Use of R-loop mapping for the assessment of human collagen mutations

Detection and localization of base changes in RNA using a chemical cleavage method

The detection of base changes in DNA and RNA is of central importance in genetic research. Mismatched cytosines and thymines in heteroduplex DNA molecules show increased chemical reactivity with hydroxylamine and osmium tetroxide, respectively, and the DNA can then be specifically cleaved at the modified nucleotides. We show here that mismatched cytosines and thymines can be detected and located directly in RNA: DNA heteroduplex molecules. In order to detect guanosine and adenosine base changes the complementary cDNA strand must be analyzed. In addition, the sensitivity of the technique can be increased by employing the polymerase chain reaction. To test the fidelity of this method a number of known or predicted mutations were analyzed. These include single point mutations in the human collagen alpha 1(I) and rat phenylalanine hydroxylase mRNA, two engineered point mutations in a mouse collagen alpha 1(I) mRNA, and a deletion in a human collagen alpha 2(I) mRNA. All known base changes were detected and correctly localized. In addition, the predicted base changes were confirmed.

Inherited disorders of collagen gene structure and expression

As a result of investigations completed during the last 15 years, the molecular bases of most form of osteogenesis imperfecta (OI) and of some forms of the Ehlers-Danlos syndrome (EDS) are now known. Most forms of OI result from point mutations in the genes (COL1A1 and COL1A2) that encode the chains of type I procollagen or mutations that affect the expression of these genes. Less frequently, mutations that affect the size of the chain can also result in these phenotypes. The phenotypic presentation appears to be determined by the nature of the mutation, the chain in which it occurs, and, for point mutations, the position of the substitution and the nature of the substituting amino acid in the protein product. Similar mutations in the gene (COL3A1) that encodes the chains of type III procollagen result in the EDS type IV phenotype. Mutations which result in deletion of the cleavage site for the aminoterminal procollagen protease result in the EDS type VII phenotype and other mutations which affect the structure of the triple-helical domain by deletions and alter the conformation of the substrate at the site of proteolytic conversion can produce mixed phenotypes. Alterations in post-translational processing of collagenous proteins can result in the EDS type VI and EDS type IX phenotypes. Linkage analysis and study of type II collagen proteins from individuals with a variety of skeletal dysplasias suggest that similar mutations in these genes also result in clinically apparent phenotypes. Mutations in the majority of the 20 known collagen genes have not yet been identified.

Osteogenesis imperfecta

Major advances have occurred in the classification of OI and in the definition of underlying molecular defects. A clearer understanding of the pathogenesis of OI and of the relationships between the phenotypes and genotypes should emerge. The study of induced mutations in selected regions of the collagen genes with expression in cultured cells or transgenic mice should hasten this process. These advances will also provide a basis for studies into the large number of other genetically determined connective tissue disorders that are grouped together as the skeletal dysplasias. The results of recent studies in OI are providing a unique insight into many aspects of collagen and connective tissue biochemistry, physiology and pathology.