MACRORESTRICTION ANALYSIS OF CAENORHABDITIS-ELEGANS GENOMIC DNA

The usefulness of genomic physical maps is greatly enhanced by linkage of the physical map with the genetic map. We describe a ''macrorestri ction mapping'' procedure for Caenorhabditis elegans that we have appl ied to this endeavor. High molecular weight, genomic DNA is digested w ith infrequently cutting restriction enzymes and size-fractionated by pulsed field gel electrophoresis. Southern blots of the gels are probe d with clones from the C. elegans physical map. This procedure allows the construction of restriction maps covering several hundred kilobase s and the detection of polymorphic restriction fragments using probes that map several hundred kilobases away. We describe several applicati ons of this technique. (1) We determined that the amount of DNA in a p reviously uncloned region is <220 kb. (2) We mapped the mes-l gene to a cosmid, by detecting polymorphic restriction fragments associated wi th a deletion allele of the gene. The 25-kb deletion was initially det ected using as a probe sequences located similar to 400 kb away from t he gene. (3) We mapped the molecular endpoint of the deficiency hDf6, and determined that three spontaneously derived duplications in the un c-38-dpy-5 region have very complex molecular structures, containing i nternal rearrangements and deletions.