Worm Breeder's Gazette 13(4): 27 (October 1, 1994)

These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.

DNA Fingerprinting in C. elegans - An Approach.

Mark Benecke1, Jorg T. Epplen2, Einhard Schierenberg3

Hybridization of short oligonucleotides against Southerns blots of digested genomic DNA allows identification of individual as well as clone specific characteristics within a population (DNA fingerprinting)(1). Our oligonucleotide probes, due to their structure, detect long tandem repeated non-coding sequences which vary in length from individual to individual (variable number of tandem repeats or VNTRs) They are found frequently in all organisms from prokaryotes up to vertebrates(2). The C. elegans genome is known to have low repetition frequencies; in general, the core sequences are repeated less than hundred-fold and show a low level of associated restriction fragment length polymorphisms (RFLPs)(3, 4). Only some species of whales, a teleost fish, northern elephant seals and marmots appear to be as monomorphic (low number of VNTRs, low degree of variation) as C. elegans(5,6,7,8). Probes which detect loci of low variability might be a convenient tool not only for individual-specific studies but also on a phylogenetic level. One advantage of this method over sequencing of specific RNA325s or genes is that many loci spread over the entire genome can be visualized in one working step. Neglecting potential differences between individuals within essentially homogeneous worm populations we have started to compare hybridization patterns of various C. elegans strains. Worms grown on plates were harvested, cleaned from bacteria by centrifugation in a sucrose solution, dissolved with Proteinase K, and finally DNA was isolated by phenol extraction. Using DIG- and radioactively labeled probes (15 to 18 oligonucleotides in length) and a set of abundant restriction enzymes we found that at least 3 out of 15 probes tested so far hybridize against 10-30 potentially polymorphic loci in the range of 1 to 22 kb. The number of informative bands appears to be sufficient for a useful statistical similarity analysis(9). Our results confirm that the C. elegans genome contains a low number of long tandem repeats and their high monomorphism. Nevertheless, fingerprint analysis is possible. We can distinguish strains by their defined fingerprint patterns. Our results do not seem to support the fingerprint-based finding that C. elegans strains are not distinguishable on a molecular level(10). For the future we plan to use PCR-based fingerprinting methods together with a light-microscopic comparison of developmental features(11). From this combined effort we expect to obtain additional information on phylogenetic relationships between nematodes. (1)JEFFREYS AJ, WILSON V, THEIN SL (1985) Nature 316, 76-79 (2) BURKE T, DOLF G, JEFFREYS AJ, WOLFF R (eds.) (1991) DNA Fingerprinting. Approaches and Applications. Birkhauser. Basel (3) EMMONS SW, ROSENZWEIG B, HIRSH D (1980) J Mol Bio 144, 481-500 (4) NACLERIO G, CANGIANO G, COULSON A. LEVITT A, RUVOLVO V, LA VOLPE A (1992) J Mol Biol 226, 159-168 (5) SCHARTL M, NANDA I. SCHLUPP I, PARZEFALL J, SCHMID M, EPPLEN JT (1990) Fingerprint News 2(4), 22-24 (6) HOELZEL R AMOS W (1988) Nature 333, 305 (7) HOELZEL AR, LE BOEF B (1990) Fingerprint News 2(1), 10 (8) RASSMANN C, ARNOLD W, TAUTZ D (1994) Molecular Ecology 3, in press (9) LYNCH M (1990) Mol Biol Evol 7. 478-484 ( l0 )UITTERLINDENAG, SLAGBOOM PE, JOHNSON TE. VIJG J (1989) NAR 17, 9572-9530 (11) SKIBA F, SCHIERENBERG E ( l992 )Developmental Biology 151, 597-610