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Volumn 10, Issue 5, 2007, Pages 534-542

Mapping the genome landscape using tiling array technology

Author keywords

[No Author keywords available]

Indexed keywords

DNA METHYLATION; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GENOME; METHODOLOGY; PLANT; REVIEW;

EID: 34848925793     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2007.07.006     Document Type: Review
Times cited : (57)

References (77)
  • 1
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • Schena M., Shalon D., Davis R.W., and Brown P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270 (1995) 467-470
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 2
    • 0029748326 scopus 로고    scopus 로고
    • Parallel human genome analysis: microarray-based expression monitoring of 1000 genes
    • Schena M., Shalon D., Heller R., Chai A., Brown P.O., and Davis R.W. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci U S A 93 (1996) 10614-10619
    • (1996) Proc Natl Acad Sci U S A , vol.93 , pp. 10614-10619
    • Schena, M.1    Shalon, D.2    Heller, R.3    Chai, A.4    Brown, P.O.5    Davis, R.W.6
  • 5
    • 10644247621 scopus 로고    scopus 로고
    • Applications of DNA tiling arrays for whole-genome analysis
    • Mockler T.C., and Ecker J.R. Applications of DNA tiling arrays for whole-genome analysis. Genomics 85 (2005) 1-15
    • (2005) Genomics , vol.85 , pp. 1-15
    • Mockler, T.C.1    Ecker, J.R.2
  • 7
    • 0037012922 scopus 로고    scopus 로고
    • Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays
    • Clark T.A., Sugnet C.W., and Ares Jr. M. Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296 (2002) 907-910
    • (2002) Science , vol.296 , pp. 907-910
    • Clark, T.A.1    Sugnet, C.W.2    Ares Jr., M.3
  • 13
    • 33745068992 scopus 로고    scopus 로고
    • Development of Arabidopsis whole-genome microarrays and their application to the discovery of binding sites for the TGA2 transcription factor in salicylic acid-treated plants
    • Thibaud-Nissen F., Wu H., Richmond T., Redman J.C., Johnson C., Green R., Arias J., and Town C.D. Development of Arabidopsis whole-genome microarrays and their application to the discovery of binding sites for the TGA2 transcription factor in salicylic acid-treated plants. Plant J 47 (2006) 152-162
    • (2006) Plant J , vol.47 , pp. 152-162
    • Thibaud-Nissen, F.1    Wu, H.2    Richmond, T.3    Redman, J.C.4    Johnson, C.5    Green, R.6    Arias, J.7    Town, C.D.8
  • 15
    • 1842450809 scopus 로고    scopus 로고
    • Identifying transcriptional targets
    • Taverner N., Smith J., and Wardle F. Identifying transcriptional targets. Genome Biol 5 (2004) 210
    • (2004) Genome Biol , vol.5 , pp. 210
    • Taverner, N.1    Smith, J.2    Wardle, F.3
  • 16
    • 1242316281 scopus 로고    scopus 로고
    • ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
    • Buck M.J., and Lieb J.D. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83 (2004) 349-360
    • (2004) Genomics , vol.83 , pp. 349-360
    • Buck, M.J.1    Lieb, J.D.2
  • 19
    • 33748629119 scopus 로고    scopus 로고
    • Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis
    • This is the first combinatorial study of the DNA methylome and transcriptome using whole-genome tiling microarrays in any organism.
    • Zhang X., Yazaki J., Sundaresan A., Cokus S., Chan S.W.L., Chen H., Henderson I.R., Shinn P., Pellegrini M., Jacobsen S.E., et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126 (2006) 1189-1201. This is the first combinatorial study of the DNA methylome and transcriptome using whole-genome tiling microarrays in any organism.
    • (2006) Cell , vol.126 , pp. 1189-1201
    • Zhang, X.1    Yazaki, J.2    Sundaresan, A.3    Cokus, S.4    Chan, S.W.L.5    Chen, H.6    Henderson, I.R.7    Shinn, P.8    Pellegrini, M.9    Jacobsen, S.E.10
  • 20
    • 33845880624 scopus 로고    scopus 로고
    • Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
    • This paper reports whole DNA methylome and transcriptome maps for Arabidopsis. Thsestudies demonstrated that gene expression and DNA methylation are closely interwoven processes.
    • Zilberman D., Gehring M., Tran R.K., Ballinger T., and Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39 (2007) 61-69. This paper reports whole DNA methylome and transcriptome maps for Arabidopsis. Thsestudies demonstrated that gene expression and DNA methylation are closely interwoven processes.
    • (2007) Nat Genet , vol.39 , pp. 61-69
    • Zilberman, D.1    Gehring, M.2    Tran, R.K.3    Ballinger, T.4    Henikoff, S.5
  • 21
    • 23444432370 scopus 로고    scopus 로고
    • Epigenomic mapping in Arabidopsis using tiling microarrays
    • Martienssen R., Doerge R., and Colot V. Epigenomic mapping in Arabidopsis using tiling microarrays. Chromosome Res 13 (2005) 299-308
    • (2005) Chromosome Res , vol.13 , pp. 299-308
    • Martienssen, R.1    Doerge, R.2    Colot, V.3
  • 24
    • 17744364327 scopus 로고    scopus 로고
    • Gardening the genome: DNA methylation in Arabidopsis thaliana
    • Chan S.W.L., Henderson I.R., and Jacobsen S.E. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6 (2005) 351-360
    • (2005) Nat Rev Genet , vol.6 , pp. 351-360
    • Chan, S.W.L.1    Henderson, I.R.2    Jacobsen, S.E.3
  • 26
    • 23044497893 scopus 로고    scopus 로고
    • Poetry of b1 Paramutation: cis- and trans-chromatin communication
    • Chandler V.L. Poetry of b1 Paramutation: cis- and trans-chromatin communication. Cold Spring Harb Symp Quant Biol 69 (2004) 355-362
    • (2004) Cold Spring Harb Symp Quant Biol , vol.69 , pp. 355-362
    • Chandler, V.L.1
  • 27
    • 3042801584 scopus 로고    scopus 로고
    • Chromatin conversations: mechanisms and implications of paramutation
    • Chandler V.L., and Stam M. Chromatin conversations: mechanisms and implications of paramutation. Nat Rev Genet 5 (2004) 532-544
    • (2004) Nat Rev Genet , vol.5 , pp. 532-544
    • Chandler, V.L.1    Stam, M.2
  • 30
    • 0037067658 scopus 로고    scopus 로고
    • DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis
    • Choi Y., Gehring M., Johnson L., Hannon M., Harada J.J., Goldberg R.B., Jacobsen S.E., and Fischer R.L. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell 110 (2002) 33-42
    • (2002) Cell , vol.110 , pp. 33-42
    • Choi, Y.1    Gehring, M.2    Johnson, L.3    Hannon, M.4    Harada, J.J.5    Goldberg, R.B.6    Jacobsen, S.E.7    Fischer, R.L.8
  • 31
    • 33845866061 scopus 로고    scopus 로고
    • The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis
    • Zhu J., Kapoor A., Sridhar V.V., Agius F., and Zhu J.K. The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis. Current Biol 17 (2007) 54-59
    • (2007) Current Biol , vol.17 , pp. 54-59
    • Zhu, J.1    Kapoor, A.2    Sridhar, V.V.3    Agius, F.4    Zhu, J.K.5
  • 32
    • 34249853277 scopus 로고    scopus 로고
    • DNA demethylation in the Arabidopsis genome
    • The authors identified regions of active demethylation mediated by DNA glycosylases throughout the entire Arabidopsis genome. Additionally, they also assert that demethylation by DNA glycosylases is required to edit the pattern of DNA methylation within genomes to protect genes from potentially deleterious methylation.
    • Penterman J., Zilberman D., Huh J.H., Ballinger T., Henikoff S., and Fischer R.L. DNA demethylation in the Arabidopsis genome. Proc Natl Acad Sci U S A 104 (2007) 6752-6757. The authors identified regions of active demethylation mediated by DNA glycosylases throughout the entire Arabidopsis genome. Additionally, they also assert that demethylation by DNA glycosylases is required to edit the pattern of DNA methylation within genomes to protect genes from potentially deleterious methylation.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 6752-6757
    • Penterman, J.1    Zilberman, D.2    Huh, J.H.3    Ballinger, T.4    Henikoff, S.5    Fischer, R.L.6
  • 33
    • 0030769859 scopus 로고    scopus 로고
    • Hypermethylated SUPERMAN epigenetic alleles in Arabidopsis
    • Jacobsen S.E., and Meyerowitz E.M. Hypermethylated SUPERMAN epigenetic alleles in Arabidopsis. Science 277 (1997) 1100-1103
    • (1997) Science , vol.277 , pp. 1100-1103
    • Jacobsen, S.E.1    Meyerowitz, E.M.2
  • 35
    • 0028885673 scopus 로고
    • Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of Arabidopsis
    • Bender J., and Fink G.R. Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of Arabidopsis. Cell 83 (1995) 725-734
    • (1995) Cell , vol.83 , pp. 725-734
    • Bender, J.1    Fink, G.R.2
  • 36
    • 0032829710 scopus 로고    scopus 로고
    • Arabidopsis PAI gene arrangements, cytosine methylation and expression
    • Melquist S., Luff B., and Bender J. Arabidopsis PAI gene arrangements, cytosine methylation and expression. Genetics 153 (1999) 401-413
    • (1999) Genetics , vol.153 , pp. 401-413
    • Melquist, S.1    Luff, B.2    Bender, J.3
  • 37
    • 0037080492 scopus 로고    scopus 로고
    • Epigenetic variation in Arabidopsis disease resistance
    • Stokes T.L., Kunkel B.N., and Richards E.J. Epigenetic variation in Arabidopsis disease resistance. Genes Dev 16 (2002) 171-182
    • (2002) Genes Dev , vol.16 , pp. 171-182
    • Stokes, T.L.1    Kunkel, B.N.2    Richards, E.J.3
  • 38
    • 4644312235 scopus 로고    scopus 로고
    • The role of RNA interference in heterochromatic silencing
    • Lippman Z., and Martienssen R. The role of RNA interference in heterochromatic silencing. Nature 431 (2004) 364-370
    • (2004) Nature , vol.431 , pp. 364-370
    • Lippman, Z.1    Martienssen, R.2
  • 39
    • 0035837378 scopus 로고    scopus 로고
    • Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis
    • Miura A., Yonebayashi S., Watanabe K., Toyama T., Shimada H., and Kakutani T. Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411 (2001) 212-214
    • (2001) Nature , vol.411 , pp. 212-214
    • Miura, A.1    Yonebayashi, S.2    Watanabe, K.3    Toyama, T.4    Shimada, H.5    Kakutani, T.6
  • 40
    • 0034103860 scopus 로고    scopus 로고
    • Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation
    • Hirochika H., Okamoto H., and Kakutani T. Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation. Plant Cell 12 (2000) 357-369
    • (2000) Plant Cell , vol.12 , pp. 357-369
    • Hirochika, H.1    Okamoto, H.2    Kakutani, T.3
  • 41
    • 0035282119 scopus 로고    scopus 로고
    • Robertson's mutator transposons in A. thaliana are regulated by the chromatin-remodeling gene decrease in DNA methylation (DDM1)
    • Singer T., Yordan C., and Martienssen R.A. Robertson's mutator transposons in A. thaliana are regulated by the chromatin-remodeling gene decrease in DNA methylation (DDM1). Genes Dev 15 (2001) 591-602
    • (2001) Genes Dev , vol.15 , pp. 591-602
    • Singer, T.1    Yordan, C.2    Martienssen, R.A.3
  • 42
    • 33745726564 scopus 로고    scopus 로고
    • RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in Arabidopsis
    • Chan S.W.L., Henderson I.R., Zhang X., Shah G., Chien J.S.C., and Jacobsen S.E. RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in Arabidopsis. PLoS Genet 2 (2006) e83
    • (2006) PLoS Genet , vol.2
    • Chan, S.W.L.1    Henderson, I.R.2    Zhang, X.3    Shah, G.4    Chien, J.S.C.5    Jacobsen, S.E.6
  • 43
    • 33847037497 scopus 로고    scopus 로고
    • Noncoding RNAs and gene silencing
    • A comprehensive review of non-protein-coding transcripts (ncRNAs) and gene silencing in various organisms. The authors review the role of ncRNA in heterochromatic silencing, the silencing of transposable elements. Furthermore, they discussed the role of co-transcriptional processing by RNA interference and other mechanisms, as well as parallels of RNA silencing with the processes of imprinting, paramutation, polycomb silenecing, and X inactivation.
    • Zaratiegui M., Irvine D.V., and Martienssen R.A. Noncoding RNAs and gene silencing. Cell 128 (2007) 763-776. A comprehensive review of non-protein-coding transcripts (ncRNAs) and gene silencing in various organisms. The authors review the role of ncRNA in heterochromatic silencing, the silencing of transposable elements. Furthermore, they discussed the role of co-transcriptional processing by RNA interference and other mechanisms, as well as parallels of RNA silencing with the processes of imprinting, paramutation, polycomb silenecing, and X inactivation.
    • (2007) Cell , vol.128 , pp. 763-776
    • Zaratiegui, M.1    Irvine, D.V.2    Martienssen, R.A.3
  • 44
    • 24644519490 scopus 로고    scopus 로고
    • The transcriptional landscape of the mammalian genome
    • The FANTOM Consortium. The authors provide a comprehensive description of transcription start and termination sites using a massive full-length cDNA collection.
    • Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., et al., The FANTOM Consortium. The transcriptional landscape of the mammalian genome. Science 309 (2005) 1559-1563. The authors provide a comprehensive description of transcription start and termination sites using a massive full-length cDNA collection.
    • (2005) Science , vol.309 , pp. 1559-1563
    • Carninci, P.1    Kasukawa, T.2    Katayama, S.3    Gough, J.4    Frith, M.C.5    Maeda, N.6    Oyama, R.7    Ravasi, T.8    Lenhard, B.9    Wells, C.10
  • 45
    • 33747603960 scopus 로고    scopus 로고
    • The imprinted Air ncRNA is an atypical RNAPII transcript that evades splicing and escapes nuclear export
    • Seidl C.I., Stricker S.H., and Barlow D.P. The imprinted Air ncRNA is an atypical RNAPII transcript that evades splicing and escapes nuclear export. EMBO J 25 (2006) 3565-3575
    • (2006) EMBO J , vol.25 , pp. 3565-3575
    • Seidl, C.I.1    Stricker, S.H.2    Barlow, D.P.3
  • 46
    • 2942560254 scopus 로고    scopus 로고
    • Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene
    • Martens J.A., Laprade L., and Winston F. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429 (2004) 571-574
    • (2004) Nature , vol.429 , pp. 571-574
    • Martens, J.A.1    Laprade, L.2    Winston, F.3
  • 47
    • 33846156841 scopus 로고    scopus 로고
    • Tsix defective in splicing is competent to establish Xist silencing
    • Sado T., Hoki Y., and Sasaki H. Tsix defective in splicing is competent to establish Xist silencing. Development 133 (2006) 4925-4931
    • (2006) Development , vol.133 , pp. 4925-4931
    • Sado, T.1    Hoki, Y.2    Sasaki, H.3
  • 48
    • 34250160256 scopus 로고    scopus 로고
    • RNA maps reveal new RNA classes and a possible function for pervasive transcription
    • This study investigated the genomic origins and relationships of human nuclear and cytosolic polyadenylated RNAs both longer and shorter than 200 nucleotides in length. From their results, the authors suggest a role for some unannotated RNAs as primary transcripts for the production of short RNAs.
    • Kapranov P., Cheng J., Dike S., Nix D.A., Duttagupta R., Willingham A.T., Stadler P.F., Hertel J., Hackermueller J., Hofacker I.L., et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (2007) 1138341. This study investigated the genomic origins and relationships of human nuclear and cytosolic polyadenylated RNAs both longer and shorter than 200 nucleotides in length. From their results, the authors suggest a role for some unannotated RNAs as primary transcripts for the production of short RNAs.
    • (2007) Science , pp. 1138341
    • Kapranov, P.1    Cheng, J.2    Dike, S.3    Nix, D.A.4    Duttagupta, R.5    Willingham, A.T.6    Stadler, P.F.7    Hertel, J.8    Hackermueller, J.9    Hofacker, I.L.10
  • 49
    • 0038360922 scopus 로고    scopus 로고
    • Epigenetic gene regulation by noncoding RNAs
    • Andersen A.A., and Panning B. Epigenetic gene regulation by noncoding RNAs. Curr Opin Cell Biol 15 (2003) 281-289
    • (2003) Curr Opin Cell Biol , vol.15 , pp. 281-289
    • Andersen, A.A.1    Panning, B.2
  • 50
    • 0023797123 scopus 로고
    • Genetic evidence for promoter competition in Saccharomyces cerevisiae
    • Hirschman J.E., Durbin K.J., and Winston F. Genetic evidence for promoter competition in Saccharomyces cerevisiae. Mol Cell Biol 8 (1988) 4608-4615
    • (1988) Mol Cell Biol , vol.8 , pp. 4608-4615
    • Hirschman, J.E.1    Durbin, K.J.2    Winston, F.3
  • 51
    • 25444452651 scopus 로고    scopus 로고
    • A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription
    • Babak T., Blencowe B., and Hughes T. A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription. BMC Genom 6 (2005) 104
    • (2005) BMC Genom , vol.6 , pp. 104
    • Babak, T.1    Blencowe, B.2    Hughes, T.3
  • 52
    • 34147112685 scopus 로고    scopus 로고
    • Noncoding RNA transcription beyond annotated genes
    • Carninci P., and Hayashizaki Y. Noncoding RNA transcription beyond annotated genes. Curr Opin Genet Dev 17 (2007) 139-144
    • (2007) Curr Opin Genet Dev , vol.17 , pp. 139-144
    • Carninci, P.1    Hayashizaki, Y.2
  • 53
    • 29444457713 scopus 로고    scopus 로고
    • Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function
    • Pang K.C., Frith M.C., and Mattick J.S. Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet 22 (2006) 1-5
    • (2006) Trends Genet , vol.22 , pp. 1-5
    • Pang, K.C.1    Frith, M.C.2    Mattick, J.S.3
  • 55
    • 4344692339 scopus 로고    scopus 로고
    • Mouse-centric comparative transcriptomics of protein coding and non-coding RNAs
    • Suzuki M., and Hayashizaki Y. Mouse-centric comparative transcriptomics of protein coding and non-coding RNAs. Bioessays 26 (2004) 833-843
    • (2004) Bioessays , vol.26 , pp. 833-843
    • Suzuki, M.1    Hayashizaki, Y.2
  • 56
    • 24644505259 scopus 로고    scopus 로고
    • Fewer genes, more noncoding RNA
    • Claverie J.M. Fewer genes, more noncoding RNA. Science 309 (2005) 1529-1530
    • (2005) Science , vol.309 , pp. 1529-1530
    • Claverie, J.M.1
  • 57
    • 24644472515 scopus 로고    scopus 로고
    • Antisense transcription in the mammalian transcriptome
    • RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group) and the FANTOM Consortium. The authors demonstrate a global analysis of the mouse transcriptome, which provides evidence that a large proportion of the genome can produce transcripts from both strands (anti-sense gene pairs). Additionally, the researchers find that anti-sense transcripts commonly join neighboring 'genes' into complex loci of linked transcription.
    • Katayama S., Tomaru Y., Kasukawa T., Waki K., Nakanishi M., Nakamura M., Nishida H., Yap C.C., Suzuki M., Kawai J., et al., RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group) and the FANTOM Consortium. Antisense transcription in the mammalian transcriptome. Science 309 (2005) 1564-1566. The authors demonstrate a global analysis of the mouse transcriptome, which provides evidence that a large proportion of the genome can produce transcripts from both strands (anti-sense gene pairs). Additionally, the researchers find that anti-sense transcripts commonly join neighboring 'genes' into complex loci of linked transcription.
    • (2005) Science , vol.309 , pp. 1564-1566
    • Katayama, S.1    Tomaru, Y.2    Kasukawa, T.3    Waki, K.4    Nakanishi, M.5    Nakamura, M.6    Nishida, H.7    Yap, C.C.8    Suzuki, M.9    Kawai, J.10
  • 58
    • 29244490062 scopus 로고    scopus 로고
    • Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis
    • This paper describes an over-lapping anti-sense gene pair that generates a region of dsRNA. This dsRNA region initiates a series of siRNA processing steps that ultimately result in the downregulation of P5CDH in response to salt stress. From their results, the authors suggest that anti-sense transcripts can regulate neighboring genes through formation of regions of dsRNA that subsequently recruit various RNA silencing pathways.
    • Borsani O., Zhu J., Verslues P.E., Sunkar R., and Zhu J.K. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123 (2005) 1279-1291. This paper describes an over-lapping anti-sense gene pair that generates a region of dsRNA. This dsRNA region initiates a series of siRNA processing steps that ultimately result in the downregulation of P5CDH in response to salt stress. From their results, the authors suggest that anti-sense transcripts can regulate neighboring genes through formation of regions of dsRNA that subsequently recruit various RNA silencing pathways.
    • (2005) Cell , vol.123 , pp. 1279-1291
    • Borsani, O.1    Zhu, J.2    Verslues, P.E.3    Sunkar, R.4    Zhu, J.K.5
  • 59
    • 33847611493 scopus 로고    scopus 로고
    • Small RNA-mediated chromatin silencing directed to the 3′ region of the Arabidopsis gene encoding the developmental regulator, FLC
    • The authors report the identification of two smRNAs corresponding to the reverse strand 3′ to the canonical poly(A) site of the gene encoding a repressor of flowering in Arabidopsis, FLOWEING LOCUS C (FLC), using whole genome tiling array data. These smRNAs are required for proper regulation of FLC expression and ultimately flowering time.
    • Swiezewski S., Crevillen P., Liu F., Ecker J.R., Jerzmanowski A., and Dean C. Small RNA-mediated chromatin silencing directed to the 3′ region of the Arabidopsis gene encoding the developmental regulator, FLC. Proc Natl Acad Sci U S A 104 (2007) 3633-3638. The authors report the identification of two smRNAs corresponding to the reverse strand 3′ to the canonical poly(A) site of the gene encoding a repressor of flowering in Arabidopsis, FLOWEING LOCUS C (FLC), using whole genome tiling array data. These smRNAs are required for proper regulation of FLC expression and ultimately flowering time.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 3633-3638
    • Swiezewski, S.1    Crevillen, P.2    Liu, F.3    Ecker, J.R.4    Jerzmanowski, A.5    Dean, C.6
  • 61
    • 0021924990 scopus 로고
    • Effect of regional DNA methylation on gene expression
    • Keshet I., Yisraeli J., and Cedar H. Effect of regional DNA methylation on gene expression. Proc Natl Acad Sci U S A 82 (1985) 2560-2564
    • (1985) Proc Natl Acad Sci U S A , vol.82 , pp. 2560-2564
    • Keshet, I.1    Yisraeli, J.2    Cedar, H.3
  • 62
    • 0027215524 scopus 로고
    • Methylation induced premeiotically in ascobolus: coextension with DNA repeat lengths and effect on transcript elongation
    • Barry C., Faugeron G., and Rossignol J. Methylation induced premeiotically in ascobolus: coextension with DNA repeat lengths and effect on transcript elongation. Proc Natl Acad Sci U S A 90 (1993) 4557-4561
    • (1993) Proc Natl Acad Sci U S A , vol.90 , pp. 4557-4561
    • Barry, C.1    Faugeron, G.2    Rossignol, J.3
  • 63
    • 33745080545 scopus 로고    scopus 로고
    • RNA interference is not involved in natural antisense mediated regulation of gene expression in mammals
    • Faghihi M., and Wahlestedt C. RNA interference is not involved in natural antisense mediated regulation of gene expression in mammals. Genome Biol 7 (2006) R38
    • (2006) Genome Biol , vol.7
    • Faghihi, M.1    Wahlestedt, C.2
  • 64
    • 24644448635 scopus 로고    scopus 로고
    • Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana
    • Wang X.J., Gaasterland T., and Chua N.H. Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome Biol 6 (2005) R30
    • (2005) Genome Biol , vol.6
    • Wang, X.J.1    Gaasterland, T.2    Chua, N.H.3
  • 65
    • 34848815710 scopus 로고    scopus 로고
    • Gehring M, Henikoff S. DNA methylation dynamics in plant genomes. Biochim Biophys Acta, In press. A comprehensive review on the functions of DNA methylation in plants. The authors review the impact of DNA methylation on transposable elements, genes, and on the genome as a whole. Additionally, the extent to which changes in DNA methylation are part of the plant life cycle are also discussed.
  • 69
    • 23944444785 scopus 로고    scopus 로고
    • Epigenetic control of plant development by Polycomb-group proteins
    • Schubert D., Clarenz O., and Goodrich J. Epigenetic control of plant development by Polycomb-group proteins. Curr Opin Plant Biol 8 (2005) 553-561
    • (2005) Curr Opin Plant Biol , vol.8 , pp. 553-561
    • Schubert, D.1    Clarenz, O.2    Goodrich, J.3
  • 72
    • 34249068213 scopus 로고    scopus 로고
    • Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis
    • The authors report identification of regions containing tri-methylation of histone H3 lysine 27 (H3K27me3) in the Arabidopsis genome using whole genome tiling arrays. They suggest that H3K27me3 is a major silencing mechanism in plants that regulates an unexpectedly large number of genes, and this silencing pathway is unrelated to others that have been previously identified.
    • Zhang X., Clarenz O., Cokus S., Bernatavichute Y.V., Pellegrini M., Goodrich J., and Jacobsen S.E. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 5 (2007) e129. The authors report identification of regions containing tri-methylation of histone H3 lysine 27 (H3K27me3) in the Arabidopsis genome using whole genome tiling arrays. They suggest that H3K27me3 is a major silencing mechanism in plants that regulates an unexpectedly large number of genes, and this silencing pathway is unrelated to others that have been previously identified.
    • (2007) PLoS Biol , vol.5
    • Zhang, X.1    Clarenz, O.2    Cokus, S.3    Bernatavichute, Y.V.4    Pellegrini, M.5    Goodrich, J.6    Jacobsen, S.E.7
  • 75
    • 34249026300 scopus 로고    scopus 로고
    • High-resolution profiling of histone methylations in the human genome
    • This is the first, comprehensive, whole-genome mapping of numerous histone modifications as well as binding sites for histone variant H2A.Z, RNA polymerase II, and the insulator binding protein CTCF in any organism using ultra high-throughput Solexa 1G sequencing technology.
    • Barski A., Cuddapah S., Cui K., Roh T.Y., Schones D.E., Wang Z., Wei G., Chepelev I., and Zhao K. High-resolution profiling of histone methylations in the human genome. Cell 129 (2007) 823-837. This is the first, comprehensive, whole-genome mapping of numerous histone modifications as well as binding sites for histone variant H2A.Z, RNA polymerase II, and the insulator binding protein CTCF in any organism using ultra high-throughput Solexa 1G sequencing technology.
    • (2007) Cell , vol.129 , pp. 823-837
    • Barski, A.1    Cuddapah, S.2    Cui, K.3    Roh, T.Y.4    Schones, D.E.5    Wang, Z.6    Wei, G.7    Chepelev, I.8    Zhao, K.9
  • 76
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • The authors develop a large-scale chromatin immunoprecipitation assay (ChIP-Seq) for the transcription factor neuron-restrictive silencer factor (NRSF; also known as REST, for repressor element-1 silencing transcription factor), and then utilized ultra-high-throughput DNA Solexa 1G sequencing technology to map a genome-wide binding profile for this transcription factor. They find that NRSF binds to 1946 locations within the human genome, including a number of novel genomic locations. Additionally, they use this high-density data to map an extremely accurate consensus recognition sequence for this very important transcription factor.
    • Johnson D.S., Mortazavi A., Myers R.M., and Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316 (2007) 1497-1502. The authors develop a large-scale chromatin immunoprecipitation assay (ChIP-Seq) for the transcription factor neuron-restrictive silencer factor (NRSF; also known as REST, for repressor element-1 silencing transcription factor), and then utilized ultra-high-throughput DNA Solexa 1G sequencing technology to map a genome-wide binding profile for this transcription factor. They find that NRSF binds to 1946 locations within the human genome, including a number of novel genomic locations. Additionally, they use this high-density data to map an extremely accurate consensus recognition sequence for this very important transcription factor.
    • (2007) Science , vol.316 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.