A transposon-based strategy for sequencing repetitive DNA in eukaryotic genomes.

Repetitive DNA is a significant component of eukaryotic genomes. We have developed a strategy to efficiently and accurately sequence repetitive DNA in the nematode Caenorhabditis elegans using integrated artificial transposons and automated fluorescent sequencing. Mapping and assembly tools represent important components of this strategy and facilitate sequence assembly in complex regions. We have applied the strategy to several cosmid assembly gaps resulting from repetitive DNA and have accurately recovered the sequences of these regions. Analysis of these regions revealed six novel transposon-like repetitive elements, IR-1, IR-2, IR-3, IR-4, IR-5, and TR-1. Each of these elements represents a middle-repetitive DNA family in C. elegans containing at least 3-140 copies per genome. Copies of IR-1, IR-2, IR-4, and IR-5 are located on all (or most) of the six nematode chromosomes, whereas IR-3 is predominantly located on chromosome X. These elements are almost exclusively interspersed between predicted genes or within the predicted introns of these genes, with the exception of a single IR-5 element, which is located within a predicted exon. IR-1, IR-2, and IR-3 are flanked by short sequence duplications resembling the target site duplications of transposons. We have established a website database (http:(/)/www.welch.jhu.edu/approximately devine/RepDNAdb.html) to track and cross-reference these transposon-like repetitive elements that contains detailed information on individual element copies and provides links to appropriate GenBank records. This set of tools may be used to sequence, track, and study repetitive DNA in model organisms and humans.

[1]  N. Shimizu,et al.  [Shotgun sequencing]. , 2019, Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme.

[2]  A. Smit,et al.  The origin of interspersed repeats in the human genome. , 1996, Current opinion in genetics & development.

[3]  Jef D Boeke,et al.  High Frequency Retrotransposition in Cultured Mammalian Cells , 1996, Cell.

[4]  S. Devine,et al.  Integration of the yeast retrotransposon Ty1 is targeted to regions upstream of genes transcribed by RNA polymerase III. , 1996, Genes & development.

[5]  A. Smit,et al.  Tiggers and DNA transposon fossils in the human genome. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[6]  S. Devine,et al.  Efficient integration of artificial transposons into plasmid targets in vitro: a useful tool for DNA mapping, sequencing and genetic analysis. , 1994, Nucleic acids research.

[7]  P. Anderson,et al.  The Tc5 family of transposable elements in Caenorhabditis elegans. , 1994, Genetics.

[8]  R. Durbin,et al.  2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans , 1994, Nature.

[9]  R. Plasterk,et al.  Target site choice of the related transposable elements Tc1 and Tc3 of Caenorhabditis elegans. , 1994, Nucleic acids research.

[10]  R. Levis,et al.  Transposons in place of telomeric repeats at a Drosophila telomere , 1993, Cell.

[11]  Wei Li,et al.  A variant Tc4 transposable element in the nematode C. elegans could encode a novel protein , 1993, Nucleic Acids Res..

[12]  D. Botstein,et al.  Maize transposable elements: a story in four parts. , 1992 .

[13]  N. Fedoroff.  Maize Transposable Elements , 2015 .

[14]  R. Staden,et al.  A sequence assembly and editing program for efficient management of large projects. , 1991, Nucleic acids research.

[15]  D. Hartl,et al.  Evolution of the transposable element mariner in Drosophila species. , 1991, Genetics.

[16]  S. W. Emmons,et al.  A transposon-related palindromic repetitive sequence from C. elegans. , 1991, Nucleic acids research.

[17]  H. Horvitz,et al.  Tc4, a Caenorhabditis elegans transposable element with an unusual fold-back structure. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[18]  M V Olson,et al.  Physical map of the Saccharomyces cerevisiae genome at 110-kilobase resolution. , 1991, Genetics.

[19]  M. Palazzolo,et al.  Transposon-facilitated DNA sequencing. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[20]  D. Berg,et al.  Tn5supF, a 264-base-pair transposon derived from Tn5 for insertion mutagenesis and sequencing DNAs cloned in phage lambda. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[21]  S. W. Emmons,et al.  The Tc2 transposon in Caenorhabditis elegans. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[22]  P. Anderson,et al.  The Tc3 family of transposable genetic elements in Caenorhabditis elegans. , 1989, Genetics.

[23]  D. Finnegan.  The I factor and I-R hybrid dysgenesis in Drosophila melanogaster , 1989 .

[24]  E. Appella,et al.  DNA sequence of the E. coli gyrB gene: application of a new sequencing strategy. , 1987, Nucleic acids research.

[25]  Asad Ahmed,et al.  A rapid procedure for DNA sequencing using transposon-promoted deletions in Escherichia coli. , 1985, Gene.

[26]  C. M. Joyce,et al.  Method for determining whether a gene of Escherichia coli is essential: application to the polA gene , 1984, Journal of bacteriology.

[27]  J. Summerton,et al.  A rapid method for preparation of bacterial plasmids. , 1983, Analytical biochemistry.

[28]  S. W. Emmons,et al.  Evidence for a transposon in caenorhabditis elegans , 1983, Cell.

[29]  D. Holmes,et al.  A rapid boiling method for the preparation of bacterial plasmids. , 1981, Analytical biochemistry.

[30]  S. W. Emmons,et al.  Arrangement of repeated sequences in the DNA of the nematode Caenorhabditis elegans. , 1980, Journal of molecular biology.

[31]  J. Sulston,et al.  The DNA of Caenorhabditis elegans. , 1974, Genetics.

[32]  R. Britten,et al.  Repeated Sequences in DNA , 1968 .