Isolation and characterization of overlapping genomic clones covering the chicken alpha 2 (type I) collagen gene

[50 years of connective tissue research: from the French Connective Tissue Club to the French Society of Extracellular Matrix Biology]

The history of connective tissue research began in the late 18th century. However, it is only 50 years later that the concept of connective tissue was shaped. It took another fifty years before biochemical knowledge of extracellular matrix macromolecules began to emerge in the first half of the 20th century. In 1962, thanks to Ladislas and Barbara Robert, back from the US, the first society called "French Connective Tissue Club" was created in Paris. The first board was constituted of Albert Delaunay, Suzanne Bazin and Ladislas Robert. Very quickly, under the influence of these pioneers, national and international meetings were organized and, in 1967, a "Federation of the European Connective Tissue Clubs" was created at the initiative of Ladislas Robert (Paris) and John Scott (Manchester). It spread rapidly to the major European nations. In 1982 the transformation of "Clubs" in "Societies" occurred, a name more in line with the requirements of the time. In 2008, the "French Connective Tissue Society" became the "French Society of Extracellular Matrix Biology" ("Société Française de Biologie de la Matrice Extracellulaire", SFBMEc), to better highlight the importance of the extracellular matrix in the biology of living organisms. The SFBMEc's mission today is to promote and develop scientific exchanges between academic, industrial, and hospital laboratories involved in research on the extracellular matrix. SFBMEc organizes or subsidizes scientific meetings and awards scholarships to Ph.D. students or post-docs to participate in international conferences. It includes 200 to 250 members from different disciplines, developing strong interactions between scientists, clinicians and pathologists. It is present all around the French territory in many research laboratories. During these last 50 years, the extraordinary advances made possible by the development of new investigation techniques, in particular molecular biology, cell and tissue imaging, molecular modeling, etc., have permitted a considerable increase of the knowledge in the field of connective tissue.

Structural and functional studies on the interstitial collagen genes

An understanding of the molecular mechanisms which control expression of the type I and III collagen genes may provide a rational basis for the design of more effective therapeutic approaches to fibrotic diseases. The structure of the interstitial collagen genes is reviewed and potential sites which could control their expression are examined. One approach to the study of the regulation of these genes consists in DNA-mediated gene transfection experiments and is discussed in this paper.

The chick alpha2(I) collagen gene contains two functional promoters, and its expression in chondrocytes is regulated at both transcriptional and post-transcriptional levels

Embryonic chick cartilages contain transcripts derived from the alpha2(I) collagen gene, although type I collagen is not normally found in these tissues; most of these RNAs are alternative transcripts initiating within intron 2. Use of the internal start site results in replacement of exons 1 and 2 with a previously undescribed exon and a change in the translational reading frame; thus, the alternative transcript cannot encode alpha2(I) collagen. We have demonstrated that production of the alternative transcript is due to activation of an internal promoter in chondrocytes and have identified a 179-base pair domain that is required for its activity. Furthermore, we have shown that the alternative transcript resulting from activation of the internal promoter turns over relatively rapidly; thus, the steady-state level of this transcript is less than predicted based on the transcription rate. The upstream promoter is only partially repressed in chondrocytes, suggesting that the lack of authentic alpha2(I) collagen mRNA may also be due in part to decreased mRNA stability. Thus, repression of alpha2(I) collagen synthesis in cartilage involves both transcriptional and post-transcriptional mechanisms. In contrast, repression of alpha1(I) collagen synthesis appears to be mediated primarily at the level of transcription.

Expression of collagenlike sequences by a tumor virus, herpesvirus saimiri

Sequencing demonstrates that the oncogenic regions of a group A strain and a group C strain of herpesvirus saimiri are nonhomologous. A bicistronic viral mRNA from this region is transcribed in tumor cells transformed by a highly oncogenic group C virus. The first open reading frame is homologous to collagen; no such sequences were found in group A or B strains. This is the first report that a virus encodes for sequences similar to those of a connective tissue protein.

The chicken alpha-globin gene domain is transcribed into a 17-kilobase polycistronic RNA

The 5' start sites and the 3' ends of giant transcripts of the approximately 20-kilobase (kb)-long chicken alpha-globin gene domain were identified by reverse transcription with specific primers and by nuclease S1 mapping using cloned and sequenced restriction fragments of the domain. A transcriptional unit of approximately 17 kb was found that includes all three embryonic and adult genes of the cluster. The largest transcript initiates 8 kb upstream of the gene, within a cluster of A + T-rich sequences placed upstream of a matrix attachment point, at one of several CAA(A)T boxes framing a cluster of four TATA boxes. The 5' ends of a group of 2.5-, 5-, and 12-kb globin transcripts accumulating in avian erythroblastosis virus-transformed cells, which transcribe globin genes abortively, map to the sequence ATATATAATAA 1 kb upstream of the embryonic pi-globin gene. This sequence might correspond to a site of RNA processing or of alternative transcription initiation. Transcription of the domain ends about 2 kb downstream of the last gene of the cluster, downstream of an enhancer and immediately upstream of a CR1 repetitive element in an A + T-rich sequence that includes a matrix attachment site. These data indicate that full-domain transcripts including embryonic as well as adult alpha-globin genes exist, and that the region transcribed is framed by A + T-rich linkers and matrix attachment points.

Structure of a full-length cDNA clone for the prepro alpha 2(I) chain of human type I procollagen. Comparison with the chicken gene confirms unusual patterns of gene conservation

A cDNA clone from a human placental library was found to consist of an essentially full-length cDNA of 4.6 kb for the prepro alpha 2(I) chain of type I procollagen. Nucleotide sequencing of the 5'-end of the cDNA provided a sequence of 1617 nucleotide residues and codons for 539 amino acid residues not previously defined. Comparison of the complete structure of the prepro alpha 2(I) cDNA with previously reported sequences for the chicken pro alpha 2(I) gene indicated that 83% of 1366 total amino acid residues were conserved. In the alpha-chain domain 84% of 1014 amino acid residues were conserved. Also, there was conservation of the previously noted preference for U and C in the third position of codons for glycine, proline and alanine. One major difference between the human and the chicken prepro alpha 2(I) chain was that the human chain contained 21 fewer proline residues, an observation that probably explains why the triple helix of human type I procollagen unfolds at temperatures that are 1-2 degrees C lower. In parallel experiments, sequencing of intron-exon boundaries for nine exons of genomic subclones confirmed and extended previous observations that the pro alpha 2(I) gene, like other genes from fibrillar collagens, has an unusual 54-base pattern of exon sizes that is highly conserved through evolution.

Structure of the human hemopexin gene and evidence for intron-mediated evolution

The human hemopexin gene was isolated and its structure determined. The gene spans approximately 12 kb and is interrupted by nine introns. When the intron/exon pattern was examined with respect to the polypeptide segments they encode, a direct correspondence between exons and the 10 repeating units in the protein was observed. The introns are not randomly placed; they fall in the middle of the region of amino acid sequence homology in strikingly similar locations in 6 of the 10 units and in a symmetrical position in the two halves of the coding sequence. These features strongly support the hypothesis that the gene evolved through intron-mediated duplications of a primordial sequence to a five-exon cluster. A more recent gene duplication led to the present-day gene organization.

Do exons code for structural or functional units in proteins?

In considering the origin and evolution of proteins, the possibility that proteins evolved from exons coding for specific structure-function modules is attractive for its economy and simplicity but is not systematically supported by the available data. However, the number of correspondences between exons and units of protein structure-function that have so far been identified appears to be greater than expected by chance alone. The available data also show (i) that exons are fairly limited in size but are large enough to specify structure-function modules in proteins; (ii) that the position of introns for homologous domains in the same gene is reasonably stable, but there is also evidence for mechanisms that alter the position or existence of introns; and (iii) that it is possible that the observed relationship of exons to protein structure represents a degenerate state of an ancestral correspondence between exons and structure-function modules in proteins.

Periodicities in introns

The sequence information for the splicing process of introns is found in the consensus sequences at the two splice sites. For long introns, of 300 or more nucleotides, the middle regions may provide additional specificity for splicing which can be investigated by defining an adequate quantitative parameter. This methodology permits to retrieve the coding periodicity in the viral and mitochondrial introns and to identify with a statistical significance, a surprising alternating purine-pyrimidine base sequence -i.e. a modulo 2 periodicity- in the eukaryotic introns, and particularly in the vertebrate introns. This alternating structure suggests that the vertebrate introns do not have the genetic information to code for proteins, they carry structural and regulatory functions.

Identification of a cell-specific transcriptional enhancer in the first intron of the mouse alpha 2 (type I) collagen gene

A transcriptional enhancer has been identified in the first intron of the mouse alpha 2 (type I) collagen gene in a region between +418 and +1524 base pairs from the transcriptional start site. The enhancer functions both when it is located 5' and 3' to the promoter that it activates and is independent of the orientation of the element. The enhancer stimulates both the homologous alpha 2 type I [alpha 2(I)] collagen promoter and the heterologous early simian virus 40 promoter. In transient expression experiments, enhancer-dependent transcription from the alpha 2(I) collagen promoter utilizes the same transcriptional start site as the one used in the endogenous alpha 2(I) collagen gene. The enhancer activates transcription at a distance of at least 3 kilobase pairs from the transcriptional start site. The alpha 2(I) collagen enhancer displays cell specificity, since it is functional in NIH 3T3 fibroblasts but completely inactive in a lymphoid cell line, in contrast to two immunoglobulin gene enhancers that show the opposite behavior. We find several areas of sequence homology with viral enhancers, particularly the enhancer of simian virus 40.

Transcriptional control of the mouse alpha 2(I) collagen gene: functional deletion analysis of the promoter and evidence for cell-specific expression

A chimeric gene was constructed in which sequences between 2,000 base pairs upstream of the start of transcription of the mouse alpha 2(I) collagen gene and 54 base pairs downstream of this site were fused to the chloramphenicol acetyltransferase (CAT) gene. We present evidence suggesting that this collagen gene segment is sufficient for cell-specific expression of the chimeric gene. Indeed, the levels of CAT activity in transient expression experiments were at least 10 times higher after transfection of NIH 3T3 cells than after transfection of a mouse myeloma cell line, whereas much less difference was found after transfection of these two cell types with pSV2-CAT, a plasmid in which the early simian virus 40 promoter is fused to the CAT gene. Several deletions were introduced in the same 5'-flanking segment of the alpha 2(I) collagen gene, and the effects of these deletions were examined after DNA transfection of the chimeric collagen-CAT gene into NIH 3T3 cells. At least two segments broadly located between -979 and -502 and between -346 and -104 are needed for optimal expression of the chimeric gene. These results were obtained both in transient expression experiments and by analysis of pools of NIH 3T3 cells that were stably transfected with the different mutants. In general, the effects of the deletions on the activity of the alpha 2(I) collagen promoter were analogous, whether the plasmids harbored the simian virus 40 enhancer sequence or not, although the overall levels of expression of the chimeric gene were increased when the recombinant plasmids contained this sequence.

Exon/intron organization of the chicken type II procollagen gene: intron size distribution suggests a minimal intron size

Overlapping genomic clones have been isolated that contain the alpha chain and COOH-terminal propeptide coding regions of the chicken type II procollagen gene. All type II procollagen exon sequences present in these clones have been identified and mapped by DNA sequencing. These include 43 exons coding for the alpha-chain triple helix, 1 exon coding for the junction between the COOH-terminal propeptide and the alpha-chain region, and 3 exons coding for the COOH-terminal propeptide and 3' noncoding sequences. With the exception of one additional intron between 2 exons coding for amino acids 568-585 and 586-603, exon-intron boundaries have been conserved when compared with genes for all other characterized genes for fibrillar collagens. The chicken type II procollagen gene differs from most other collagen genes in having introns of considerably smaller average size. The size distribution of the introns suggests that approximately equal to 80 base pairs may be a minimal functional size for introns in this gene. This size of intron may be necessary in a gene with a very large number of small exons to prevent aberrant splicing from removing exon sequence together with intron sequence.

Developmental and tissue-specific expression directed by the alpha 2 type I collagen promoter in transgenic mice

Eight transgenic mice were generated in which the promoter of the mouse alpha 2(I) collagen gene (nucleotides -2000 to +54), linked to the bacterial gene for chloramphenicol acetyltransferase (CAT), is stably integrated in the germ line. These strains contain from 1 to 20 copies of the alpha 2(I) collagen-CAT chimeric gene per haploid genome. In seven of the eight strains, the CAT gene is expressed, although the levels of CAT enzyme activity vary considerably from one strain to the other. In six of these strains, the expression of the CAT gene follows the expected tissue distribution pattern of expression of the alpha 2(I) collagen gene. In these six strains, the level of CAT activity is much higher in extracts of tail, a tissue that is very rich in tendons, than in any other tissue that was tested. This distribution parallels the much higher levels of alpha 2(I) collagen RNA that are found in the tail as compared to other tissues. Expression of the chimeric gene is detected in the embryo after 8.5 days of gestation, at approximately the same time that the endogenous type I genes become active. We conclude that the alpha 2(I) collagen promoter sequences present in the recombinant plasmid used for our experiments contain sufficient information to ensure stage- and tissue-specific activity of this promoter.

Transcriptional control of the mouse alpha 2(I) collagen gene: functional deletion analysis of the promoter and evidence for cell-specific expression

A chimeric gene was constructed in which sequences between 2,000 base pairs upstream of the start of transcription of the mouse alpha 2(I) collagen gene and 54 base pairs downstream of this site were fused to the chloramphenicol acetyltransferase (CAT) gene. We present evidence suggesting that this collagen gene segment is sufficient for cell-specific expression of the chimeric gene. Indeed, the levels of CAT activity in transient expression experiments were at least 10 times higher after transfection of NIH 3T3 cells than after transfection of a mouse myeloma cell line, whereas much less difference was found after transfection of these two cell types with pSV2-CAT, a plasmid in which the early simian virus 40 promoter is fused to the CAT gene. Several deletions were introduced in the same 5'-flanking segment of the alpha 2(I) collagen gene, and the effects of these deletions were examined after DNA transfection of the chimeric collagen-CAT gene into NIH 3T3 cells. At least two segments broadly located between -979 and -502 and between -346 and -104 are needed for optimal expression of the chimeric gene. These results were obtained both in transient expression experiments and by analysis of pools of NIH 3T3 cells that were stably transfected with the different mutants. In general, the effects of the deletions on the activity of the alpha 2(I) collagen promoter were analogous, whether the plasmids harbored the simian virus 40 enhancer sequence or not, although the overall levels of expression of the chimeric gene were increased when the recombinant plasmids contained this sequence.

A distinct class of vertebrate collagen genes encodes chicken type IX collagen polypeptides

Type IX collagen is a disulfide-bonded protein first isolated from hyaline cartilage. The structure of this collagen is unusual in that the molecules contain three triple-helical domains interspersed with noncollagenous regions. The molecules are heterotrimers composed of three genetically distinct polypeptide chains. In our laboratory, cDNAs specific for two of these polypeptide chains have recently been isolated. Here we report on the isolation of genomic clones by use of these cDNAs as probes for screening a chicken genomic library. Nucleotide sequence analysis of these clones shows that the exon structure of type IX collagen genes is fundamentally different from the exon structure of the genes for the fibrillar collagen types I-III. Whereas the sizes of exons in fibrillar collagen genes are related to a basic 54-base-pair coding unit, the exons of type IX collagen genes show a large variation in size and do not appear to be related to a 54-base-pair unit. We propose, therefore, that type IX collagen genes belong to a class of vertebrate collagen genes distinct from that of fibrillar collagens.

Regulation of a collagen gene promoter by the product of viral mos oncogene

Oncogenic transformation of cells produces important changes in the biosynthetic pattern of certain cellular proteins. For example, the synthesis of type I collagen in transformed fibroblasts is severely reduced as a result of changes in transcription. Here we report the results of DNA-mediated transfection experiments using recombinant plasmids in which the promoter region of the alpha 2(I) collagen gene is fused to an easily recognizable marker gene, and cell lines expressing the marker gene are isolated. Our data show that the expression of the marker gene fused to the cloned alpha 2(I) collagen promoter is strongly inhibited by v-mos transformation, suggesting that a common mechanism inhibits both the transfected and endogeneous alpha 2(I) collagen promoters.

Intron-dependent evolution of chicken glyceraldehyde phosphate dehydrogenase gene

The function of introns in the evolution of genes can be explained in at least two ways: either introns appeared late in evolution and therefore could not have participated in the construction of primordial genes, or RNA splicing and introns existed in the earliest organisms but were lost during the evolution of the modern prokaryotes. The latter alternative allows the possibility of intron participation in the formation of primordial genes before the divergence of modern prokaryotes and eukaryotes. Blake suggested that evidence for intron-facilitated evolution of a gene might be found by comparing the borders of functional protein domains with the placement of introns. We therefore examined glyceraldehyde phosphate dehydrogenase (GAPDH), a glycolytic enzyme, because it is the first protein for which the following data are available: X-ray crystallographic studies demonstrating structurally independent protein 'domains' which were highly conserved during the divergence of prokaryotes and eukaryotes; and a study of genomic organization which mapped introns in the gene. Sequencing of the chicken GAPDH gene revealed 11 introns. We report here that sites of three of the introns (IV, VI and XI) correspond closely with the borders of the NAD-binding, catalytic and helical tail domains of the enzyme, supporting the hypothesis that introns did have a role in the evolution of primitive genes. In addition, other biochemical and structural data were used to construct a model of the intron-mediated assembly of the GAPDH gene that explains the existence of 10 introns.

Peptide-maps of procollagen (I) from corneas and tendons of 17-day-old chick embryos

Corneas and tendons dissected from 17-day-old chick embryos were labeled with [35S]methionine in the presence of 0.3 mM alpha,alpha'-dipyridyl. The unhydroxylated, 35S-labeled pro alpha chains and alpha chains were isolated by polyacrylamide gel electrophoresis in sodium dodecyl sulfate. The pro alpha and alpha chains were then subjected to peptide-map analysis by proteolytic digestion with trypsin and alpha-chymotrypsin, papain or proteinase K. The peptide-maps derived from cornea and tendon pro alpha 1(I) chains are identical. Similar results were obtained from cornea and tendon alpha 1(I) chains. There were differences in the peptide maps derived from cornea and tendon pro alpha 2(I) chains. However, no difference was observed in alpha 2(I) chains. These results suggest that cornea and tendon pro alpha 1(I) chains are probably identical in primary structures, whereas the cornea pro alpha 2(I) chain may be different from the tendon pro alpha 2(I) chain within pepsin sensitive regions of the procollagen molecule. The reason for difference in the peptide-maps of pro alpha 2(I) chains remain unknown. One of the possible explanations is the variation of posttranslational modification within the propeptides of the pro alpha 2(I) chain. However, this hypothesis needs to be further investigated. Nevertheless, the finding that the peptide-maps of alpha 2(I) chains from tendons and corneas are identical fail to support the two genes hypothesis for pro alpha 2(I) chains.

Number and organization of collagen genes in Caenorhabditis elegans

We analyzed the number and organization of collagen genes in the nematode Caenorhabditis elegans. Genomic Southern blot hybridization experiments and recombinant phage library screenings indicated that C. elegans has between 40 and 150 distinct collagen genes. A large number of recombinant phages containing collagen genes were isolated from C. elegans DNA libraries. Physical mapping studies indicated that most phage contained a single small collagen gene less than 3 kilobases in size. A few phage contained multiple collagen hybridizing regions and may contain a larger collagen gene or several tightly linked small collagen genes. No overlaps were observed between phages containing different collagen genes, implying that the genes are dispersed in the C. elegans genome. Consistent with the small size of most collagen genes, we found that the predominant class of collagen mRNA in C. elegans is 1.2 to 1.4 kilobases in length. Genomic Southern blot experiments under stringent hybridization conditions revealed considerable sequence diversity among collagen genes. Our data suggest that most collagen genes are unique or are present in only a few copies.

Number and organization of collagen genes in Caenorhabditis elegans

We analyzed the number and organization of collagen genes in the nematode Caenorhabditis elegans. Genomic Southern blot hybridization experiments and recombinant phage library screenings indicated that C. elegans has between 40 and 150 distinct collagen genes. A large number of recombinant phages containing collagen genes were isolated from C. elegans DNA libraries. Physical mapping studies indicated that most phage contained a single small collagen gene less than 3 kilobases in size. A few phage contained multiple collagen hybridizing regions and may contain a larger collagen gene or several tightly linked small collagen genes. No overlaps were observed between phages containing different collagen genes, implying that the genes are dispersed in the C. elegans genome. Consistent with the small size of most collagen genes, we found that the predominant class of collagen mRNA in C. elegans is 1.2 to 1.4 kilobases in length. Genomic Southern blot experiments under stringent hybridization conditions revealed considerable sequence diversity among collagen genes. Our data suggest that most collagen genes are unique or are present in only a few copies.

Conservation of the sizes for one but not another class of exons in two chick collagen genes

Type III collagen is often found in the same tissues as type I collagen, yet the function and nature of the fibrils formed by the two collagens differ markedly. To understand the evolutionary history of the collagen gene family in more detail, we isolated the gene for type III collagen and compared its structure with that of the gene for alpha 2(I) collagen. This comparison points to a remarkable conservation in the size distribution of the exons coding for the helical part of these two collagen polypeptides: equivalent amino acid segments in the helical domain of each polypeptide are encoded by exons of equal sizes in each gene. This suggests that after the interstitial collagen genes had been duplicated from a common ancestor about 2-5 X 10(8) years ago, no recombinations between these exons were tolerated, although the same recombinational phenomena must have played an important part in shaping the structure of the progenitor for these genes. This fixation of the size distribution of the exons which code for the interstitial collagen helical domains is found despite the persistence in these exons of sequence elements that should have favoured recombinational rearrangements, and contrasts with the variations in the pattern of sizes of some exons coding for the amino and carboxyl propeptides of these collagens.

Isolation of cDNA and genomic DNA clones encoding type II collagen

A cDNA library constructed from total chick embryo RNA was screened with an enriched fraction of type II collagen mRNA. Two overlapping cDNA clones were characterized and shown to encode the COOH propeptide of type II collagen. In addition, a type II collagen clone was isolated from a Charon 4A library of chick genomic fragments. Definitive identification of the clones was based on DNA sequence analysis. The 3' end of the type II collagen gene appears to be similar to that of other interstitial collagen genes. Northern hybridization data indicates that there is a marked decrease in type II collagen mRNA levels in chondrocytes treated with the dedifferentiating agent 5-bromodeoxyuridine. The major type II collagen mRNA species is 5300 bases long, similar to that of other interstitial collagen RNAs.

DNase I sensitivity of the alpha 2(I) collagen gene: correlation with its expression but not with its methylation pattern

The chromatin structure of the chick alpha 2(I) collagen gene was probed with DNase I. Because our previous work strongly suggested that the 5' end of this gene is not methylated whereas the rest of the gene is methylated whether or not the gene is expressed, we compared the relative DNase I sensitivity of the methylated and unmethylated segments. Both regions demonstrate similar relative DNase I sensitivities within a given tissue. In chromatin of chick embryo fibroblasts, we find a DNase I hypersensitive site which maps between 100 and 300 bp preceding the start of transcription. This site is not found in brain chromatin but is present in chick embryo fibroblasts transformed by Rous Sarcoma virus although the rate of transcription of the alpha 2(I) collagen gene is greatly reduced in these cells. Hence, the mechanism responsible for the large decrease in alpha 2(I) collagen gene expression in RSV transformed cells is different from the mechanism that is responsible for the presence of a DNase I hypersensitive site in the promoter. Furthermore, changes in the DNase I sensitivity of the chromatin of the alpha 2(I) collagen promoter occur without changes in the methylation pattern of the gene.

Construction and characterization of type II collagen complementary deoxyribonucleic acid clones

The mRNA for type II collagen was purified from embryonic chick sternum or from purified sternal chondrocytes with guanidine thiocyanate as the extractant. Double-stranded cDNAs to procollagen mRNAs from sternum were synthesized and dC-tailed. After annealing with PstI-cleaved, dG-tailed pBR322, this DNA was used to transform Escherichia coli X1776. Transformed colonies were screened by colony hybridization to type I and II collagen cDNAs. Clones that preferentially hybridized to type II cDNA were characterized further. Four such cDNA clones, pCgII-2, 3, 10 and 12, with inserts of 400, 320, 260 and 750 bp, have been identified as type II collagen cDNA clones by several criteria, including their preference for hybridizing with type II rather than type I collagen mRNAs in hybrid-selected translation experiments.

Multiple 3' ends of the chicken pro alpha 2(I) collagen gene

The precise location of the 3' ends of the chicken pro alpha 2(I) collagen gene have been identified by S1 nuclease protection of overlapping genomic fragments by calvaria poly A containing RNA and size determination of the protected fragments on DNA sequencing gels. The gene ends 300 and 306 bp and 754 and 777 bp from the translation stop codon. The two sets of ends explain the major and minor pro alpha 2(I) collagen mRNAs previously observed, which may result from either RNA polymerase readthrough of the first termination site and/or different processing sites.

Internal deletion in a collagen gene in a perinatal lethal form of osteogenesis imperfecta

Cloned probes specific for unique genes have proven to be powerful tools in defining the nature of genetic diseases such as the thalassaemias and growth hormone deficiencies. A similar approach should be useful in defining heritable diseases of type I collagen, the heterotrimer of two alpha 1(I) chains and one alpha 2(I) chain, which is the most abundant member of the collagen family of proteins. Recently, cloned cDNAs and genomic DNAs for the two polypeptide chains of the type I collagen have become available and have been used to elucidate the chromosomal location of the corresponding genes. Here, we have used several of these cloned DNAs to demonstrate the presence of an internal deletion of about 0.5 kilobases (kb) in one allele for the pro alpha 1(I) chain in a patient with osteogenesis imperfecta (OI), a group of heritable disorders which are characterized by brittle bones but which are highly heterogeneous both phenotypically and biochemically.

A conserved nucleotide sequence, coding for a segment of the C-propeptide, is found at the same location in different collagen genes

The nucleotide sequence of a segment of the chick alpha 1 type III collagen gene which codes for the C-propeptide was determined and compared with the corresponding sequence in the alpha 1 type I and alpha 2 type I collagen genes. As in the alpha 2 type I gene the coding information for the C-propeptide of the type III collagen gene is subdivided in four exons. Similarly, the amino proximal exon contains sequences for both the carboxy terminal end of the alpha-helical segment of collagen and for the beginning of the C-propeptide in both genes. Therefore, this organization of exons must have been established before these two collagen genes arose by duplication of a common ancestor. In several subsegments the deduced amino acid sequence for the C-propeptide of type III collagen shows a strong homology with the corresponding amino acid sequence in alpha 1 and alpha 2 type I. For one of these homologous amino acid sequences, however, the nucleotide sequence is much better conserved than for the others. It is possible that a mechanism of gene conversion has maintained the homogeneity of this nucleotide sequence among the interstitial collagen genes. Alternatively, the conserved nucleotide sequence may represent a regulatory signal which could function either in the DNA or in the RNA.

Chick pro alpha 2 (I) collagen gene: exon location and coding potential for the prepropeptide

We report the DNA sequence of a cDNA clone complementary to the 5' end of the chick pro alpha 2(I) mRNA. The sequence enables us to deduce the amino acid sequence of this region, which has been refractory to conventional protein sequencing techniques. Its importance lies in the role of the prepropeptide in secretion, triple helix formation of the mature protein and initiation of fibrillogenesis. We have also located four of the five exons which code for this region on the genome. One exon is only 11bp in size and appears to code exclusively for the signal propeptidase cleavage site. This is an extreme example of an exon defining a functional unit.

Isolation of genomic DNA clones spanning the entire fibronectin gene

Overlapping recombinant clones that appear to encompass the entire fibronectin gene have been isolated by step-wise screening of a library of chicken genomic DNA fragments. The first genomic clone was isolated by using a cloned fibronectin cDNA hybridization probe. The remaining clones were obtained by using defined fragments of this and successive genomic clones as probes. Their relationships and overlaps were determined by electron microscopy, restriction mapping, and heteroduplex analysis. Based on electron microscopic analysis of hybrids between these clones and fibronectin mRNA, the gene is approximately 48 kilobases long, more than 5 times larger than the corresponding mRNA. This large gene contains at least 48 exons interrupted by introns of highly variable size. The total exon size as estimated by R-loop analysis is 8 kilobases, similar to the mRNA for fibronectin. With the exception of the 3'- and 5'-terminal exons, the exons are small and roughly similar in size. The average exon size is 147 +/- 37 base pairs, corresponding to a protein unit of 50 amino acids. The nucleotide sequence of one of these exons was determined. The deduced amino acid sequence has marked homologies with one type of repetitive protein sequence unit known to exist in bovine fibronectin. These results suggest that the gene for fibronectin may have arisen by multiple gene duplications of a primordial gene or genes approximately equal to 150 base pairs long.