Characterization of an HLA DR beta pseudogene.

Abstract

The class II molecules of the human major histocompatibility complex include the DR, DC, and SB antigens, each composed of an a and a 13 polypeptide chain. We have isolated a DR13 gene in overlapping cosmid clones made from genomic DNA of a Dw4/DR4 homozygous individual. This gene consists of six exons and spans >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 (3 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(3 pseudogene seems to be present also in other DR4 individuals.The class II antigens of the major histocompatibility tomplex are expressed on some cell types involved in the immune response, such as B lymphocytes and macrophages (1). They participate in the presentation of foreign antigens in cellular interactions (2). In man, associations between class II antigen alleles and a large number of diseases have been described (3).The human major histocompatibility complex contains the genes of at least three types of class II antigens-i.e., DR, DC, and SB (4, 5). All three are cell-surface glycoprotein heterodimers, consisting of an a chain of -z35,000 Da noncovalently associated with a 13 chain of --28,000 Da (6). A characteristic property of the class II antigens is their extensive genetic polymorphism. The variability of the DR antigens is provided exclusively by the 13 chains (7) whose polymorphism resides primarily in the amino-terminal domains (8, 9).Cloning of cDNA (10) and protein sequencing (11,12) have shown that in some cell lines, DR13-like genes of at least two distinct loci are expressed. Hybridizations to genomic DNA with DR1B probes reveal even further complexity, inasmuch as individuals of different DR specificities seem to display distinct numbers of DR13 genes, some having at least three DRP-like genes (J. Bohme, personal communication).Class II antigen DNA probes are now being used in hybridizations to genomic DNA in search for more specific correlations of various diseases with class II loci and alleles, detected as restriction fragment length polymorphisms (13, 14). However, the hybridization patterns obtained often reveal a more complex genetic organization than expected from phenotypic observations (15). Molecular characterization of the many class II genes should help simplify interpretation...

Molecular characterization of the murine cytotoxic T-cell membrane glycoprotein Ly-3 (CD8).

“…1). The finding of a murine BJ repeat in the 3' untranslated region is rare, but it is also seen in some mRNA transcripts encoding murine histocompatibility antigen H-2 (36), human histocompatibility antigen HLA (37), and human low density lipoprotein receptor (38). In the latter, Alu/Alu recombination has been shown to occur leading to an alteration in mRNA transcript size (38).…”

DNA binding of the mouse class II major histocompatibility CCAAT factor depends on two components.

“…33). One of these elements is the Y box, which is located 50 to 120 base pairs upstream of the transcription start site and contains an inverted CCAAT sequence that is well conserved among all class II major histocompatibility genes (17,20,22,24,27,31). Recently, a number of proteins that footprint to CCAAT sequences have been described and, in some cases, purified (1, 3-6, 10, 11, 15, 16.…”

DNA and Protein Studies of HLA Class II Molecules: Their Relationship to T Cell Recognition

“…However, the *possibility remains that the clones we have sequenced represent transcripts of * a relatively conserved gene which is apparently not recognized by available T lymphocyte typing reagents. Indeed, sequencing of 3 DR 8 genes at the genomic level in a DR4-Dw4 ITC (Larhammar et al 1985, and personal communication) has not turned up sequences showing, as compared to our clones or that of Long, minimal differences such as those we have described.…”