Tyrosine aminotransferase and chymotrypsinogen B are linked to haptoglobin on human chromosome 16q: comparison of genetic and physical distances

Insights on N-glycosylation of human haptoglobin and its association with cancers

Protein glycosylation is one of the most significant post-translation modifications and plays a critical role in various biological functions. Haptoglobin (Hp) is one of the acute-phase response proteins secreted by liver. Its glycosylation could be analyzed by many analytical techniques qualitatively and quantitatively. The glycosylation alterations of Hp are reported to be associated with different kinds of diseases. The main glycosylation alterations of Hp in cancer appear to be the presence of aberrantly fucosylated and sialylated structures as well as increased branching. In this mini review, we provided a brief overview of Hp structure and biological function, discussed its glycosylation alterations in different cancers, and described the existing technologies for analyzing glycosylation site and glycan of Hp. Given the importance of Hp glycosylation, its unknown and unclear biological complexity and significances, Hp glycosylation has become a major target in cancer research. Development of sensitive and specific detection of Hp glycosylation including large-scale validation may be significant steps forward to its clinical application.

High resolution localization of recombination hot spots using sperm typing

We have applied sperm DNA typing to determine the distribution of crossover events within a one megabase region of the short arm of human chromosome 4 near the locus for Huntington disease. A total of 29 recombinants were detected among 602 sperm typed after whole genome amplification. These recombinants were typed for seven polymorphic markers. The 280 kilobase D4S10-D4S126 interval was found to undergo recombination at a 6-9-fold greater rate per unit of physical distance than the adjacent 720 kb D4S126-D4S127 interval. Sperm typing has the potential to dissect mammalian recombination hot spots to the point where DNA sequence analysis may reveal the molecular basis for hyperrecombination.

Genomic cloning and partial characterization of human chymotrypsinogen gene

Chymotrypsinogen is a principal precursor of pancreatic proteolytic enzymes. We previously isolated a cDNA clone for human prechymotrypsinogen from a human pancreatic cDNA library. In the present study, we used this cDNA sequences to isolate genomic DNA clones. Three overlapping cosmid clones spanning approximately 65-kb genomic sequences were isolated from a human cosmid library. The genomic DNA clones were characterized by restriction enzyme mapping and by hybridizing them to subfragments of the cDNA. The sequence tagged sites for human chymotrypsinogen gene were created by designing two oligonucleotides. Furthermore, the isolated genomic clones were confirmed to be localized on chromosome 16q23 by fluorescence in situ hybridization and G-banding analysis.

Point mutations in the tyrosine aminotransferase gene in tyrosinemia type II

Tyrosinemia type II (Richner-Hanhart syndrome, RHS) is a disease of autosomal recessive inheritance characterized by keratitis, palmoplantar hyperkeratosis, mental retardation, and elevated blood tyrosine levels. The disease results from deficiency in hepatic tyrosine aminotransferase (TAT; L-tyrosine:2-oxoglutarate aminotransferase, EC 2.6.1.5), a 454-amino acid protein encoded by a gene with 12 exons. To identify the causative mutations in five TAT alleles cloned from three RHS patients, chimeric genes constructed from normal and mutant TAT alleles were tested in directing TAT activity in a transient expression assay. DNA sequence analysis of the regions identified as nonfunctional revealed six different point mutations. Three RHS alleles have nonsense mutations at codons 57, 223, and 417, respectively. One "complex" RHS allele carries a GT----GG splice donor mutation in intron 8 together with a Gly----Val substitution at amino acid 362. A new splice acceptor site in intron 2 of the fifth RHS allele leads to a shift in reading frame.

Gene mapping of ocular diseases

Increasing awareness of the role of genetic factors in the causation of many human eye diseases has made ocular genetics one of the fastest growing areas of ophthalmology. The objective of this paper is to present the basic principles of gene mapping and their application to ophthalmology. The techniques used to map the genome are reviewed with emphasis placed on molecular genetics. The advances in this area have already provided the major impetus to the areas of diagnosis and prevention of some genetic eye disorders. Tables are presented that list the autosomal, X-linked and mitochondrial assignment of eye genes and disorders with ocular involvement.

Genomic organization and chromosomal mapping of the mouse P-cadherin gene

Cadherins are a family of Ca(2+)-dependent cell adhesion molecules, that includes P-cadherin, E-cadherin, N-cadherin and L-CAM. In this study, the genomic organization of the mouse P-cadherin gene was determined by analyzing overlapping DNA clones obtained from a mouse genomic library. The results showed that this gene spans over 45 kb and consists of 15 exons. A marked feature of this gene is that the first intron is 23 kbp long accounting for half its length. Comparisons of this structure with that of L-CAM, a chicken cadherin, revealed that the exon-intron boundaries are conserved between the two genes except that the P-cadherin first exon includes the correspoding first and second exons of the L-CAM gene. This gene was also similar to the other in that the second intron, which corresponds to the P-cadherin first intron, is exceptionally longer than other introns. These results suggest that the exon-intron pattern conserved in these genes is of significance for generation of domain structure of cadherin molecules or for their transcriptional regulation. We also determined the chromosomal localization of the P-cadherin gene by interspecific backcross analysis, and found that this gene is located in the central region of mouse chromosome 8 and linked with the E-cadherin locus. This is the first evidence for the linkage of different cadherin genes.

Allele loss on chromosome 16 associated with progression of human hepatocellular carcinoma

Loss of heterozygosity on chromosome 16 is a common genetic alteration in human hepatocellular carcinoma (HCC). To clarify the pathogenetic significance of allele loss on chromosome 16, we performed restriction fragment length polymorphism analysis of 70 surgically resected tumors by using 15 polymorphic DNA markers for chromosome 16. Loss of heterozygosity on chromosome 16 was detected in 36 (52%) of 69 informative cases, and the common region of allele loss in these 36 tumors was located between the HP locus (16q22.1) and the CTRB locus (16q22.3-q23.2). These losses occurred more frequently in HCCs of poor differentiation, of larger size, and with metastasis, whereas they were not detected in HCC at the earliest stage. In addition, these losses were not associated with presence or absence of hepatitis B virus DNA integration or hepatitis C virus infection. These results show that loss of heterozygosity on chromosome 16 is a late event occurring after hepatocarcinogenesis and strongly suggest that this phenomenon is involved in enhancement of tumor aggressiveness during progression of HCC.

Isolation and characterization of the human tyrosine aminotransferase gene

Structure and sequence of the human gene for tyrosine aminotransferase (TAT) was determined by analysis of cDNA and genomic clones. The gene extends over 10.9 kbl and consists of 12 exons giving rise to a 2,754 nucleotide long mRNA (excluding the poly(A)tail). The human TAT gene is predicted to code for a 454 amino acid protein of molecular weight 50,399 dalton. The overall sequence identity within the coding region of the human and the previously characterized rat TAT genes is 87% at the nucleotide and 92% at the protein level. A minor human TAT mRNA results from the use of an alternative polyadenylation signal in the 3' exon which is present but not used at the corresponding position in the rat TAT gene. The non-coding region of the 3' exon contains a complete Alu element which is absent in the rat TAT gene but present in apes and old world monkeys. Two functional glucocorticoid response elements (GREs) reside 2.5 kb upstream of the rat TAT gene. The DNA sequence of the corresponding region of the human TAT gene shows the distal GRE mutated and the proximal GRE replaced by Alu elements.

Gene mapping on mouse chromosome 8 by interspecific crosses: new data on a linkage group conserved on human chromosome 16q

A large conserved linkage group exists on mouse chromosome 8 and human chromosome 16q, including the loci for chymotrypsinogen B (Ctrb), haptoglobin (Hp), lecithin:cholesterol acyltransferase (Lcat), metallothionein-1,-2 (Mt-1,-2), tyrosine aminotransferase (Tat), and uvomorulin (Um). Using cloned gene probes, these six loci were mapped in M. m. domesticus X M. spretus interspecific crosses relative to a number of chromosome 8 anchor loci resulting in the gene order Es-1,Es-9-Mt-1,-2-Got-2-Es-2,Es-7,Lcat,Um-Hp,Tat,Ctrb-e. These results complement earlier studies and redefine the conserved segment on mouse chromosome 8, previously defined by the Hp-Tat interval, by the 24-cM interval between Mt-1,-2 and the conserved locus for adenine phosphoribosyltransferase, Aprt, mapped at 25 cM from Es-1 by T. B. Nesterova, P. M. Borodin, S. M. Zakian, and O. L. Serov (1987, Biochem. Genet. 25: 563-568). Within this segment, the gene order appears the same in man and mouse. While map distances between HP-TAT,HP-CTRB, and TAT-CTRB of respectively 7, 11, and 9 cM have previously been measured in man, no crossovers between Hp, Tat, and Ctrb were observed in over 100 meioses in the mouse.

A genetic linkage map of five marker loci in and around the Duchenne muscular dystrophy locus

Linkage analysis of five marker loci in and around the Duchenne muscular dystrophy (DMD) locus, DXS84, DXS206, DXS164, DXS270, and DXS28, was conducted with 499 families. Overall, the best multipoint distances were found to be DXS84-3.7 +/- 0.6 cM-DXS206-1.0 +/- 0.4 cM-DXS164-1.9 +/- 0.6 cM-DXS270-12.0 +/- 1.1 cM-DXS28. A comparison of this linkage map with the established physical map suggests the presence of hot spots for recombination in the DMD locus.

The human tyrosine aminotransferase gene: characterization of restriction fragment length polymorphisms and haplotype analysis in a family with tyrosinemia type II

Deficiency in hepatic tyrosine aminotransferase (TAT) causes tyrosinemia type II, an autosomal recessively inherited disorder. Using a TAT cosmid clone, we have identified an MspI restriction fragment length polymorphism (RFLP) 5' to the TAT gene, with allele frequencies of 0.63 and 0.37. Analysis of the cloned maternal and paternal TAT alleles from a patient with tyrosinemia type II led to the identification of a HaeIII RFLP at the 3' end of the TAT gene, with allele frequencies of 0.94 and 0.06. The two RFLPs are 27 kb apart and in no allelic association. From haplotype frequencies, a polymorphism information content (PIC) value of 0.44 was obtained. The two RFLPs have allowed the unambiguous identification of the mutant TAT alleles in the patient's pedigree by haplotype analysis.