides (24 bases long), derived from these polymorphic areas, have been synthesized. Each oligonucleotide was hybridized to BamHI-digested DNA samples from eight families with HLA-DR4 individuals. Four polymorphic BamHI fragments were detected. Two of eight oligonucleotides gave a single signal (8.9 kilobases) on DQw3.2-positive haplotypes. We used one of these oligonucleotides in a genomic DNA dot hybridization and detected a hybridization signal only in DQw3.2-positive individuals. A very simple test like this allows the screening of a large population sample within a very short period.

Structure of vertebrate genes: a statistical analysis implicating selection

This paper conducts a statistical analysis of the size distribution of exons and six other gene parts [the transcription unit, introns, intervening DNA (sum of introns), mRNA (sum of exons), and leader and trailer regions of mRNA] as well as the number of exons, the percentage of introns, the placement of introns within the gene, and the potential for frameshifts from coding exon shifts. The first seven variables measured in base pairs fit log-normal distributions. Significant correlations between the sizes of intervening DNA and mRNA, the sizes of leader and trailer regions, and the sizes of introns and flanking exons exist. Introns occur at nonrandom frequencies within the codon frame, in untranslated regions, and relative to the frameshift potential from exon movement or duplication. These nonrandom patterns in gene structure demonstrate that models of gene evolution must incorporate selective processes.

Identification of linear HLA class II amino acid sequences recognized by rabbit antisera against native molecules

A rabbit was immunized with B lymphoblastoid cells, and subsets of the antibodies produced were isolated on affinity columns made from synthetic peptides corresponding to known amino acid sequences from the human class II antigens DQ and DP. Those peptides for which specific antibodies were isolated could be assumed to contribute to the antigenic properties of the intact antigen. The antibody subsets were tested for binding to synthetic peptides, to glycoprotein fractions isolated from cells with different DR and DQ specificities, and to the cells used for immunization of the rabbit. The isolation of those antibodies directed against well-defined amino acid stretches of the histocompatibility antigens is proof of the role of those regions in determining the antigenic properties of these molecules.

HLA-DQ beta gene contributes to susceptibility and resistance to insulin-dependent diabetes mellitus

Over half of the inherited predisposition to insulin-dependent diabetes mellitus maps to the region of chromosome 6 that contains the highly polymorphic HLA class II genes which determine immune responsiveness. Analysis of DNA sequences from diabetics indicates that alleles of HLA-DQ beta determine both disease susceptibility and resistance, and that the structure of the DQ molecule, in particular residue 57 of the beta-chain, specifies the autoimmune response against the insulin-producing islet cells.

Characterization of an HLA-DR beta pseudogene in the DRw52 supertypic group

The nature of the DR beta II pseudogene in a haplotype of the DRw52 supertypic group was investigated by nucleotide sequence analysis. It revealed several deleterious mutations in the signal sequence and second domain regions in addition to the complete absence of the first domain and adjacent sequences. No expression of DR beta II pseudogene mRNA can be detected. The same DR beta II pseudogene is probably present in other members of the DRw52 supertypic group. The pattern of mutations in this DR beta II pseudogene is different from that observed in the DR beta pseudogene of the DRw53 supertypic group, indicating a distinct evolutionary pathway for these two groups of DR haplotypes.

Structure of the rat platelet factor 4 gene: a marker for megakaryocyte differentiation

A rat platelet factor 4 (PF4) cDNA has been isolated by immunoscreening a g lambda 11 rat megakaryocyte cDNA expression library. Sequence analysis of the rat PF4 cDNA revealed that this megakaryocyte protein is composed of a leader sequence of 29 amino acid residues and a mature protein sequence of 76 amino acid residues. The structure of rat PF4 derived from its cDNA shows a marked homology with the amino acid sequence of human PF4 obtained by classical protein chemistry techniques. This observation is particularly striking with regard to the carboxy-terminal region of rat and human PF4, where 28 of the last 31 C-terminal residues are identical. The rat PF4 gene was obtained from a rat genomic library by using rat PF4 cDNA as a hybridization probe. Sequence analysis showed that the gene is constructed of three exons and two short introns. The transcriptional start site is located 73 base pairs upstream of the translational start codon as judged by S1 nuclease mapping and primer extension. The 5' noncoding region of the gene also exhibited a sequence homologous to the TATA box at -31, as well as a series of direct and inverted repeat sequences and a cluster of 26 T residues at -155 to -218. This latter domain may be involved in regulating PF4 gene expression during megakaryocytopoiesis.

Molecular cloning of a polymorphic DNA endonuclease fragment associates insulin-dependent diabetes mellitus with HLA-DQ

A BamHI 3.7-kilobase (kb) fragment detected by an HLA-DQ beta-chain complementary DNA (cDNA) probe and negatively associated with insulin-dependent diabetes mellitus (IDDM) was cloned and sequenced to localize the polymorphism to BamHI sites in intervening sequences of an HLA-DQ beta-chain gene. A probe of the first intervening sequence (IVS 1) showed the BamHI 3.7-kb fragment in 6 of 17 HLA-DR3/4 controls but in 0 of 13 DR-identical IDDM patients. All IDDM patients (13 of 13) had BamHI fragments of 12 and 4 kb, detected in 9 of 17 controls (P less than 0.02). The simple restriction fragment length polymorphism pattern of the IVS 1 probe was exploited by comparing 113 IDDM patients with 177 healthy controls to show increased prevalences in IDDM of the 12-kb (P less than 0.0001) and 4-kb (P less than 0.0001) fragments. In IDDM patients younger than 20 yr at onset, 98% were 12- and/or 4-kb positive, compared with 63% of controls (P less than 0.0001), giving a relative risk of 91.8 for individuals with both fragments. The 12-kb fragment was linked to HLA-DR4, and the 4-kb fragment to HLA-DR3. Both serologic markers were split and a non-DR3/non-DR4 IDDM patient was 4-kb positive. HLA-DQ seems therefore closer, than HLA-DR, to an IDDM susceptibility gene.

An epitope common to HLA class I and class II antigens, Ig light chains, and beta 2-microglobulin

The homology of class I major histocompatibility complex (MHC) antigens, class II MHC antigens, and immunoglobulin molecules has suggested their divergence from a common ancestral gene. We report here a monoclonal antibody (mAb), PAC.M1, which reacts with HLA class I heavy chains, HLA class II alpha and beta chains, and the light chain of human immunoglobulin by Western blot analysis. PAC.M1 reacted with 44 kd, 33 kd, and 29 kd species when tested on membrane glycoproteins from TRal, a B-lymphoblastoid cell line (B-LCL). Two-dimensional electrophoresis and Western blotting of TRal glycoproteins showed that these species had the appropriate electrophoretic mobilities for class I heavy chain and class II alpha and beta subunits. The presence of the epitope was verified on class II alpha and beta subunits by Western blotting of purified alpha beta-invariant chain complexes, and on class I heavy chains by Western blotting of purified class I antigens. The PAC.M1 mAb also reacted with immunoglobulin light chains when Western blotting was performed with normal human serum and purified IgG and IgM as antigens. While reactivity of the mAb with beta-2 microglobulin (beta 2m) was difficult to detect by Western blotting, binding of PAC.M1 to purified beta 2m was detectable in a solid-phase binding assay. Thus, PAC.M1 reacts with a determinant shared by a number of members of the immunoglobulin superfamily.

Structure of the rat platelet factor 4 gene: a marker for megakaryocyte differentiation

A rat platelet factor 4 (PF4) cDNA has been isolated by immunoscreening a g lambda 11 rat megakaryocyte cDNA expression library. Sequence analysis of the rat PF4 cDNA revealed that this megakaryocyte protein is composed of a leader sequence of 29 amino acid residues and a mature protein sequence of 76 amino acid residues. The structure of rat PF4 derived from its cDNA shows a marked homology with the amino acid sequence of human PF4 obtained by classical protein chemistry techniques. This observation is particularly striking with regard to the carboxy-terminal region of rat and human PF4, where 28 of the last 31 C-terminal residues are identical. The rat PF4 gene was obtained from a rat genomic library by using rat PF4 cDNA as a hybridization probe. Sequence analysis showed that the gene is constructed of three exons and two short introns. The transcriptional start site is located 73 base pairs upstream of the translational start codon as judged by S1 nuclease mapping and primer extension. The 5' noncoding region of the gene also exhibited a sequence homologous to the TATA box at -31, as well as a series of direct and inverted repeat sequences and a cluster of 26 T residues at -155 to -218. This latter domain may be involved in regulating PF4 gene expression during megakaryocytopoiesis.

Genetic organization of the ovine MHC class II region

To study the class II genes of the major histocompatibility region of the sheep genome, human HLA class II genes corresponding to the known subregions in man (DR, DQ, DP, DO, and DZ) were used for Southern hybridization analysis of sheep DNA and to probe a sheep genomic library. Hybridizing bands were noted for all probes except DP alpha. DQ alpha and beta and DR beta appear to be present as multicopy genes, while DR alpha-, DZ alpha-, and DO beta- like genes appear to be single copy. All bands detected with the DP beta probe were also detectable with other beta chain probes. From eight lambda-bacteriophage clones of a sheep genomic library nine distinct class II genes were identified. These genes were characterized by differential hybridization analysis and restriction mapping. Two genes were DR beta-like, three DQ alpha-like and four DQ beta-like. The extensive cross-hybridization observed with beta chain probes was not seen with alpha chain probes. The results of this study suggest that the major histocompatibility complex class II region of the sheep has a similar genetic organization to that of man, with the provisional exception of the DP subregion.

Exon-specific oligonucleotide probes localize HLA-DQ beta allelic polymorphisms

The HLA genetic region consists of a large multigene complex which includes a number of highly homologous alpha and beta genes encoding class II polypeptides, clustered in three major loci, DP, DQ, and DR. Analysis of genomic polymorphisms at each of these loci is of considerable interest due to the role of particular structural polymorphisms in immune function, but this analysis has been hampered by difficulty in distinguishing between such highly homologous loci. We have identified locus-specific and exon-specific class II gene sequences in order to produce synthetic oligonucleotide probes which hybridize specifically to DQ beta genes. Two such oligonucleotide probes are described which are specific for the beta 1 and beta 2 exons of DQ (DC) beta, which identify DQ beta genes in digests of cellular DNA and which can be used to characterize restriction sites flanking the two oligonucleotide-specific regions. By sequentially hybridizing these probes in modified Southern analyses, we have been able to generate a tentative "restriction map" of a newly identified DQ beta allele from digests of total genomic DNA. This oligonucleotide mapping technique discriminates between two HLA-DQw3+ alleles, DQ3.1 and DQ3.2, permitting the recognition of structural polymorphisms with DQ beta which are highly associated with type I diabetes mellitus.

Characterization of three HLA-DR beta genes isolated from an HLA-DR 3/4 insulin-dependent diabetic patient

Three HLA-DR beta genes were isolated from a Swedish HLA-DR3/4 insulin-dependent diabetes mellitus (IDDM) patient and characterized by restriction endonuclease mapping and nucleotide sequence analysis. Two out of the three DNA sequences differed from those of published DR beta-chain sequences. A DR beta-gene probe prepared from exon 4 and flanking sequences was used in a Southern blot analysis of blood donors' DNA and DNA from HLA-DR3/4 IDDM patients and HLA-DR-matched healthy control subjects. This probe differentiated HLA-DR3/4 IDDM patients and HLA-DR-matched controls in the Scandinavian population but not in the North American Caucasoid population.

Structure and evolution of the HLA class II SX beta gene

The class II major histocompatibility complex antigens are cell-surface heterodimers consisting of an alpha and a beta chain. Cosmid cloning has shown that the three families of class II antigens, DR, DQ, and DP, are encoded within the HLA-D region of chromosome 6 as a series of discrete gene clusters. The DP cluster contains two pairs of alpha and beta genes, one of which encodes the biochemically-defined DP antigen. In order to assess whether the other two genes, SX alpha and SX beta, are also expressed, potential coding regions have been subcloned and sequenced. The SX3 beta gene is shown to contain regions closely homologous to all six exons of DP beta. A 1 bp deletion in the beta 2 exon, also observed for the SX4 beta allele, causes a translational frameshift, suggesting that SX beta is a pseudogene. However, all the other exons, as well as their splice sites and the putative promoter region, appear to be intact.

Molecular diversity of HLA-DR4 haplotypes

Complementary DNA (cDNA) clones encoding beta chains of the DR and DQ regions and alpha chains of the DQ region were isolated and sequenced from four homozygous DR4 cell lines of different HLA-D types: GM3103(Dw4), FS(Dw10), BIN(Dw14), and KT3(Dw15). When compared with each other and with a previously published sequence from a DR4 (Dw13 cell line), the variability of DR beta 1 gene products is generally restricted to the region around amino acid position 70, with an additional polymorphism at position 86. Many of these differences, including an unusual amino acid substitution at position 57 in the Japanese cell line KT3(Dw15), may be due to gene conversion events from the DR beta 2 or DX beta genes. In contrast, DR beta 2 molecules are identical in Dw15, Dw10, and Dw4 cell lines. DQ beta chains isolated from GM3103(Dw4), FS(Dw10), and BIN40(Dw14) are also identical. However, the DQ beta sequence from cell line KT3(Dw15) differs substantially from all other previously reported DQ beta alleles, consistent with its serological designation, DQ "blank." The first domain sequences of DQ alpha chains were identical in all four cell lines. The data suggest that relatively circumscribed amino acid changes in the DR beta 1 molecule are responsible for the HLA-D typing differences between some haplotypes.

An isolated beta 1 exon next to the DR alpha gene in the HLA-D region

A cosmid clone containing the DR alpha gene and a beta 1 exon of a DR beta-related gene was isolated from a human cosmid clone bank made from the consanguineous DR7 cell line MANN. No other DR beta-related exons were found on this clone. The beta 1 exon was located about 15 kb away from the DR alpha gene in a tail-to-tail (3' to 3') orientation. The exon contained several deleterious mutations: a defective splice site at the 5' end, two translational frame shifts (a 1 bp deletion and a 1 bp insertion), and three extra cysteine residues. Nucleotide and amino acid sequence comparisons of the beta 1 exon indicated that although it is substantially different from other class II beta-chain genes, it is slightly more related to DR than to any other class II gene. The DR beta-related sequence was on a DNA fragment which showed no polymorphism on a panel of cell lines with Eco RI or Pst I. These Southern blots, however, revealed a related, polymorphic sequence in the human genome. Nucleotide sequences in the intron flanking the beta 1 exon shared greater sequence homology than the beta 1 exon itself when compared with the DR beta genomic sequence. The exon may play a role in the generation of variation in expressed class II beta-chain genes and it may be a relic of a different subset of class II products.

Recognition of class II molecules by human T cells. I. Analysis of epitopes of DR and DQ molecules in a DRw11, DRw52, DQw3 haplotype

The HLA-D region of individuals with the DRw11, w52, DQw3 haplotype encodes multiple molecular products of three distinct subregions, DR, DP, and DQ. Since each molecule can carry multiple stimulatory epitopes, the repertoire of allogeneic T-cell responses to determinants of this haplotype can be quite large. In the present experiments, alloreactive cloned T-cell lines recognized six distinct epitopes associated with DRw11, DRw52, DQw3 haplotypes. Panel studies established that three epitopes were DRw11-like and three were DRw52-like. Blocking with monoclonal antibodies showed that two DRw11-like epitopes were carried by DR-subregion products and one DRw11-like epitope was carried by DQ-subregion molecules. DRw52-like epitopes were detected on separate DR subregion-encoded molecules. One of them carried both DRw11- and DRw52-like epitopes, the other carried two of the DRw52-like epitopes. These epitopes, which represent functional units that trigger T-cell responses, can be detected at the present time only with the methods used in this report. Conventional allogeneic T-cell responses represent the summation of responses to multiple epitopes encoded by different D-subregion genes.

DNA sequence analysis of a rat RT1 class II A beta gene

The rat major histocompatibility complex (RT1) encodes twin sets of class II molecules, each consisting of two polypeptide chains referred to as A alpha and A beta, and E alpha and E beta. A gene encoding the RT1.A beta chain was isolated from a rat genomic library using an HLA-DQ beta chain cDNA as a probe. The nucleotide sequence of the coding regions of this gene was determined. Comparison of this sequence with those of the corresponding genes of mouse (H-2A beta) and human (HLA-DQ beta) revealed that this gene has been highly conserved during evolution, and that some parts of the molecule are more conserved than others. Analysis of the nucleotide sequence encoding the two external domains suggests that the membrane proximal domain has been subject to conservative selection, whereas replacement substitutions have been selected positively at certain residues within the amino terminal domain. The overall organization of the RT1.A beta gene is similar to that of the H-2A beta gene.

DO beta: a new beta chain gene in HLA-D with a distinct regulation of expression

The HLA-D region of the human major histocompatibility complex encodes the genes for the alpha and beta chains of the DP, DQ and DR class II antigens. A cDNA clone encoding a new class II beta chain (designated DO) was isolated from a library constructed from mRNA of a mutant B-cell line having a single HLA haplotype. Complete cDNA clones encoding the four isotypic beta chains of the DR1, DQw1, DPw2 and putative DO antigens were sequenced. The DO beta gene was mapped in the D region by hybridization with DNA of HLA-deletion mutants. DO beta mRNA expression is low in B-cell lines but remains in mutant lines which have lost expression of other class II genes. Unlike other class II genes DO beta is not induced by gamma-interferon in fibroblast lines. The DO beta gene is distinct from the DP beta, DQ beta and DR beta genes in its pattern of nucleotide divergence. The independent evolution and expression of DO beta suggest that it may be part of a functionally distinct class II molecule.

Locus-specific detection of HLA-DQ and -DR antigens by antibodies against synthetic N-terminal octapeptides of the beta chain

Antibodies against synthetic peptides representing the class-II antigen HLA-DR and -DQ beta chain N-terminal sequences were prepared in rabbits. The two octapeptides only share two amino acids and enzyme-linked immuno-assays showed the antisera only to bind to its own antigen. Both peptide antisera detected a 29 kDa component in immunoblots of Raji and AL-34 cell plasma membrane proteins separated by SDS gel electrophoresis. The binding of either N-terminal peptide antiserum was selectively inhibited only by the peptide used as antigen. Indirect immunofluorescence analysis by flow cytofluorometry showed specific surface immunofluorescence in 1:100-1:1000 dilutions in lymphoblastoid and blood mononucleated cells. In the latter the binding was primarily confined to monocytes and a subpopulation of lymphocytes. It is concluded that locus-specific immunological reagents to distinguish between beta chains of HLA-DR and -DQ have been prepared by the preparation by the production of antibodies against the N-terminal sequences of each polypeptide.

The I region of the C57BL/10 mouse: characterization and physical linkage to H-2K of an SB beta-like class II pseudogene, psi A beta 3

In the C57BL/10 mouse, 140 kilobases (kb) of the I region (I-Ab, I-Eb) were isolated as recombinant cosmids. The class II genes A beta 2, A beta 1, A alpha,E beta 1, E beta 2, and E alpha are located from centromere to telomere in a region of approximately equal to 110 kb, which shows that the I region in the b haplotype has a similar overall organization to those described for the d, k, and wr7 haplotypes. In addition to these genes, we have also isolated a class II gene, psi A beta 3, which is physically linked to the class I H-2K region, 75 kb telomeric to the H-2Kb gene. This orients the H-2K region on the genetic map with the H-2Kb gene being located toward the I region. The sequence of the beta 2 domain of psi A beta 3 is similar to the immunoglobulin-like domain of other class II genes. Interestingly, it shows 83% nucleotide homology to the human SB beta gene, the same homology that was seen previously between the immunoglobulin-like exons of A beta 1 and DC beta and between E beta 1 and DR beta, respectively. It is likely, therefore, that psi A beta 3 represents a member of a third SB-like class II gene family present in addition to I-A and I-E genes and that the divergence of the SB family predates the speciation of rodents and primates. Comparison of the DNA sequence of the exon encoding the beta 2 domain of psi A beta 3 in the b or k haplotypes with functional class II genes shows that a deletion of eight nucleotides has occurred, such that the psi A beta 3 sequence cannot be translated into a functional class II protein. This suggests that psi A beta 3 is a pseudogene.

Genetic complexity and expression of human class II histocompatibility antigens

The genes encoding nearly all of the serologically defined class II antigens of the major histocompatibility complex have been isolated. Three class II loci have been studied in great detail. The DR region contains a single alpha gene and 3 beta chain genes, 1 of which is a pseudogene. The DR alpha chain gene has been linked to a DR beta gene which encodes a beta protein which contains the serological determinant MT3. A second cosmid cluster contains 2 beta genes, 1 of which encodes the DR4 allospecificity. The identification of these genes has been made by the comparison of amino terminal sequences of DR molecules obtained from a DR4 cell line and the deduced protein sequences of the beta 1 exons from cosmid and phage clones. A conserved element including the promoter and signal sequence is found at the 5' end of each of the 3 DR beta genes. Additionally, this element occurs three more times in the DR region, raising the question of whether additional beta chain genes might be found. The DQ region contains 2 pairs of genes, 1 of which encodes the DQ antigen. The 2nd pair of genes, called DX alpha and beta, appears to be capable of expressing a DQ-related product, although, to date, there is no evidence for its expression. The DP region also contains 2 pairs of genes. One pair encodes the DP antigen while the 2nd alpha-beta pair is shown to be composed of pseudogenes. The location of polymorphic regions in these genes and aspects of their relationship to the serology, evolution, and function of the class II MHC are discussed. The control of expression of class II genes by gamma-interferon has been examined. The promoters of class II genes are characterized by two conserved sequences common to all alpha and beta chain genes as well as by conserved sequences specific for either alpha or beta chain genes. In addition to studies of expression by DNA-mediated gene transformation, a system for the gene transfer of MHC antigens utilizing transmissible retrovirus vectors is described. Retrovirus vectors have been used to transmit DR alpha, DR beta, and the invariant chain (gamma) sequences to recipient cells with resultant expression of these proteins.

Structure, sequence and polymorphism in the HLA-D region

Molecular analysis of the HLA-D region has uncovered a complex array of related genes encompassing a minimum of 6 alpha and 7 beta chain sequences. A high level of polymorphism is characteristic of the DQ alpha and beta genes, as well as DR beta. The DP genes, both alpha and beta, are also polymorphic, though to a lesser extent. The genes fit into the previously established loci: DP, DQ and DR, except for a newly-discovered sequence, DZ alpha, which is approximately equally related to all of the other alpha chain genes. Analysis of the polymorphism and evolution of the HLA-D region, by examination of the sequences, calls for several independent duplication events in the generation of this family of genes.

Structure and polymorphism of murine and human class II major histocompatibility antigens

The molecular analysis of the Class II region of the MHC of mice and of humans has to date led to some important conclusions. These regions encode sizeable families of related loci, at least 2 alpha and 6 beta in mice and 6 alpha and 7 beta in man. In addition to the sizeable number of potential molecules that could be expressed by the loci of this region, all the beta chains and both A alpha and DC alpha have extensive amounts of polymorphism. This polymorphism is strikingly similar at Class II loci in mouse and man. The majority of the variability is found in the first domain and consists of discrete regions of variability. These variable regions appear to be important functionally in presenting antigen, as evidenced by the bm12 mutant. The allotypy of these molecules is complex and is presumably generated by a combination of gene conversion and point mutation followed by selection. Final definition of the range of allelic variability and further insights into the mechanism by which it was generated are still to be resolved, as in a complete map of all the Class II loci in both mouse and man. The data available at present pose certain questions that now need to be addressed. The precise functional role of individual regions or residues of the Class II molecules can now be analyzed using the available sequence data and site specific mutagenesis. Fine structural analysis of these molecules is impossible at present using only sequence data, and X-ray crystallography will be required to answer fundamental questions about 3-dimensional structure. Finally, disease-specific sequences may be uncovered on particular haplotypes which permit the production of disease-specific probes. The molecular revelations of the last few years have resolved many questions about the polymorphisms of Class II products, but many new questions need to be resolved before these molecules and their extensive polymorphism can be properly understood.

Gene organization of DC and DX subregions of the human major histocompatibility complex

The DC and DX subregions of the human major histocompatibility complex (MHC) have been cloned from a cosmid library made from a human B-cell line, Priess. The DC subregion, 48 kilobases, includes the DC alpha and DC beta genes. A second DC-like region, the DX subregion, 35 kilobases, contains the DX alpha gene and a newly found beta gene termed DX beta. Since the DC and DX genes are highly homologous in nucleotide sequence, gene size, exon-intron organization, and direction of transcription, the DC and DX subregions were presumably generated by duplication of an ancestral alpha-beta gene pair. Nucleotide sequencing indicates that all four genes have intact coding sequences and promoter regions. Homology between the upstream promoter sequences of these four genes and seven other class II genes at nucleotides -69 to -78 and -98 to -110 highlights these previously described conserved elements. Moreover, a striking conservation of flanking alpha-gene-specific and beta-gene-specific sequences has been observed. Comparison of Southern blots of Priess DNA with DC alpha and DC beta cDNA probes with isolated cosmid clones showed that (i) the human chromosome encodes only two DC alpha-related and two DC beta-related genes, namely, DC alpha, DX alpha, DC beta, and DX beta, and (ii) the DC and DX subregions are homozygous in Priess cells.

Nucleotide sequence of an HLA-DQ alpha chain derived from a DRw9 cell line: genetic and evolutionary implications

Three families of human Ia molecules, DP, DQ, and DR, have previously been defined. A cDNA clone, pDSH-9.1, encoding the alpha chain of a DQ molecule derived from an HLA-DRw9 homozygous cell line has been isolated and sequenced. Comparison of the nucleotide and predicted protein sequence to those of other DQ alpha subunits reveals that DQ alpha subunits derived from DR4, -7, and -9 cells are very similar to each other but quite different from a DQ alpha subunit derived from a DRw6 cell line. These studies suggest that certain Ia haplotypes have a common evolutionary history. Furthermore, in the context of current serologic and biochemical knowledge, they suggest that the gene encoding the DQ alpha subunit is in strong linkage disequilibrium with the DR locus.

Characterization of an HLA DR beta pseudogene

The class II molecules of the human major histocompatibility complex include the DR, DC, and SB antigens, each composed of an alpha and a beta polypeptide chain. We have isolated a DR beta gene in overlapping cosmid clones made from genomic DNA of a Dw4/DR4 homozygous individual. This gene consists of six exons and spans greater than 20 kilobases. Upon sequencing, it was found to possess several deleterious mutations, each capable of rendering the gene nonfunctional: (i) four splice junctions deviate from the G-T/A-G rule; (ii) two premature termination codons are present in the first domain exon; (iii) a 2-base-pair insertion causes a translational frame shift in the second domain exon. In addition, several amino acid residues that are conserved in all known expressed beta chains have been replaced in the amino acid sequence predicted from the pseudogene. Analysis of the pattern of nucleotide substitutions in the second domain exon suggests that most amino acid replacements occurred after the gene was inactivated. The inactivation may have been caused by insertion of a Kpn I repeat 5' to the promoter region, thereby interfering with transcription of the gene through removal of transcriptional enhancer elements. The DR beta pseudogene seems to be present also in other DR4 individuals.

SB subregion of the human major histocompatibility complex: gene organization, allelic polymorphism and expression in transformed cells

The SB region of the human major histocompatibility complex (MHC) has been cloned from cosmid and lambda phage libraries made from the human B-lymphoblastoid cell line Priess (DR4/4, DC4/4, SB3/4). Two alpha genes and two beta genes are encoded in the 100 kb long SB region in the order SB alpha-SB beta-SX alpha-SX beta. The SB alpha and SB beta genes encode the alpha and beta subunits of the SB subset of class II MHC molecules. Both the SX alpha and the SX beta genes are pseudogenes in the haplotype examined. From the isolated clones, the two haplotypes of the Priess cell line, SB3 and SB4, are distinguished by nucleotide sequencing and blot hybridization analyses. Restriction site polymorphisms between the SB3 and SB4 clones were observed only in relatively small regions of the SB beta and SX beta genes. A mouse macrophage cell line was transfected with one of the cosmid clones containing both SB alpha and SB beta genes. Expression of the alpha and beta genes was detected by fluorescene-activated cell sorting (FACS) and two-dimensional gel electrophoresis using SB-specific monoclonal antibodies.

Structure and polymorphism of the HLA class II SB light chain genes

The HLA Class II region contains at least three groups of loci, DR, DC and SB, which play an important role in the immune response. The antigens encoded at these loci are heterodimers composed of an alpha and a beta chain. The sequence of a complete Class II beta cDNA clone whose sequence agrees closely with the limited N-terminal protein sequence available for the SB beta chain is reported. In addition the structure and coding sequence of genomic SB beta clones of two different SB haplotypes has been obtained and allows definition of some polymorphic regions. The SB beta gene appears to undergo alternate splicing at its 3' end, resulting in expression of two different intracytoplasmic regions. Partial sequencing of a second non-allelic SB beta-like gene, SX beta, indicates that it is a pseudogene.

Analysis of the distribution of charged residues in the N-terminal region of signal sequences: implications for protein export in prokaryotic and eukaryotic cells

A statistical analysis of the distribution of charged residues in the N-terminal region of 39 prokaryotic and 134 eukaryotic signal sequences reveals a remarkable similarity between the two samples, both in terms of net charge and in terms of the position of charged residues within the N-terminal region, and suggests that the formyl group on Metf is not removed in prokaryotic signal sequences.