Structural comparison of the chicken genes for alpha 1(VI) and alpha 2(VI) collagen

Phylogenetic distribution of intron positions in alpha-amylase genes of bilateria suggests numerous gains and losses

Most eukaryotes have at least some genes interrupted by introns. While it is well accepted that introns were already present at moderate density in the last eukaryote common ancestor, the conspicuous diversity of intron density among genomes suggests a complex evolutionary history, with marked differences between phyla. The question of the rates of intron gains and loss in the course of evolution and factors influencing them remains controversial. We have investigated a single gene family, alpha-amylase, in 55 species covering a variety of animal phyla. Comparison of intron positions across phyla suggests a complex history, with a likely ancestral intronless gene undergoing frequent intron loss and gain, leading to extant intron/exon structures that are highly variable, even among species from the same phylum. Because introns are known to play no regulatory role in this gene and there is no alternative splicing, the structural differences may be interpreted more easily: intron positions, sizes, losses or gains may be more likely related to factors linked to splicing mechanisms and requirements, and to recognition of introns and exons, or to more extrinsic factors, such as life cycle and population size. We have shown that intron losses outnumbered gains in recent periods, but that "resets" of intron positions occurred at the origin of several phyla, including vertebrates. Rates of gain and loss appear to be positively correlated. No phase preference was found. We also found evidence for parallel gains and for intron sliding. Presence of introns at given positions was correlated to a strong protosplice consensus sequence AG/G, which was much weaker in the absence of intron. In contrast, recent intron insertions were not associated with a specific sequence. In animal Amy genes, population size and generation time seem to have played only minor roles in shaping gene structures.

Complete exon-intron organization and chromosomal location of the gene for mouse type XIII collagen (col13a1) and comparison with its human homologue

Recent findings indicate that type XIII collagen is a transmembrane protein with a short N-terminal sytocsolic domain, a single transmembrane domain and a large, mainly collagenous ectodomain. The complete exon-intron structure of the gene coding for the mouse alpha1(XIII) collagen chain, col13a1, has now been characterized from genomic clones spanning over 180 kilobases (kb) and shown to be approximately 135 kb in size and to contain 42 exons varying between 8 base pairs (bp), the shortest exon in the genes encoding the various collagens, and 836 bp. Nuclease S1 mapping and 5'RACE resulted in identification of multiple transcription initiation points in the mouse gene, ranging between 470 and 548 bp upstream from the initiation methionine. This is in good agreement with a recently identified human EST clone extending 537 bp upstream from the initiation methionine. The 836-bp first exon of the mouse gene covers both the long 5' untranslated region and also a 36-residue cytosolic portion, a 23-residue transmembrane domain, and 37 residues of the 60-residue non-collagenous ectodomain immediately adjacent to the plasma membrane. One striking feature of the exons encoding solely collagenous sequences is the abundance of 27-bp exons, half the ancestral 54-bp size characteristic of fibrillar collagen genes, while the others vary between 8 and 144 bp, including instances of 36-, 45- and 54-bp exons. Determination of approximately 2.6 kb of sequences upstream of the initiation methionine of both the mouse and human genes and the identification of a clone containing four exons and spanning a gap in the previously characterized human clones allowed detailed comparison of the two genes. The exon-intron structures were found to be completely conserved between the species, and both genes have their 5' untranslated region preceded by a highly homologous apparent promoter region of approximately 350 bp containing a modified TATAA motif and several GC boxes. The chromosomal location of the mouse gene was determined by SSCP and fluorescence in situ hybridization and found to be at chromosome 10, band 4, between markers D1OMit5 -2.3 +/- 1.6 cM -col13a1 - 3.4+/-1.9 cM - D1OMit15. This result indicates that the mouse type XIII collagen gene and its human counterpart are located in chromosomal segments with conserved syntenies (The GenBank accession numbers for the mouse gene are AF063666-AF063693. The new GenBank accession number for the 5' end of the human type XIII collagen gene is AF071009).

Human COL6A1: genomic characterization of the globular domains, structural and evolutionary comparison with COL6A2

The alpha1(VI) and alpha2(VI) chains of type VI collagen (nonfibrillar) are highly similar and are encoded by single-copy genes in close proximity on human Chromosome (Chr) 21q22.3, a gene-rich region that has proved refractory to cloning. For the alpha1(VI) chain, only the regions encoding the triple-helical and the promoter have been characterized hitherto.To facilitate our study of the role of this gene in the phenotype of Down syndrome, we have cloned and sequenced the amino- and carboxyl-terminal globular domains of COL6A1. The amino-terminal domain consists of seven exons and the carboxyl-terminal globular domain of nine exons. Together with the exons of the triple-helical domain, COL6A1 is encoded by a total of 36 exons spanning approximately 30 kb. Comparison of the genomic organization of COL6A1 and COL6A2 revealed that despite the similarity within their triple-helical domains, the intron-exon structures of their globular domains differ markedly. Conservation is limited to the exons encoding amino acids immediately adjacent to the triple-helical region, including the cysteine residues essential for the structure of mature collagen VI. The intron-exon structures of these two genes are highly similar to the collagen VI genes of chicken. These data suggest that COL6A1 and COL6A2 arose from a gene duplication before the divergence of the reptilian and mammalian lineages.

Expression and distribution of two alternatively spliced transcripts from the chicken alpha 2 (VI) collagen gene

Two types of mRNA molecules with different 3' ends are transcribed from the chicken alpha 2(VI) collagen gene. The major splice variant encodes a polypeptide with a von Willebrand factor A domain at its carboxyl terminus. In the minor splice variant, this A domain is replaced by a novel motif which reveals some similarity to a fibronectin type III repeat. In situ hybridization experiments demonstrate that the major transcript is ubiquitously expressed. Substantial amounts are found in skeletal and cardiac muscle, gizzard, skin, tendon, liver, the wall of blood vessels, and the connective tissue of peripheral nerves. In contrast, the minor transcript is expressed at a very low level and can hardly be detected in any tissue by in situ hybridization. Only the aortic wall contains a considerable amount of this splice variant. However, no difference is observed by Northern blotting and the polymerase chain reaction in the ratio of the two transcripts when aorta and the other tissues are compared. Thus, the minor splice variant is not expressed in a tissue specific manner and, consequently, it is unlikely that it plays a tissue specific role. It might rather serve a general function in the structure and assembly of type VI collagen microfibrils.

Characterization of the human alpha 1(VI) collagen promoter and its comparison with human alpha 2(VI) promoters

From a human cosmid library, we isolated a clone (5B) with an insert of 32 kb, encoding the amino-terminal and the 5'-end flanking region of the alpha 1(VI) collagen gene. Exon 1 was found to be 194 bp and contain the 5' untranslated region plus 97 bp coding sequence. Exon 2 consists of 130 bp, a size that is conserved across the chicken and mouse species. S1-nuclease-protection assays and primer-extension analysis, using mRNA from human dermal fibroblasts, show the presence of multiple transcription start sites located in a region of approximately 20 nucleotides. Canonical TATA and CAAT boxes, as found in the chicken and mouse alpha 1 promoters, were absent in the human alpha 1(VI) promoter. The promoter region from positions -1 to -190, is a polypyrimidine/polypurine-rich region containing 12 CCCTCCCC (CT element consensus) sequences and has multiple potential binding sites for the Sp1, and AP2 transcription factors. These regulatory proteins bind to the alpha 2(VI) promoters [Saitta, B. & Chu, M.-L. (1994) Eur. J. Biochem. 223, 675-682]. To test the transcriptional activity of the alpha 1 promoter, transient transfection experiments of the DNA constructs were performed in human dermal fibroblasts and in human fibrosarcoma (HT1080) cell lines. The DNA constructs drive the expression of the chloramphenicol acetyl transferase (CAT) gene. The results show strong CAT activity for the constructs at positions -1700, -298 and -257, while low activity was found for the constructs at positions -4400, -142 and -5 when transfected in fibroblasts. The experiments also identified positive and negative regulatory regions in the alpha 1(VI) promoter CAT constructs when transfected in fibroblasts, but did not identify them in the fibrosarcoma cells.

A novel transcription factor and two members of the Sp 1 multigene family regulate the activity of the alpha 2 (VI) collagen promoter

For a better understanding of the processes that lead to the activation or inhibition of type VI collagen synthesis, we have identified and characterized the cis-acting elements of the chicken alpha 2 (VI) collagen promoter. This promoter encompasses four sites, termed S1, S2, X and S3, which interact with nuclear factors. Sites S1, S2 and S3 are each recognized by the same two proteins that belong to the Sp 1 multigene family. Site X appears to interact with a novel transcription factor of 43 kDa. When a fragment containing all four of the elements is placed in front of a reporter gene, the resulting construct is able to induce a high level of transcription in chicken fibroblasts. As soon as a single element is deleted from this construct, the activity decreases drastically. Thus, the four elements are essential for the transcriptional activation of the alpha 2 (VI) collagen gene.

Type A modules: interacting domains found in several non-fibrillar collagens and in other extracellular matrix proteins

A 200-amino acid long motif first recognized in von Willebrand Factor (type A module) has been found in components of the extracellular matrix, hemostasis, cellular adhesion, and immune defense mechanisms. At present the extracellular matrix is the predominant site of expression of type A modules since at least four non-fibrillar collagens and two non-collagenous proteins contain a variable number of modules ranging from one to twelve. The modules conform to a consensus motif made of short conserved subregions separated by stretches of variable length. The proteins that incorporate type A modules participate in numerous biological events such as cell adhesion, migration, homing, pattern formation, and signal transduction after interaction with a large array of ligands.

Murine alpha 1(VI) collagen chain. Complete amino acid sequence and identification of the gene promoter region

The entire primary structure of the murine alpha 1(VI) collagen chain was deduced from cloned cDNA. The predicted polypeptide consists of 1025 amino acids and shows extensive homology with the corresponding human and chicken chains. A genomic clone isolated with a cDNA probe was found to contain about 13 kilobases of the 5'-flanking region and the first and second exon, coding for the 5'-untranslated sequence and signal peptide and part of the N-terminal portion of the mature protein, respectively. Polymerase chain reaction and primer extension analyses revealed two major and several minor transcription start sites distributed over 76 base pairs (bp). The region just upstream of the transcription initiation sites lacks canonical TATA and CAAT boxes and Sp1 binding sites, but contains putative binding sites for other transcription factors and a 90-bp polypyrimidine tract with elements of dyad symmetry. Chimeric constructs were derived from different fragments of the 5'-flanking genomic region and the chloramphenicol acetyltransferase (CAT) gene and expression of the reporter gene was assayed following transfection of various cell types. A construct containing sequences extending from -215 to +41 directed high levels of CAT expression. The data indicate that this region harbours a functional promoter.

Characterization of the chicken alpha 1(VI) collagen promoter

The promoter of the chicken alpha 1(VI) collagen gene resembles the 5'-flanking regions of many housekeeping genes. It lacks a canonical TATAA box but contains potential binding sites for transcription factors AP1 and SP1. The promoter region has a relatively high GC content and forms a typical CpG island. In accordance with the absence of a TATAA element, the gene contains multiple transcription-initiation sites distributed over 80 bp genomic DNA. A 621-bp fragment derived from the 5' end of the alpha 1(VI) collagen gene is able to direct transcription of a heterologous reporter gene in transient-expression assays. Other DNA fragments that are either shorter or longer than the 621-bp fragment show markedly reduced promoter activity. Thus, the basic promoter element of the alpha 1(VI) collagen gene must reside within this 621-bp fragment.