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C W Summers

Publications and source records attributed to C W Summers.

5 recordsLinked to original sources
PubMed1993

HLA class I non-coding nucleotide sequences, 1992.

We present a compilation of the nucleotide sequences of the non-coding regions of the human HLA class I genes which complements previously published information on exon sequences. The listing includes the 5' and 3' untranslated (UT) regions, and introns 1-7. The HLA class I loci and their alleles from which non-coding sequences were derived are listed in Table 1, together with source references. Where possible, locus and allele designations follow the Nomenclature for factors of the HLA system 1991 (Bodmer et al., 1992). In aligning sequences, nucleotides which are conserved between all class I genes are specified only by the consensus sequence, and are indicated by a hyphen (-). To maintain the alignment between different alleles, an asterisk (*) is inserted where there is a gap in the sequence. An unavailable sequence is indicated by a period (.). Regions of sequence too diverse to be accurately compared are represented by an exclamation mark (!). Sequence motifs previously classified as having an important role in HLA class I regulation or processing, such as enhancer sequences, are identified at the bottom of the sequence comparison. It is not our intention in this paper to present an analysis of the many features revealed by this compilation. However, we hope that the information will provide important reference material for studies of HLA class I mRNA processing (Cianetti et al., 1989), promoter regulation (David-Watine et al., 1990) and in the design of allele, locus or region specific PCR primers (Summers et al., 1991). We hope to update this compilation in due course, and we would welcome sequence information not included in this publication, as well as comments and corrections that help to maintain the accuracy of the information.

Alleles↗
PubMed1991

Polymerase chain reaction analysis of transcriptional patterns of expression of class I HLA genes.

In order to study transcriptional patterns of expression of individual class I HLA genes we have constructed a series of cDNA libraries from human cell lines including normal lymphoblastoid cell lines MANN and HOM2, two colorectal carcinoma cell lines, WiDr and SW480, and a fetal lung fibroblast cell line, MRC-5. Between 0.5 and 1 x 10(6) independent clones were screened in each library using a class I HLA-specific DNA probe and the frequency of class I HLA cDNA clones was found to vary between 0.23% (WiDr) and 0.76% (HOM2). Polymerase chain reaction (PCR)-based analyses of possible alternative splicing events showed that each of 161 class I HLA cDNA clones which had insert sizes exceeding 0.6 kb exhibited normal splicing patterns for exons 5 and 6. Similar PCR-based analyses in clones with appropriately large inserts revealed no exceptions to the normal splicing patterns for each of exons 2, 3, 4, and 7. Sixty of the class I HLA cDNA clones selected from the WiDr, MRC-5, and MANN cDNA libraries were assigned to individual loci following identification of locus-specific DNA sequences by PCR sequencing across exon 5. The sequences obtained from the 60 clones were each interpreted to correspond to one of the classical loci, HLA-A, HLA-B, and HLA-C. While representatives of the HLA-A locus predominated in the MANN library, HLA-B-specific clones were the most abundant in the WiDr and MRC-5 libraries.

Base Sequence↗
PubMed1991

Characterization of an expressible nonclassical class I HLA gene.

Screening of a human cosmid library representing genomic DNA from an individual homozygous for the HLA-DR2 B7 A2 haplotype yielded 109 class I HLA-specific clones. One cosmid clone, Ice 6.23, had a full-length nonclassical class I gene within a 5.4-kb HindIII fragment. The Ice 6.23-5.4H gene was cloned into the unique NotI site of an expression vector pSV2.Not, a derivative of pSV2neo, which was constructed to contain a second SV40 early region promoter adjacent to an introduced NotI site. The resulting construct was transfected into the P815-B2M cell line, a derivative of the mouse mastocytoma P815 (HTR) line which expressed human beta2-microglobulin following stable transfection with a cloned human beta2-microglobulin gene. Following transfection the Ice 6.23-5.4 H gene was found to be expressed at both the mRNA and cell surface product levels. DNA sequencing of this gene suggests that it is allelic to the HLA-6.0 gene clone (HLA-G) of Geraghty et al. (Proceedings of the National Academy of Sciences USA, 84:9145, 1987); thereby revealing a HindIII restriction fragment length polymorphism at the HLA-G locus. An extraordinarily high degree of sequence similarity (99.92%) between these two genes, which derive from unrelated HLA haplotypes, suggests strong conservative selection pressure at the HLA-G locus. A flanking single copy sequence probe 4 kb distant from the Ice 6.23-5.4H gene was used to generate long-range restriction mapping at the HLA-G locus.

Amino Acid Sequence↗
PubMed1987

Restriction fragment length polymorphism at the HLA-C locus.

We have used the HLA-C-specific DNA probe pC250 to investigate restriction fragment length polymorphism (RFLP) at the HLA-C locus. Genomic Southern blot hybridization included DNA prepared from a panel of homozygous typing cells representing serological specificities Cw1 to Cw8 and also from samples representing Cw blanks. Although many restriction nucleases failed to reveal any polymorphism, RFLPs were evident with Taq I, Pvu II, Bst XI, Nde I, and Nci I in addition to the previously reported Eco RI. In the case of Bst XI, a unique RFLP defined a subset of serologically defined Cw blanks. Comparison of RFLP sizes with restriction fragment lengths obtained from the known HLA-Cw3 gene sequence permitted the localization of intragenic C locus RFLPs and the identification of a variable Taq I site in the second intron, a variable Nci I site near the end of the fourth exon, and a variable Pvu II site in the fifth intron.

Chromosome Mapping↗