메뉴 건너뛰기




Volumn 2, Issue 5, 2016, Pages

Unique cell-type-specific patterns of DNA methylation in the root meristem

Author keywords

[No Author keywords available]

Indexed keywords

PLANT PROTEIN; TRANSCRIPTOME;

EID: 84979284341     PISSN: None     EISSN: 20550278     Source Type: Journal    
DOI: 10.1038/NPLANTS.2016.58     Document Type: Article
Times cited : (144)

References (50)
  • 1
    • 77249170184 scopus 로고    scopus 로고
    • Establishing maintaining and modifying DNA methylation patterns in plants and animals
    • Law, J. A. & Jacobsen, S. E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Rev. Genet. 11, 204-220 (2010).
    • (2010) Nature Rev. Genet , vol.11 , pp. 204-220
    • Law, J.A.1    Jacobsen, S.E.2
  • 2
    • 84901041535 scopus 로고    scopus 로고
    • RNA-directed DNA methylation: An epigenetic pathway of increasing complexity
    • Matzke, M. A. & Mosher, R. A. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nature Rev. Genet. 15, 394-408 (2014).
    • (2014) Nature Rev. Genet , vol.15 , pp. 394-408
    • Matzke, M.A.1    Mosher, R.A.2
  • 3
    • 84875741680 scopus 로고    scopus 로고
    • The arabidopsis nucleosome remodeler ddm1 allows DNA methyltransferases to access h1-containing heterochromatin
    • Zemach, A. et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153, 193-205 (2013).
    • (2013) Cell , vol.153 , pp. 193-205
    • Zemach, A.1
  • 4
    • 84893716683 scopus 로고    scopus 로고
    • Non-cg methylation patterns shape the epigenetic landscape in arabidopsis
    • Stroud, H. et al. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nature Struct. Mol. Biol. 21, 64-72 (2014).
    • (2014) Nature Struct. Mol. Biol , vol.21 , pp. 64-72
    • Stroud, H.1
  • 5
    • 0033539183 scopus 로고    scopus 로고
    • An epigenetic mutation responsible for natural variation in floral symmetry
    • Cubas, P., Vincent, C. & Coen, E. An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401, 157-161 (1999).
    • (1999) Nature , vol.401 , pp. 157-161
    • Cubas, P.1    Vincent, C.2    Coen, E.3
  • 6
    • 84939516199 scopus 로고    scopus 로고
    • Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements
    • Secco, D. et al. Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. eLife 4, e09343 (2015).
    • (2015) ELife , vol.4 , pp. e09343
    • Secco, D.1
  • 7
    • 84864679478 scopus 로고    scopus 로고
    • Widespread dynamic DNA methylation in response to biotic stress
    • Dowen, R. H. et al.Widespread dynamic DNA methylation in response to biotic stress. Proc. Natl Acad. Sci. USA 109, E2183-E2191 (2012).
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. E2183-E2191
    • Dowen, R.H.1
  • 8
    • 84906325490 scopus 로고    scopus 로고
    • Natural epigenetic polymorphisms lead to intraspecific variation in arabidopsis gene imprinting
    • Pignatta, D. et al. Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprinting. eLife 3, e03198 (2014).
    • (2014) ELife , vol.3 , pp. e03198
    • Pignatta, D.1
  • 9
    • 59349118366 scopus 로고    scopus 로고
    • Epigenetic reprogramming and small RNA silencing of transposable elements in pollen
    • Slotkin, R. K. et al. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136, 461-472 (2009).
    • (2009) Cell , vol.136 , pp. 461-472
    • Slotkin, R.K.1
  • 10
    • 84867053720 scopus 로고    scopus 로고
    • Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA
    • Calarco, J. P. et al. Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 151, 194-205 (2012).
    • (2012) Cell , vol.151 , pp. 194-205
    • Calarco, J.P.1
  • 11
    • 84866140080 scopus 로고    scopus 로고
    • Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes
    • Ibarra, C. A. et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 337, 1360-1364 (2012).
    • (2012) Science , vol.337 , pp. 1360-1364
    • Ibarra, C.A.1
  • 12
    • 70349278339 scopus 로고    scopus 로고
    • Selective epigenetic control of retrotransposition in arabidopsis
    • Mirouze, M. et al. Selective epigenetic control of retrotransposition in Arabidopsis. Nature 461, 427-430 (2009).
    • (2009) Nature , vol.461 , pp. 427-430
    • Mirouze, M.1
  • 13
    • 70349276670 scopus 로고    scopus 로고
    • Bursts of retrotransposition reproduced in arabidopsis
    • Tsukahara, S. et al. Bursts of retrotransposition reproduced in Arabidopsis. Nature 461, 423-426 (2009).
    • (2009) Nature , vol.461 , pp. 423-426
    • Tsukahara, S.1
  • 14
    • 84898620330 scopus 로고    scopus 로고
    • Meristem-specific expression of epigenetic regulators safeguards transposon silencing in arabidopsis
    • Baubec, T., Finke, A., Mittelsten Scheid, O. & Pecinka, A. Meristem-specific expression of epigenetic regulators safeguards transposon silencing in Arabidopsis. EMBO Rep. 15, 446-452 (2014).
    • (2014) EMBO Re , vol.15 , pp. 446-452
    • Baubec, T.1    Finke, A.2    Mittelsten Scheid, O.3    Pecinka, A.4
  • 15
    • 84912120604 scopus 로고    scopus 로고
    • Evolution of DNA methylation patterns in the brassicaceae is driven by differences in genome organization
    • Seymour, D. K., Koenig, D., Hagmann, J., Becker, C. & Weigel, D. Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization. PLoS Genet. 10, e1004785 (2014).
    • (2014) PLoS Genet , vol.10 , pp. e1004785
    • Seymour, D.K.1    Koenig, D.2    Hagmann, J.3    Becker, C.4    Weigel, D.5
  • 16
    • 84892581957 scopus 로고    scopus 로고
    • Epigenetic differences between shoots and roots in arabidopsis reveals tissue-specific regulation
    • Widman, N., Feng, S., Jacobsen, S. E. & Pellegrini, M. Epigenetic differences between shoots and roots in Arabidopsis reveals tissue-specific regulation. Epigenetics 9, 236-242 (2014).
    • (2014) Epigenetics , vol.9 , pp. 236-242
    • Widman, N.1    Feng, S.2    Jacobsen, S.E.3    Pellegrini, M.4
  • 17
    • 80054837794 scopus 로고    scopus 로고
    • Transgenerational epigenetic instability is a source of novel methylation variants
    • Schmitz, R. J. et al. Transgenerational epigenetic instability is a source of novel methylation variants. Science 334, 369-373 (2011).
    • (2011) Science , vol.334 , pp. 369-373
    • Schmitz, R.J.1
  • 18
    • 80054718602 scopus 로고    scopus 로고
    • Spontaneous epigenetic variation in the arabidopsis thaliana methylome
    • Becker, C. et al. Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480, 245-249 (2011).
    • (2011) Nature , vol.480 , pp. 245-249
    • Becker, C.1
  • 19
    • 84874991260 scopus 로고    scopus 로고
    • Patterns of population epigenomic diversity
    • Schmitz, R. J. et al. Patterns of population epigenomic diversity. Nature 495, 193-198 (2013).
    • (2013) Nature , vol.495 , pp. 193-198
    • Schmitz, R.J.1
  • 20
    • 84872614860 scopus 로고    scopus 로고
    • Comprehensive analysis of silencing mutants reveals complex regulation of the arabidopsis methylome
    • Stroud, H., Greenberg, M. V., Feng, S., Bernatavichute, Y. V. & Jacobsen, S. E. Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 152, 352-364 (2013).
    • (2013) Cell , vol.152 , pp. 352-364
    • Stroud, H.1    Greenberg, M.V.2    Feng, S.3    Bernatavichute, Y.V.4    Jacobsen, S.E.5
  • 21
    • 84877040915 scopus 로고    scopus 로고
    • The initiation of epigenetic silencing of active transposable elements is triggered by rdr6 and 21-22 nucleotide small interfering rnas
    • Nuthikattu, S. et al. The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21-22 nucleotide small interfering RNAs. Plant Physiol. 162, 116-131 (2013).
    • (2013) Plant Physiol , vol.162 , pp. 116-131
    • Nuthikattu, S.1
  • 22
    • 33748629119 scopus 로고    scopus 로고
    • Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis
    • Zhang, X. et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126, 1189-1201 (2006).
    • (2006) Cell , vol.126 , pp. 1189-1201
    • Zhang, X.1
  • 23
    • 33845880624 scopus 로고    scopus 로고
    • Genomewide analysis of arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
    • Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T. & Henikoff, S. Genomewide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genet. 39, 61-69 (2007).
    • (2007) Nature Genet , vol.39 , pp. 61-69
    • Zilberman, D.1    Gehring, M.2    Tran, R.K.3    Ballinger, T.4    Henikoff, S.5
  • 24
    • 12544254467 scopus 로고    scopus 로고
    • DNA methylation profiling identifies cg methylation clusters in arabidopsis genes
    • Tran, R. K. et al. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr. Biol. 15, 154-159 (2005).
    • (2005) Curr. Biol , vol.15 , pp. 154-159
    • Tran, R.K.1
  • 25
    • 19344374219 scopus 로고    scopus 로고
    • Genetic and functional diversification of small RNA pathways in plants
    • Xie, Z. et al. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2, E104 (2004).
    • (2004) PLoS Biol , vol.2 , pp. E104
    • Xie, Z.1
  • 26
    • 14844302397 scopus 로고    scopus 로고
    • Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation
    • Onodera, Y. et al. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120, 613-622 (2005).
    • (2005) Cell , vol.120 , pp. 613-622
    • Onodera, Y.1
  • 27
    • 33745279055 scopus 로고    scopus 로고
    • Dissecting arabidopsis thaliana dicer function in small RNA processing, gene silencing and DNA methylation patterning
    • Henderson, I. R. et al. Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nature Genet. 38, 721-725 (2006).
    • (2006) Nature Genet , vol.38 , pp. 721-725
    • Henderson, I.R.1
  • 28
    • 34347382532 scopus 로고    scopus 로고
    • An snf2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in arabidopsis
    • Smith, L. M. et al. An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell 19, 1507-1521 (2007).
    • (2007) Plant Cell , vol.19 , pp. 1507-1521
    • Smith, L.M.1
  • 29
    • 84904015315 scopus 로고    scopus 로고
    • The histone variant h2a.w defines heterochromatin and promotes chromatin condensation in arabidopsis
    • Yelagandula, R. et al. The histone variant H2A.W defines heterochromatin and promotes chromatin condensation in Arabidopsis. Cell 158, 98-109 (2014).
    • (2014) Cell , vol.158 , pp. 98-109
    • Yelagandula, R.1
  • 30
    • 67149119197 scopus 로고    scopus 로고
    • Genome-wide demethylation of arabidopsis endosperm
    • Hsieh, T. F. et al. Genome-wide demethylation of Arabidopsis endosperm. Science 324, 1451-1454 (2009).
    • (2009) Science , vol.324 , pp. 1451-1454
    • Hsieh, T.F.1
  • 31
    • 0033607276 scopus 로고    scopus 로고
    • Genetic ablation of root cap cells in arabidopsis
    • Tsugeki, R. & Fedoroff, N. V. Genetic ablation of root cap cells in Arabidopsis. Proc. Natl Acad. Sci. USA 96, 12941-12946 (1999).
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 12941-12946
    • Tsugeki, R.1    Fedoroff, N.V.2
  • 32
    • 33644764962 scopus 로고    scopus 로고
    • Root gravitropism requires lateral root cap and epidermal cells for transport and response to a mobile auxin signal
    • Swarup, R. et al. Root gravitropism requires lateral root cap and epidermal cells for transport and response to a mobile auxin signal. Nature Cell Biol. 7, 1057-1065 (2005).
    • (2005) Nature Cell Biol , vol.7 , pp. 1057-1065
    • Swarup, R.1
  • 33
    • 70049096990 scopus 로고    scopus 로고
    • Induction of RNA-directed DNA methylation upon decondensation of constitutive heterochromatin
    • Schoft, V. K. et al. Induction of RNA-directed DNA methylation upon decondensation of constitutive heterochromatin. EMBO Rep. 10, 1015-1021 (2009).
    • (2009) EMBO Re , vol.10 , pp. 1015-1021
    • Schoft, V.K.1
  • 34
    • 0027165869 scopus 로고
    • Cellular organisation of the arabidopsis thaliana root
    • Dolan, L. et al. Cellular organisation of the Arabidopsis thaliana root. Development 119, 71-84 (1993).
    • (1993) Development , vol.119 , pp. 71-84
    • Dolan, L.1
  • 35
    • 79952114001 scopus 로고    scopus 로고
    • Fluorescence-Activated cell sorting in plant developmental biology
    • Iyer-Pascuzzi, A. S. & Benfey, P. N. Fluorescence-Activated cell sorting in plant developmental biology. Methods Mol. Biol. 655, 313-319 (2010).
    • (2010) Methods Mol. Biol , vol.655 , pp. 313-319
    • Iyer-Pascuzzi, A.S.1    Benfey, P.N.2
  • 36
    • 29544440189 scopus 로고    scopus 로고
    • Transcriptional profile of the arabidopsis root quiescent center
    • Nawy, T. et al. Transcriptional profile of the Arabidopsis root quiescent center. Plant Cell 17, 1908-1925 (2005).
    • (2005) Plant Cell , vol.17 , pp. 1908-1925
    • Nawy, T.1
  • 37
    • 84863713395 scopus 로고    scopus 로고
    • D-type cyclins control cell division and developmental rate during arabidopsis seed development
    • Collins, C., Dewitte, W. & Murray, J. A. D-type cyclins control cell division and developmental rate during Arabidopsis seed development. J Exp. Bot. 63, 3571-3586 (2012).
    • (2012) J Exp. Bot , vol.63 , pp. 3571-3586
    • Collins, C.1    Dewitte, W.2    Murray, J.A.3
  • 38
    • 0033638561 scopus 로고    scopus 로고
    • A novel two-component hybrid molecule regulates vascular morphogenesis of the arabidopsis root
    • Mahonen, A. P. et al. A novel two-component hybrid molecule regulates vascular morphogenesis of the Arabidopsis root. Genes Dev 14, 2938-2943 (2000).
    • (2000) Genes Dev , vol.14 , pp. 2938-2943
    • Mahonen, A.P.1
  • 39
    • 0347447343 scopus 로고    scopus 로고
    • A gene expression map of the arabidopsis root
    • Birnbaum, K. et al. A gene expression map of the Arabidopsis root. Science 302, 1956-1960 (2003).
    • (2003) Science , vol.302 , pp. 1956-1960
    • Birnbaum, K.1
  • 40
    • 33645822943 scopus 로고    scopus 로고
    • Transcriptional and posttranscriptional regulation of transcription factor expression in arabidopsis roots
    • Lee, J. Y. et al. Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots. Proc. Natl Acad. Sci. USA 103, 6055-6060 (2006).
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 6055-6060
    • Lee, J.Y.1
  • 41
    • 0033601119 scopus 로고    scopus 로고
    • Werewolf a myb-related protein in arabidopsis, is a position-dependent regulator of epidermal cell patterning
    • Lee, M. M. & Schiefelbein, J. WEREWOLF, a MYB-related protein in Arabidopsis, is a position-dependent regulator of epidermal cell patterning. Cell 99, 473-483 (1999).
    • (1999) Cell , vol.99 , pp. 473-483
    • Lee, M.M.1    Schiefelbein, J.2
  • 42
    • 42749087226 scopus 로고    scopus 로고
    • Highly integrated single-base resolution maps of the epigenome in arabidopsis
    • Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523-536 (2008).
    • (2008) Cell , vol.133 , pp. 523-536
    • Lister, R.1
  • 43
    • 79952264847 scopus 로고    scopus 로고
    • Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells
    • Lister, R. et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471, 68-73 (2011).
    • (2011) Nature , vol.471 , pp. 68-73
    • Lister, R.1
  • 44
    • 84923804522 scopus 로고    scopus 로고
    • Methylc-seq library preparation for base-resolution whole-genome bisulfite sequencing
    • Urich, M. A., Nery, J. R., Lister, R., Schmitz, R. J. & Ecker, J. R. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nature Protoc. 10, 475-483 (2015).
    • (2015) Nature Protoc , vol.10 , pp. 475-483
    • Urich, M.A.1    Nery, J.R.2    Lister, R.3    Schmitz, R.J.4    Ecker, J.R.5
  • 45
    • 84938495948 scopus 로고    scopus 로고
    • Human body epigenome maps reveal noncanonical DNA methylation variation
    • Schultz, M. D. et al. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature 523, 212-216 (2015).
    • (2015) Nature , vol.523 , pp. 212-216
    • Schultz, M.D.1
  • 46
    • 84869092574 scopus 로고    scopus 로고
    • Leveling' the playing field for analyses of single-base resolution DNA methylomes
    • Schultz, M. D., Schmitz, R. J. & Ecker, J. R. 'Leveling' the playing field for analyses of single-base resolution DNA methylomes. Trends Genet. 28, 583-585 (2012).
    • (2012) Trends Genet , vol.28 , pp. 583-585
    • Schultz, M.D.1    Schmitz, R.J.2    Ecker, J.R.3
  • 47
    • 84855304145 scopus 로고    scopus 로고
    • High-resolution experimental and computational profiling of tissue-specific known and novel mirnas in arabidopsis
    • Breakfield, N. W. et al. High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis. Genome Res. 22, 163-176 (2012).
    • (2012) Genome Res , vol.22 , pp. 163-176
    • Breakfield, N.W.1
  • 48
    • 70450217879 scopus 로고    scopus 로고
    • Human DNA methylomes at base resolution show widespread epigenomic differences
    • Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315-322 (2009).
    • (2009) Nature , vol.462 , pp. 315-322
    • Lister, R.1
  • 49
    • 84876996918 scopus 로고    scopus 로고
    • Tophat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol.14, R36 (2013).
    • (2013) Genome Biol , vol.14 , pp. R36
    • Kim, D.1
  • 50
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with tophat and cufflinks
    • Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protoc. 7, 562-578 (2012).
    • (2012) Nature Protoc , vol.7 , pp. 562-578
    • Trapnell, C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.