Browse > Article

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

Lee, Myung-Chul (National Institute of Agricultural Biotechnology, RDA)
Wing, Rod A (Clemson University Genomics Institute)
Suh, Seok-Cheol (National Institute of Agricultural Biotechnology, RDA)
Eun, Moo-Young (National Institute of Agricultural Biotechnology, RDA)
Publication Information
Korean Journal of Plant Resources / v.20, no.6, 2007 , pp. 491-498 More about this Journal
Abstract
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.
Keywords
Methylation; Maize; Methyl-filtration; McrBC; Retroelement;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Carels, N., A. Barakat and G. Bernardi. 1995. The Gene Distribution of the Maize Genome. PNAS 92: 11057-11060   DOI
2 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   DOI   ScienceOn
3 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   DOI   ScienceOn
4 Razin, A. and H. Ceder. 1991. DNA methylation and gene expression. Microbiol. Rev. 55: 451-458
5 Springer, P. S. 1992. Genomic organization of Zea mays and its close relatives. PhD. Dissertation (West Lafayette, IN:Purdue University)
6 Sutherland, E, L. Coe and E. A. Raleigh. 1992. McrBC cleavage on distance between recognition endonuclease. J. Mol. BioI. 225: 327-348   DOI
7 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   DOI   ScienceOn
8 Yu, Y. 2000. Development and application of genomics tools for analysis of grass genome. PhD. Dissertation (Clemson, IN: Clemosn University)
9 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   DOI   ScienceOn
10 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   DOI
11 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   DOI   ScienceOn
12 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   DOI
13 Walker, E. L. 1998. Paramutation of the rl locus of maize is associated with increased cytosine methylation. Genetics 148: 1973-1981
14 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   DOI   ScienceOn
15 Burge, C. and S. Karlin. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. BioI. 268: 78-94   DOI   ScienceOn
16 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   DOI
17 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   DOI
18 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
19 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   DOI
20 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   DOI   ScienceOn
21 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   DOI   ScienceOn
22 Antequera, F. and A. P. Bird. 1988. Unmethylated CpG islands associated with genes in higher plant DNA. EMBO J. 7: 2295-2299
23 Xiong, Y. and T. H. Eickbush. 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9: 3353-62
24 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   DOI   ScienceOn
25 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
26 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   DOI
27 Hake, S. and V. Walbot. 1980. The genome of Zea mays, its organization and homology to related grasses. Chromosoma 79: 251-270   DOI
28 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   DOI
29 Constancia, M., B. Pickard, G. Kelsey and W. Reik. 1998. Imprinting Mechanisms. Genome Res. 8: 881-900   DOI
30 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   DOI   ScienceOn
31 Razin, A. 1998. CpG methylation, chromatin structure and gene silencing a three-way connection. EMBO J. 17: 4905-4908   DOI   ScienceOn
32 Pearson, W. R., T. Wood, Z. Zhang and W. Miller. 1997. Comparison of DNA sequences with protein sequences. Genomics 46: 24-36   DOI   ScienceOn
33 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   DOI
34 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   DOI   ScienceOn
35 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   DOI   ScienceOn