Transposon Tc1-Derived, Sequence-Tagged Sites in Caenorhabditis elegans as Markers for Gene Mapping

We present an approach to map large numbers of Tc1 transposon insertions in the genome of Caenorhabditis elegans. Strains have been described that contain up to 500 polymorphic Tc1 insertions. From these we have cloned and shotgun sequenced over 2000 Tc1 flanks, resulting in an estimated set of 400...

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Bibliographic Details
Published in:	Proceedings of the National Academy of Sciences - PNAS Vol. 93; no. 25; pp. 14680 - 14685
Main Authors:	Korswagen, Hendrik C., Durbin, Richard M., Smits, Miriam T., Ronald H. A. Plasterk
Format:	Journal Article
Language:	English
Published:	United States National Academy of Sciences of the United States of America 10-12-1996 National Acad Sciences National Academy of Sciences The National Academy of Sciences of the USA
Subjects:	Alleles Animals Biological Sciences Biomarkers Caenorhabditis elegans Caenorhabditis elegans - genetics Chromosome Mapping DNA DNA Transposable Elements Genetic mapping Genetic mutation Genetics Genome Genomes Genomics Mutation Polymerase chain reaction Sequence tagged sites Sequencing Worms
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Summary:	We present an approach to map large numbers of Tc1 transposon insertions in the genome of Caenorhabditis elegans. Strains have been described that contain up to 500 polymorphic Tc1 insertions. From these we have cloned and shotgun sequenced over 2000 Tc1 flanks, resulting in an estimated set of 400 or more distinct Tc1 insertion alleles. Alignment of these sequences revealed a weak Tc1 insertion site consensus sequence that was symmetric around the invariant TA target site and reads CAYATATRTG. The Tc1 flanking sequences were compared with 40 Mbp of a C. elegans genome sequence. We found 151 insertions within the sequenced area, a density of ≈ 1 Tc1 insertion in every 265 kb. As the rest of the C. elegans genome sequence is obtained, remaining Tc1 alleles will fall into place. These mapped Tc1 insertions can serve two functions: (i) insertions in or near genes can be used to isolate deletion derivatives that have that gene mutated; and (ii) they represent a dense collection of polymorphic sequence-tagged sites. We demonstrate a strategy to use these Tc1 sequence-tagged sites in fine-mapping mutations.
Bibliography:	ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 23 ObjectType-Article-1 ObjectType-Feature-2 To whom reprint requests should be addressed. William B. Wood, University of Colorado, Boulder, CO
ISSN:	0027-8424 1091-6490
DOI:	10.1073/pnas.93.25.14680