Localization of human type II procollagen gene (COL2A1) to chromosome 12

Parental somatogonadal COL2A1 mosaicism contributes to intrafamilial recurrence in a family with type 2 collagenopathy

The COL2A1 gene encodes the alpha-1 chain of procollagen type 2. Pathogenic variants in the COL2A1 gene are associated with several different types of skeletal dysplasia collectively known as type 2 collagenopathies. Type 2 collagenopathies have an autosomal dominant inheritance. Some germline or somatogonadal mosaicism cases have been reported. We investigated whether somatogonadal mosaicism occurred in a family with two children suspected of type 2 collagenopathies or related diseases. First, we detected a pathogenic variant in the COL2A1 gene in the two affected children by whole exome sequencing (WES). Next, we performed targeted deep sequencing to their parents without the variant by WES. A low level of COL2A1 mosaicism was revealed in the mother's tissues. We concluded that the mother had somatogonadal mosaicism with the COL2A1 mutation arose in the epiblast, and that the intrafamilial recurrence rate of the disease by the somatogonadal mosaicism was higher than by the germline mosaicism. This report suggests that parental low-level mosaicism should be evaluated in those parents with children carrying de novo germline mutations and the targeted deep sequencing is useful to detect them.

In situ hybridization localizes the human type II alpha 1 collagen gene (COL2A1) to 12q13

We have, using in situ hybridization technique, localized the human type II alpha 1 collagen gene (COL2A1) to chromosome band 12q13. The gene had previously been assigned to either 12q13.1-13.2 or 12q14.3. Since the chromosome segment 12q13-15 has been shown to be rearranged in several benign and malignant human neoplasms, the exact band localization of COL2A1 within this region makes it a useful marker for the molecular analysis of these tumors.

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.

Detection of sequence variants in the gene for human type II procollagen (COL2A1) by direct sequencing of polymerase chain reaction-amplified genomic DNA

The direct sequencing of the human type II procollagen (COL2A1) gene from polymerase chain reaction (PCR)-amplified genomic DNA is described. Thirty-two regions of the COL2A1 gene were asymmetrically amplified with intron primers which were specifically chosen to amplify a region spanning 500 to 800 bp of sequence encoding one or more exons and their accompanying intervening sequences. Primers for dideoxynucleotide sequencing of the PCR products were then designed to provide complete exon sequence information and to insure that intron:exon splice junction sequence data would be obtained. Amplification and sequencing reactions were performed on an automated workstation to facilitate the handling of multiple DNA templates. The procedure allowed efficient sequencing of over 25,000 bp of each allele of the COL2A1 gene per diploid genome. We used this method for the comparative analyses of COL2A1 sequences in DNA isolated from the blood of 42 unrelated individuals and we identified 21 neutral sequence variants in the gene. The sequence variations were confirmed by independent assays, including restriction enzyme digestion. The sequence variants described here will be important for identifying haplotypes of the type II procollagen gene that will be useful in defining a genetic etiology for diseases of cartilaginous tissues.

Completion of the primary structure of the human type IV collagenase preproenzyme and assignment of the gene (CLG4) to the q21 region of chromosome 16

The complete amino acid sequence of the human type IV collagenase preproenzyme was determined from cDNA and genomic clones. Primer extension and S1 nuclease analyses as well as nucleotide sequencing of a genomic clone indicate that the first exon has two closely spaced initiation sites for transcription and codes for 290 and 280 nt of a 5' untranslated region and a 29-residue signal peptide. The gene (CLG4) was localized to 16q21 using somatic cell hybrids and in situ hybridization.

Human type II collagen gene (COL2A1) assigned to chromosome 12q13.1-q13.2 by in situ hybridization with biotinylated DNA probe

We have made a regional assignment of the type II collagen gene (COL2A1) on human chromosome 12 by means of an in situ hybridization technique with a biotinylated DNA probe. The precise localization of the signal was mapped to the band 12q13.1-q13.2. This result was in agreement with the previous mapping by isotopic in situ hybridization technique (12q13.1-q13.2), but not with the result of Southern hybridization analysis using somatic cell hybrids (12q14.3).

Assignment of the human collagen alpha 1 (XIII) chain gene (COL13A1) to the q22 region of chromosome 10

Type XIII collagen is a recently described collagen that resembles in structure the short-chain collagens of types IX, X, and XII. Unlike any other collagen, the type XIII is found in several different forms generated through alternative splicing. A 2.0-kb genomic fragment from the human alpha 1 (XIII) collagen gene was isolated and shown by DNA sequencing to contain exon 12 as counted from the 3' end. This fragment was used as a probe to localize the gene. The gene (COL13A1) was assigned to chromosome 10 by hybridization of the probe to DNA isolated from a panel of human-mouse somatic cell hybrids containing different human chromosomes. Furthermore, the gene was mapped to the q22 region by in situ hybridization to metaphase chromosomes.

Molecular cloning of rat and human type IX collagen cDNA and localization of the alpha 1(IX) gene on the human chromosome 6

Type IX collagen is found in hyaline cartilage, where it is associated with type II collagen in quarter-staggered collagen fibrils. Chicken type IX collagen has been extensively characterized and shown to contain molecules with three triple-helical domains, interspersed with non-triple-helical sequences. The molecule contains three, genetically distinct, subunits and one of these subunits carries a covalently bound glycosaminoglycan side chain. In the present report, we describe for the first time the primary structure of mammalian type IX collagen chains, based on cloning and sequencing of cDNA from rat and human cDNA libraries. The results suggest that mammalian alpha 1(IX) chains have the same multi-domain structure as the avian protein. We also demonstrate, by in situ hybridization of chromosome spreads, that the human alpha 1(IX) collagen gene is located on the long arm of chromosome 6. The cloning of human type IX collagen cDNA provides a probe for molecular studies of human chondrodysplasias that may involve abnormalities in this extracellular collagen-proteoglycan.

The human alpha 2(IV) collagen gene, COL4A2, is syntenic with the alpha 1(IV) gene, COL4A1, on chromosome 13

We have previously assigned the gene for the alpha 1 chain of type IV collagen to chromosome 13. In this report we show that the gene coding for the second chain of this heterotrimer is on the same chromosome. This is the first example of the genes for both chains of one collagen molecule being syntenic.

Human collagen genes encoding basement membrane alpha 1 (IV) and alpha 2 (IV) chains map to the distal long arm of chromosome 13

At least 20 genes encode the structurally related collagen chains that comprise greater than 10 homo- or heterotrimeric types. Six members of this multigene family have been assigned to five chromosomes in the human genome. The two type I genes, alpha 1 and alpha 2, are located on chromosomes 17 and 7, respectively, and the alpha 1 (II) gene is located on chromosome 12. Our recent mapping of the alpha 1 (III) and alpha 2 (V) genes to the q24.3----q31 region of chromosome 2 provided the only evidence that the collagen genes are not entirely dispersed. To further determine their organization, we and others localized the alpha 1 (IV) gene to chromosome 13 and in our experiments sublocalized the gene to band q34 by in situ hybridization. Here we show the presence of the alpha 2 type IV locus also on the distal long arm of chromosome 13 by hybridizing a human alpha 2 (IV) cDNA clone to rodent-human hybrids and to metaphase chromosomes. To our knowledge, these studies represent the only demonstration of linkage between genes encoding both polypeptide chains of the same collagen type.

The single copy gene coding for human alpha 1 (IV) procollagen is located at the terminal end of the long arm of chromosome 13

Using dual-laser sorted chromosomes and spot-blot analysis, we have previously assigned genomic DNA sequences coding for human alpha 1 (IV) procollagen to chromosome 13 (Pihlajaniemi et al. 1985). By in situ hybridization to normal chromosomes and chromosomes with 13q deletions, we now report the localization of this gene to the terminal end of the long arm of chromosome 13. In addition, Southern and slot blot hybridization analysis clearly show that these genomic sequences are present only once per haploid genome.

The human type II collagen gene (COL2A1) assigned to 12q14.3

A cosmid clone containing the entire human type II alpha 1 collagen gene (COL2A1) was used as probe in the Southern analysis of DNA from a panel of human/hamster somatic cell hybrids containing different portions of human chromosome 12. Two of the hybrids exhibited a similar terminal deletion q14.3----qter, but one was positive for the gene while the other was negative. Therefore, the gene must reside in the region q14.3.

Structure of the type II collagen gene

In summary, the exon/intron structure of the chicken type II collagen gene is identical with that of the chicken alpha 2(I) collagen gene and differs at only one known position from the human and mouse alpha 1(I) genes. However, the chicken type II gene is different from the chicken alpha 2(I) gene in that it is considerably shorter because of a much smaller average intron size and in that the G+C composition of the introns is much higher. The codon usage of the type II genes also shows characteristic differences. There is a single copy of the chick type II gene per haploid genome.

Nonrandom association of a type II procollagen genotype with achondroplasia

Achondroplasia is an autosomal dominant disorder that involves defective endochondral bone formation. Type II collagen is the predominant collagen of cartilage. We found a HindIII polymorphic site in the normal Caucasian population by using the type II procollagen gene probe pgHCol(II)A. The presence of this site yields a 7.0-kilobase (kb) band; its absence yields a 14.0-kb band. We found a significant deviation in genotype distribution and allele frequencies in a population of unrelated individuals with sporadic achondroplasia, compared with the normal control population. The HindIII genotype frequencies in 32 individuals with achondroplasia are 0.41 for the 7/7 genotype (controls, 0.08), 0.34 for the 7/14 genotype (controls, 0.54), and 0.25 for the 14/14 genotype (controls, 0.37). The apparent equilibrium excess of the "7" allele in individuals with achondroplasia may reflect either a predisposition for the mutation that causes achondroplasia or it could be the result of the achondroplasia-causing mutation. In either case, these findings suggest an association of the type II procollagen gene with achondroplasia.

A highly polymorphic region 3' to the human type II collagen gene

We have characterised a highly polymorphic region 1.3kb downstream of the human Type II collagen gene. It consists of a highly AT-rich tandem repetitive region (minisatellite) approximately 650bp long. Two alleles had been observed previously, differing in size by approximately 300bp. When this region was cloned from four unrelated individuals carrying the larger allele, DNA sequence data identified three alleles, suggesting far higher polymorphism than was originally supposed. This minisatellite was shown to be present in a single copy in the human genome, and to have arisen after the divergence of Old and New World monkeys.

Human alpha 1(III) and alpha 2(V) procollagen genes are located on the long arm of chromosome 2

The multigene procollagen family encodes probably greater than 20 genetically distinct but structurally related polypeptide chains. Recent characterization of human procollagen clones has allowed determination of functional domains within the proteins, genomic organization, and chromosomal location. Previously, we assigned the coordinately expressed type I genes (alpha 1 and alpha 2) to chromosomes 17 and 7, respectively, and now other investigators have mapped the type II gene to chromosome 12 [Strom, C. M., Eddy, R. L. & Shows, T. B. (1984) Somatic Cell Genet. 10, 651-655]. Recently, we isolated cDNA clones encoding the fourth interstitial procollagen, type III, and the alpha 2 chain of the type V cytoskeletal components. To determine whether these genes were clustered with alpha 1(I), alpha 2(I), or alpha 1(II) or were further dispersed in the genome, in situ hybridization of the alpha 1(III) and alpha 2(V) probes to metaphase chromosomes was carried out. Here we report a fourth autosome with procollagen gene loci but the first cytological evidence for linkage. By using normal and translocated cell lines, our results show that both the alpha 1(III) and alpha 2(V) procollagen genes map to the q24.3----q31 region of chromosome 2.