Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome

Nature Genetics

Volumn 23, Issue 3, 1999, Pages 305-308

  Rabinowicz, Pablo D ^a   Schutz, Kristin ^b   Dedhia, Neilay ^b   Yordan, Cristina ^a   Parnell, Laurence D ^b   Stein, Lincoln ^a   McCombie, W Richard ^b   Martienssen, Robert A ^a  

^a Simons Center for Quantitative Biology   (United States)

^b Lita Annen Hazenburg Genome S   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; GENE INSERTION; GENE LIBRARY; GENE SEQUENCE; GENOME; MAIZE; METHYLATION; NONHUMAN; PRIORITY JOURNAL; RETROPOSON; SEQUENCE ANALYSIS;

CLONING, MOLECULAR; DNA METHYLATION; DNA RESTRICTION ENZYMES; ESCHERICHIA COLI; GENES, PLANT; GENOME, PLANT; GENOMIC LIBRARY; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; RETROELEMENTS; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; ZEA MAYS;

ANIMALIA; BACTERIA (MICROORGANISMS); EMBRYOPHYTA; ZEA MAYS;

EID: 0032743873     PISSN: 10614036     EISSN: None     Source Type: Journal    
DOI: 10.1038/15479     Document Type: Article

References (30)

1. SanMiguel, P. et al. Nested retrotransposons in the intergenic regions of the maize genome. Science 274, 765-768 (1996).
2. Martienssen, R. Transposons, DNA methylation and gene control. Trends Genet. 14, 263-264 (1998).
3. Bennetzen, J.L., Schrick, K., Springer, P.S., Brown, W.E. & SanMiguel, P. Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA. Genome 37, 565-576 (1994).
4. Moore, G. et al. Key features of cereal genome organization as revealed by the use of cytosine methylation-sensitive restriction endonucleases. Genomics 15, 472-482 (1993).
5. White, S.E., Habera, L.F. & Wessler, S.R. Retrotransposons in the flanking regions of normal plant genes: a role for copia-like elements in the evolution of gene structure and expression. Proc. Natl Acad. Sci. USA 91, 11792-11796 (1994).
6. Colot, V. & Rossignol, J.L. Eukaryotic DNA methylation as an evolutionary device. Bioessays 21, 402-411 (1999).
7. Hake, S. & Walbot, V. The genome of Zea mays, its organization and homology to related grasses. Chromosoma 79, 251-270 (1980).
8. Bennetzen, J.L. The regulation of Mutator function and Mu1 transposition. UCLA Symp. Mol. Cell. Biol. 35, 343-354 (1985).
9. Gruenbaum, Y., Naveh-Many, T., Cedar, H. & Razin, A. Sequence specificity of methylation in higher plant DNA. Nature 292, 860-862 (1981).
10. Burr, B.A., Burr, F.A., Thompson, K.H., Albertson, M.C. & Stuber, C.W. Gene mapping with recombinant inbreds in maize. Genetics 118, 519-526 (1988).
11. Blumenthal, R.M., Gregory, S.A. & Cooperider, J.S. Cloning of a restriction-modification system from Proteus vulgaris and its use in analyzing a methylase-sensitive phenotype in Escherichia coli. J. Bacteriol. 164, 501-509 (1985).
12. Raleigh, E.A. & Wilson, G. Escherichia coli K-12 restricts DNA containing 5-methylcytosine. Proc. Natl Acad. Sci. USA 83, 9070-9074 (1986).
13. Arumuganathan, K. & Earle, E.D. Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9, 208-218 (1991).
14. Gaut, B.S. & Doebley, J.F. DNA sequence evidence for the segmental allotetraploid origin of maize. Proc. Natl Acad. Sci. USA 94, 6809-6814 (1997).
15. Raleigh, E.A. et al. McrA and McrB restriction phenotypes of some E. coli strains and implications for gene cloning. Nucleic Acids Res. 16, 1563-1575 (1988).
16. Yanisch-Perron, C., Vieira, J. & Messing, J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33, 103-119 (1985).
17. Sutherland, E., Coe, L. & Raleigh, E.A. McrBC: a multisubunit GTP-dependent restriction endonuclease. J. Mol. Biol. 225, 327-348 (1992).
18. Martienssen, R.A. & Richards, E.J. DNA methylation in eukaryotes Curr. Opin. Genet. Dev. 5, 234-242 (1995).
19. SanMiguel, P., Gaut, B.S., Tikhonov, A., Nakajima, Y. & Bennetzen, J.L The paleontology of intergene retrotransposons of maize. Nature Genet. 20, 43-45 (1998).
20. Adams, M.D. et al. Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature 377 (suppl.), 3-17 (1995).
21. Yoder, J.A., Walsh, C.P. & Bestor, T.H. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 13, 335-340 (1997).
22. Kass, S.U., Pruss, D. & Wolffe, A.P. How does DNA methylation repress transcription? Trends Genet. 13, 444-449 (1997).
23. Grant, S.G., Jessee, J., Bloom, F.R. & Hanahan, D. Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. Proc. Natl Acad. Sci. USA 87, 4645-4649 (1990).
24. Doherty, J.P. et al. Effects of mcr restriction of methylated CpG islands of the L1 transposons during packaging and plating stages of mammalian genomic library construction. Gene 98, 77-82 (1991).
25. Woodcock, D.M. et al. RgIB facilitated cloning of highly methylated eukaryotic DNA: the human L1 transposon, plant DNA, and DNA methylated in vitro with human DNA methyltransferase. Nucleic Acids Res. 25, 4465-4482 (1988).
26. Wessler, S.R., Bureau, T.E. & White, S.E. LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Curr. Opin. Genet. Dev. 5, 814-821 (1995).
27. Bird, A. Does DNA methylation control transposition of selfish elements in the germline? Trends Genet. 13, 469-472 (1997).
28. Williamson, M.R., Doherty, J.P. & Woodcock, D.M. Modified-cytosine restriction-system-induced recombinant cloning artefacts in Escherichia coli. Gene 124, 37-44 (1993).
29. White, S. & Doebley, J. Of genes and genomes and the origin of maize. Trends Genet. 14, 327-332 (1998).
30. Bureau, T.E., Ronald, P.C. & Wessler, S.R. A computer based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes. Proc. Natl Acad. Sci. USA 93, 8524 (1996).