MAPPING CHROMOSOME REARRANGEMENT BREAKPOINTS TO THE PHYSICAL MAP OF CAENORHABDITIS-ELEGANS BY FLUORESCENT INSITU HYBRIDIZATION

A scheme for rapidly mapping chromosome rearrangements relative to the physical map of Caenorhabditis elegans is described that is based on hybridization patterns of cloned DNA on meiotic nuclei, as visualized by fluorescent in situ hybridization. From the nearly complete physica l map, DNA clones, in yeast artificial chromosomes (YACs), spanning th e rearrangement breakpoint were selected. The purified YAC DNAs were f irst amplified by degenerate oligonucleotide-primed polymerase chain r eaction, then reamplified to incorporate fluorescein dUTP or rhodamine dUTP. The site of hybridization was visualized directly (without the use of antibodies) on meiotic bivalents. This allows chromosome rearra ngements to be mapped readily if the duplicated, deficient or transloc ated regions do not pair with a normal homologous region, because the site or sites of hybridization of the probe on meiotic prophase nuclei will be spatially distinct. The pattern, or number, of hybridization signals from probes from within, or adjacent to, the rearranged region of the genome can be predicted from the genetic constitution of the s train. Characterization of the physical extent of the genetically mapp ed rearrangements places genetic landmarks on the physical map, and so provides linkage between the two types of map.