한국자원식물학회지 (Korean Journal of Plant Resources)

  • 제20권6호
  • /
  • Pages.491-498
  • /
  • 2007
  • /
  • 1226-3591(pISSN)
  • /
  • 2287-8203(eISSN)
한국자원식물학회 (The Plant Resources Society of Korea)
권호 표지

Comparison of Gene Coding Clones Content in In vivo and In vitro Methyl-Filtration Libraries of Maize(Zea may)

  • 발행 : 2007.12.30
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

It has been hypothesized that efficient exclusion of methylated retrotransposons and repeated DNA region is one of the rapid and cost-effective approaches for comprehensive gene discovery in large genome size of maize. Three kinds of methylation-sensitive restriction enzymes, HapII, MspI and McrBC, were used to identify the restriction frequency of cytosine methylation sites in maize genome. Roughly 60% of total maize genomic DNA was restricted less than 500bp by McrBC, and the most of restricted small size fraction was composed retrotransposon. In order to validate the efficient construction of gene-rich shotgun library, we compare two gene-rich methyl-filtration shotgun libraries using in vivo and in vitro methyl-filtration system. The size selected DNA fraction by Sau3A-McrBC enzyme treated was very stable and has not appeared modification in E. coli, but most insert DNA size of partially digested with Sau3A were decrease less than 500bp by bacterial methylation-modification system. In compare of retroelements portion, A 44.6% of the sequences were retroelement in unmethyl-filtered library, and the most of them was Copia type, such as Prem, Opie and Ji. The portion of retroelement was drastically decreased to 25% and 20% by in vivo and in vitro filtration system, respectively.

키워드

참고문헌

  1. Antequera, F. and A. P. Bird. 1988. Unmethylated CpG islands associated with genes in higher plant DNA. EMBO J. 7: 2295-2299
  2. Banks, J. A. and N. Fedoroff. 1989. Patterns of developmental and heritable change in methylation of the suppressor-mutator transposable element. Dev. Genet 10: 425-437 https://doi.org/10.1002/dvg.1020100604
  3. Bennetzen, J. L., K. Chrick, P. S. Springer, W. E. Brown and P. SanMiguel. 1994. Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA. Genome 37: 565-576 https://doi.org/10.1139/g94-081
  4. Bennetzen, J. L., K. Schrick, P. S. Springer, W. E. Brown and P. SanMiguel. 1994. Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA. Genome 37: 565-576 https://doi.org/10.1139/g94-081
  5. Burge, C. and S. Karlin. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. BioI. 268: 78-94 https://doi.org/10.1006/jmbi.1997.0951
  6. Carels, N., A. Barakat and G. Bernardi. 1995. The Gene Distribution of the Maize Genome. PNAS 92: 11057-11060 https://doi.org/10.1073/pnas.92.24.11057
  7. Constancia, M., B. Pickard, G. Kelsey and W. Reik. 1998. Imprinting Mechanisms. Genome Res. 8: 881-900 https://doi.org/10.1101/gr.8.9.881
  8. Cost, G. J. and J. D. Boeke. 1998. Targeting of human retrotransposon integration is directed by the specificity of the L 1 endonuclease for regions of unusual DNA structure. Biochemistry 37: 18018-93 https://doi.org/10.1021/bi981819g
  9. De Scenzo, R. A. and R. P. Wise. 1996. Variation in the ratio of physical to genetic distance in intervals adjacent to the Mia locus on barley chromosome 1H. Mol. & Gen. Genet 251: 472-482
  10. Duret, L., D. Mouchiroud and C. Gautier. 1995. Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC rich isochores. J. Mol. Evol. 40: 308-317 https://doi.org/10.1007/BF00163235
  11. Fu, H. and H. K. Dooner. 2000. A gene-enbriched BAC library for cloning large allele-specific fragments from maize:isolation of a 240-kb contig of the bronze region. Genome Res. 10: 866-873 https://doi.org/10.1101/gr.10.6.866
  12. Hake, S. and V. Walbot. 1980. The genome of Zea mays, its organization and homology to related grasses. Chromosoma 79: 251-270 https://doi.org/10.1007/BF00327318
  13. Jabbri, K. and G. Bernardi. 1998. CpG doublets, CpG islands and Alu repeat elements in long human DNA sequences from different isochores families. Gene 224: 123-128 https://doi.org/10.1016/S0378-1119(98)00474-0
  14. Jablonka, E., R. Goiten, M. Marcus and H. Cedar. 1985. DNA hypomethylation causes an increase in Dnase I sensitivity and advanse in the timing of replication of the entire X chromosome. Chromosoma 93: 152-156 https://doi.org/10.1007/BF00293162
  15. Llaca, V. and J. Messing. 1998. Amplicons of maize zein genes are conserved within genic but expanded and constructed in intergenic region. Plant J. 15: 211-220 https://doi.org/10.1046/j.1365-313X.1998.00200.x
  16. Lund, G., J. Messing and A. Viotti. 1995. Endosperm-specific demethylation and activation of specific alleles of alpha-tubulin genes of Zea mays L. Mol. Gen. Genet 246: 716-722 https://doi.org/10.1007/BF00290717
  17. Mayers, B. C., S. V. Tingey and M. Morgante. 2001. Abundance, distribution, and Transcriptional activaty of repetitive elements in the maize genome. Genome Research 11: 1660-1676 https://doi.org/10.1101/gr.188201
  18. Mouchiroud, D., G. D' onofrio, B. Aissanni, G. Macaya and C. Gautier. 1997. The distribution of genes in the human genome. Gene 100: 181-187 https://doi.org/10.1016/0378-1119(91)90364-H
  19. Pearson, W. R., T. Wood, Z. Zhang and W. Miller. 1997. Comparison of DNA sequences with protein sequences. Genomics 46: 24-36 https://doi.org/10.1006/geno.1997.4995
  20. Rossi, V., M. Motto and L. Pellegrini. 1997. Analysis of the methylation pattern of the maize opaque-2 (O2) promotor and in vitro binding studies indicate that the O2 B-Zip protein and other endosperm factors can bind to methylated target sequences. J. BioI. Chem. 272: 13758-13765 https://doi.org/10.1074/jbc.272.21.13758
  21. Rabinowicz, P. D., K. Schutz, N. Dedhia, C. Yordam, L. D. Parnell, L. Stein, W. R. McCombie and R. A. Martienssen. 1999. Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nat. Genet 23: 305-308 https://doi.org/10.1038/15479
  22. Razin, A. 1998. CpG methylation, chromatin structure and gene silencing a three-way connection. EMBO J. 17: 4905-4908 https://doi.org/10.1093/emboj/17.17.4905
  23. Razin, A. and H. Ceder. 1991. DNA methylation and gene expression. Microbiol. Rev. 55: 451-458
  24. SanMiguel, P. and J. L. Bennetzen. 1998. Evidence that a recent increase in maize genome size was caused by the massive amplification of inter gene retrotransposons. Ann. Bot. 82: 37-44 https://doi.org/10.1006/anbo.1998.0746
  25. SanMiguel, P., A. Tikhonov, Y. K. Jin, N. Motchoulskaia, D. Zakharov, B. A. Melake, P. S. Springer, K. J. Edwards, Z. Avramova and J. L. Bennetzen. 1996. Nested retrotransposons in the intergenic regions of the maize. Science 274: 765-768 https://doi.org/10.1126/science.274.5288.765
  26. SanMiguel, P., B. S. Gaut, A. Tikhonov, Y. Nakajima and J. L. Bennetzen. 1998. The paleontology og intergene retrotransposons of maize. Nature Genet 20: 43-45 https://doi.org/10.1038/1695
  27. Springer, P. S. 1992. Genomic organization of Zea mays and its close relatives. PhD. Dissertation (West Lafayette, IN:Purdue University)
  28. Sutherland, E, L. Coe and E. A. Raleigh. 1992. McrBC cleavage on distance between recognition endonuclease. J. Mol. BioI. 225: 327-348 https://doi.org/10.1016/0022-2836(92)90925-A
  29. Tikhonov, A. P., P. J. SanMiguel, Y. Nakajima, N. M. Gorensten, J. L. Bennetzen and Z. Avramova. 1999. Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Pro. Natl. Sci. USA 96: 7409-7414
  30. Walker, E. L. 1998. Paramutation of the rl locus of maize is associated with increased cytosine methylation. Genetics 148: 1973-1981
  31. Williamson, M. D., J. P. Doherty and D. M. Woodcock. 1993. Modified-cytosine restriction-system-induced recombinant cloning artifacts in Escherichia coli. Gene. 124: 37-44 https://doi.org/10.1016/0378-1119(93)90759-V
  32. Xiong, Y. and T. H. Eickbush. 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9: 3353-62
  33. Yang, D., A. Parco, S. Nandi, P. Subudhi, Y. Zhu, G. Wang and N. Huang. 1997. Construction of a bacterial artificial chromosome (BAC) library and identification of overlapping BAC clones with chromosome 4-specific RFLP markers in rice. Theor. Appl. Genet. 95: 1147-1154 https://doi.org/10.1007/s001220050675
  34. Yu, Y. 2000. Development and application of genomics tools for analysis of grass genome. PhD. Dissertation (Clemson, IN: Clemosn University)
  35. Zhang H.B., X. Zhao, X. Ding, A. H. Paterson and R. A.Wing. 1995. Preparation of megabase-size DNA from plant nuclei. Plant J. 7: 175-184 https://doi.org/10.1046/j.1365-313X.1995.07010175.x