Alternative splicing of transcripts for the alpha 3 chain of mouse collagen VI: identification of an abundant isoform lacking domains N7-N10 in mouse and human.

Three distinct alpha chains form the collagen VI monomer, the alpha 3(VI) chain being much larger than the alpha 1(VI) and alpha 2(VI) chains. The alpha 3(VI) chain has 10 von Willebrand Factor type A domains of approximately 200 amino acids at the N-terminus (N1-N10) compared with only one such domain in the alpha 1(VI) and alpha 2(VI) chains. Domains N10, N9, N7 and N3 of the alpha 3(VI) chain are subject to alternative splicing in chick and/or human tissues, indicating the possibility of isoforms that have different functions depending on which N-terminal domains are included or excluded. In this study we have PCR amplified and sequenced mouse alpha 3(VI) cDNA encoding the N2-N10 domains. By reverse transcription-PCR using oligonucleotides spanning different regions of the cDNA we have undertaken a comprehensive analysis of alternative splicing of the alpha 3(VI) mRNA in embryonic and adult mouse tissues. We demonstrate that domains N10, N9 and N7 are also subject to alternative splicing in mouse tissues and in addition identify an abundant novel variant transcript that lacks all four N-terminal domains (N7-N10) in mouse tissues and human cells. We also identify less abundant transcripts that lack a large part of the N3 domain, and transcripts lacking the entire N5 domain. Using specific RNase protection assays we show that the shorter transcripts containing domains (N8+N7+N6), (N8+N6) and N6 are present at higher levels than transcripts containing the N10 and/or N9 domains, with tissue-specific variation in the levels of variant transcripts. These studies demonstrate a larger range of collagen VI protein variants than previously described.