Transcription analysis, physical mapping, and molecular characterization of a nonclassical human leukocyte antigen class I gene.

Abstract

The human major histocompatibility complex contains approximately 20 class I genes, pseudogenes, and gene fragments. These include the genes for the three major transplantation antigens, HLA-A, HLA-B, and HLA-C, as well as a number of other genes or pseudogenes of unknown biological significance. Most of the latter have C + G-rich sequences in their 5' ends that are unmethylated in the B-lymphoblastoid cell line 3.1.0. We investigated one of these genes, HLA-H, in more detail. The gene is, overall, strongly homologous in sequence to HLA-A but differs in several potentially significant ways, including changes in conserved promoter sequences, a single-base deletion producing a translation termination codon in exon 4, and a region of sequence divergence downstream of the transcribed portion of the gene. Nevertheless, mouse L cells transfected with the gene accumulated small amounts of apparently full-length polyadenylated RNA. A portion of this RNA begins at the transcription site predicted by analogy to certain class I cDNA clones, while another portion appears to begin shortly upstream. L cells transfected with a hybrid gene containing the first three exons of HLA-H and the last five exons of HLA-B27 accumulated full-length HLA transcripts at the same level as cells transfected with an HLA-B27 gene; both levels are at least 15- to 20-fold higher than that directed by HLA-H alone. In addition, we isolated a cDNA clone for HLA-H that contains a portion of intron 3 attached to a normally spliced sequence comprising exons 4 through 8. These results suggest that low levels of translatable mRNA for the truncated class I heavy chain encoded by HLA-H are produced under physiologic circumstances and that sequences 3' of intron 3 decrease the levels of stable transcripts.

Construction of a uniform-abundance (normalized) cDNA library.

“…A 1.5-kbp probe was isolated from a BamHI digest of a y-actin cDNA clone constructed in pBR322 (17). HLA-H, a pseudogene (6.9 kbp) containing a fragment from the human major histocompatibility complex (18) with extensive homology to class I-like sequences, was cloned from the JY cell line (lymphoblastoid) in our laboratory. A 300-bp fragment of the Oct-I gene, a sequencespecific DNA binding protein (19), was PCR amplified by using internal primers spanning coding sequences.…”

Analysis of Major Histocompatibility Complex Gene Products in Tissues Isolated from the Developing Human Nervous System

“…MHC class I-spe cific RNA sequences were detected utilizing a 32P-radiolabeled HLA-H 6.6-kb EcoRl fragment known to be highly cross-reactive with the HLA-A, -B, -C common determi nant of the primary MHC class I-specific sequences [28]. Similarly, MHC class II-specific RNA sequences were detected utilizing a 32P-radiolabeled HLA-DR 3.1-kb EcoRl fragment with specificity for the a sequence of the MHC class II determinant [29], The assay was performed using a limiting Fig.…”

Nomenclature for Factors of the Hla System, 1990

“…A gene shown to be very closely related to HLA-A and previously known as HLA-AR, associated with a class 15.4 kb Hin dIII fragment (Malissen et al, 1982;Biro etal., 1983;Duceman & Wang, 1988;Zemmour et al, 1990;Chorney et al, 1990) has been named HLA-H, using the next letter available for a HLA gene.…”