Embryonic chicken cornea and cartilage synthesize type IX collagen molecules with different amino-terminal domains

We have analyzed embryonic chicken cornea for the presence of type IX collagen mRNA and protein. Using RNA transfer blot analysis, we demonstrate that alpha 1(IX) and alpha 2(IX) mRNAs are expressed by corneal epithelial cells at the time that the primary stromal components are synthesized. The levels of the mRNAs decrease with increasing developmental age and are barely detectable at day 11 of development. In contrast, type IX collagen protein is detectable by immunofluorescence at days 5 and 6 and undetectable by day 8. Using probes specific for alpha 1(IX) and alpha 2(IX) mRNAs, we demonstrate that the size of alpha 2(IX) mRNA is the same in cornea as in chondrocytes, the major source of type IX collagen. However, the alpha 1(IX) mRNA is about 700 nucleotides shorter in the cornea than in cartilage because the corneal form of the mRNA does not contain the 5' region that encodes the non-triple-helical amino-terminal globular domain of cartilage type IX collagen. Therefore, corneal type IX collagen must lack this domain. This structural modulation of an extracellular matrix protein is likely to contribute to the functional differences between cartilage matrix and the early corneal stroma, both of which are rich in type II collagen.