A novel noncollagenous protein encoded by an alternative transcript of the chick type III collagen gene is expressed in cartilage, bone and muscle

Nested genes: Biological implications and use of AFM for analysis

A "nested" gene is located within the boundaries of a larger gene, often within an intron and in the opposite orientation. Such structures are common in bacteria and viruses, but have also been described in higher species as diverse as Drosophila and humans. Expression of nested and host genes may be simultaneously up-regulated due to use of common enhancers, or down-regulated through steric hindrance or interference caused by annealing of the complementary RNAs, leading to degradation. Methods for RNA analysis such as RT-PCR and in situ hybridization reveal the presence of specific mRNAs, but do not address regulation of expression within a single cell at a single genetic locus. Atomic force microscopy is a relatively new technology, which allows visualization of the movement of an RNA polymerase along a DNA template. The potential of this technology includes a greater molecular understanding of cellular decision making processes, leading to enhanced opportunities to intervene in disease progression through use of novel treatment modalities.

Intervertebral disc collagen. Usage of the short form of the alpha1(IX) chain in bovine nucleus pulposus

Nucleus pulposus, the central zone of the intervertebral disc, is gel-like and has a similar collagen phenotype to that of hyaline cartilage. Amino-terminal protein sequence analysis of the alpha1(IX)COL3 domain purified from bovine nucleus pulposus gave a different sequence to that of the long alpha1(IX) transcript expressed in hyaline cartilage and matched the predicted sequence of short alpha1(IX). The findings indicate that the matrix of bovine nucleus pulposus contains only the short form of alpha1(IX) that lacks the NC4 domain. The sequence encoded by exon 7, predicted from human COL9A1, is absent from both short and long forms of alpha1(IX) from bovine nucleus pulposus and articular cartilage. A structural analysis of the cross-linking sites occupied in type IX collagen from nucleus pulposus showed that usage of the short alpha1(IX) transcript in disc tissue had no apparent effect on cross-linking behavior. As in cartilage, type IX collagen of nucleus pulposus was heavily cross-linked to type II collagen and to other molecules of type IX collagen with a similar site occupancy.