The ultimate goal of this research is to create a retroposon map of the human genome. Mapping will be approached using techniques of high resolution in situ hybridization and quantitative image analysis, combined with Southern blot analysis of somatic cell hybrids containing single human chromosomes or chromosome bands. There are two major retroposon families and 6 minor families in humans accounting for 15-20% of the mass of the genome and occurring in 1,000-1,000,000 copies per haploid genome. Although these elements are actively shaping the genome and are known to be associated with insertional and deletional mutations in humans, the process of retroposition, and the functions of the progenitor sequences and of their descendants are unknown. We have recently confirmed that the two major retroposons, Alu and L1 are not randomly distributed throughout the genome but instead are clustered in regions defined by the human metaphase chromosome bands, the domains related to DNA replication, prophase condensation, crossing over, gene density, and fragile sites.
The aims of this proposal are: 1. To determine the retroposon map of human chromosomes using high resolution in situ hybridization and computer aided image analysis. Biotinylated probes for 8 families of human retroposons will be investigated, including Alu, MstII, SINE-R, O-LTR, L1 and its subfragments, L2HS, THE-1 and HSRTVL-H. 2. To create a retroposon map of single human chromosomes 17 and 21 and their chromosome bands using Southern blot hybridization of the above retroposon families to somatic cell hybrids carrying single human chromosomes or bands. A panel of restriction enzymes will be used to screen each chromosome for distinct retroposon subfamilies. 3. To create a retroposon map of the human X chromosome, and to identify and clone a subfamily of putatively full length L1 retroposons visible on Southern blots as a single band and concentrated in the centromeric region bordering the region of the putative X inactivation center. Using this specific subfamily of retroposons of L1 as markers for the region, the neighboring non L1 sequences will be identified to help elucidate the molecular structure of the region. These studies should provide further molecular information on the basis of chromosome organization and may help close the gap in genome analysis to allow the identification of new DNA sequences in defined chromosomal regions, and the detection and cloning of some chromosomal changes below the limit of cytogenetic analysis.
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