메뉴 건너뛰기




Volumn 4, Issue MAY, 2015, Pages

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation

Author keywords

[No Author keywords available]

Indexed keywords

DNA METHYLTRANSFERASE; ARABIDOPSIS PROTEIN; DNA (CYTOSINE 5) METHYLTRANSFERASE; TRANSPOSON;

EID: 84930663528     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.05255     Document Type: Article
Times cited : (377)

References (47)
  • 2
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biology 11:R106. doi: 10.1186/gb-2010-11-10-r106.
    • (2010) Genome Biology , vol.11
    • Anders, S.1    Huber, W.2
  • 3
    • 78449299668 scopus 로고    scopus 로고
    • R/qtl: High-throughput multiple QTL mapping
    • Arends D, Prins P, Jansen RC, Broman KW. 2010. R/qtl: high-throughput multiple QTL mapping. Bioinformatics 26: 2990-2992. doi: 10.1093/bioinformatics/btq565.
    • (2010) Bioinformatics , vol.26 , pp. 2990-2992
    • Arends, D.1    Prins, P.2    Jansen, R.C.3    Broman, K.W.4
  • 5
    • 84883685094 scopus 로고    scopus 로고
    • Estimating and interpreting FST: The impact of rare variants
    • Bhatia G, Patterson N, Sankararaman S, Price AL. 2013. Estimating and interpreting FST: the impact of rare variants. Genome Research 23:1514-1521. doi: 10.1101/gr.154831.113.
    • (2013) Genome Research , vol.23 , pp. 1514-1521
    • Bhatia, G.1    Patterson, N.2    Sankararaman, S.3    Price, A.L.4
  • 6
    • 0037958742 scopus 로고    scopus 로고
    • R/qtl: QTL mapping in experimental crosses
    • Broman KW, Wu H, Sen S, Churchill GA. 2003. R/qtl: QTL mapping in experimental crosses. Bioinformatics 19: 889-890. doi: 10.1093/bioinformatics/btg112.
    • (2003) Bioinformatics , vol.19 , pp. 889-890
    • Broman, K.W.1    Wu, H.2    Sen, S.3    Churchill, G.A.4
  • 8
    • 84901060300 scopus 로고    scopus 로고
    • Estimating heritability of complex traits from genome-wide association studies using IBS-based Haseman-Elston regression
    • Chen GB. 2014. Estimating heritability of complex traits from genome-wide association studies using IBS-based Haseman-Elston regression. Frontiers in Genetics 5:107. doi: 10.3389/fgene.2014.00107.
    • (2014) Frontiers in Genetics , vol.5 , pp. 107
    • Chen, G.B.1
  • 15
    • 84866853818 scopus 로고    scopus 로고
    • BSmooth: From whole genome bisulfite sequencing reads to differentially methylated regions
    • Hansen KD, Langmead B, Irizarry RA. 2012. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biology 13:R83. doi: 10.1186/gb-2012-13-10-r83.
    • (2012) Genome Biology , vol.13
    • Hansen, K.D.1    Langmead, B.2    Irizarry, R.A.3
  • 16
    • 0031832432 scopus 로고    scopus 로고
    • A DNA methyltransferase homolog with a chromodomain exists in multiple polymorphic forms in Arabidopsis
    • Henikoff S, Comai L. 1998. A DNA methyltransferase homolog with a chromodomain exists in multiple polymorphic forms in Arabidopsis. Genetics 149:307-318.
    • (1998) Genetics , vol.149 , pp. 307-318
    • Henikoff, S.1    Comai, L.2
  • 17
    • 84910671594 scopus 로고    scopus 로고
    • Keeping it local: Evidence for positive selection in Swedish Arabidopsis thaliana
    • Huber CD, Nordborg M, Hermisson J, Hellmann I. 2014. Keeping it local: evidence for positive selection in Swedish Arabidopsis thaliana. Molecular Biology and Evolution 31:3026-3039. doi: 10.1093/molbev/msu247.
    • (2014) Molecular Biology and Evolution , vol.31 , pp. 3026-3039
    • Huber, C.D.1    Nordborg, M.2    Hermisson, J.3    Hellmann, I.4
  • 18
    • 79953746026 scopus 로고    scopus 로고
    • An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress
    • Ito H, Gaubert H, Bucher E, Mirouze M, Vaillant I, Paszkowski J. 2011. An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature 472:115-119. doi: 10.1038/ nature09861.
    • (2011) Nature , vol.472 , pp. 115-119
    • Ito, H.1    Gaubert, H.2    Bucher, E.3    Mirouze, M.4    Vaillant, I.5    Paszkowski, J.6
  • 23
    • 84874188531 scopus 로고    scopus 로고
    • Q(ST)-F(ST) comparisons: Evolutionary and ecological insights from genomic heterogeneity
    • Leinonen T, McCairns RJ, O'Hara RB, Merila J. 2013. Q(ST)-F(ST) comparisons: evolutionary and ecological insights from genomic heterogeneity. Nature Reviews Genetics 14:179-190. doi: 10.1038/nrg3395.
    • (2013) Nature Reviews Genetics , vol.14 , pp. 179-190
    • Leinonen, T.1    McCairns, R.J.2    O'Hara, R.B.3    Merila, J.4
  • 24
    • 84897145969 scopus 로고    scopus 로고
    • Inheritance patterns and stability of DNA methylation variation in maize near-isogenic lines
    • Li Q, Eichten SR, Hermanson PJ, Springer NM. 2014. Inheritance patterns and stability of DNA methylation variation in maize near-isogenic lines. Genetics 196:667-676. doi: 10.1534/genetics.113.158980.
    • (2014) Genetics , vol.196 , pp. 667-676
    • Li, Q.1    Eichten, S.R.2    Hermanson, P.J.3    Springer, N.M.4
  • 27
    • 84863565553 scopus 로고    scopus 로고
    • Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data
    • Liu Y, Siegmund KD, Laird PW, Berman BP. 2012. Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biology 13:R61. doi: 10.1186/gb-2012-13-7-r61.
    • (2012) Genome Biology , vol.13
    • Liu, Y.1    Siegmund, K.D.2    Laird, P.W.3    Berman, B.P.4
  • 29
    • 78049460068 scopus 로고    scopus 로고
    • Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis
    • Pecinka A, Dinh HQ, Baubec T, Rosa M, Lettner N, Mittelsten Scheid O. 2010. Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis. The Plant Cell 22:3118-3129. doi: 10.1105/tpc. 110.078493.
    • (2010) The Plant Cell , vol.22 , pp. 3118-3129
    • Pecinka, A.1    Dinh, H.Q.2    Baubec, T.3    Rosa, M.4    Lettner, N.5    Mittelsten Scheid, O.6
  • 32
    • 84885997727 scopus 로고    scopus 로고
    • NextGenMap: Fast and accurate read mapping in highly polymorphic genomes
    • Sedlazeck FJ, Rescheneder P, von Haeseler A. 2013. NextGenMap: fast and accurate read mapping in highly polymorphic genomes. Bioinformatics 29:2790-2791. doi: 10.1093/bioinformatics/btt468.
    • (2013) Bioinformatics , vol.29 , pp. 2790-2791
    • Sedlazeck, F.J.1    Rescheneder, P.2    von Haeseler, A.3
  • 33
    • 84862991434 scopus 로고    scopus 로고
    • An efficient multi-locus mixedmodel approach for genome-wide association studies in structured populations
    • Segura V, Vilhjálmsson BJ, Platt A, Korte A, Seren Ü, Long Q, Nordborg M. 2012. An efficient multi-locus mixedmodel approach for genome-wide association studies in structured populations. Nature Genetics 44:825-830. doi: 10.1038/ng.2314.
    • (2012) Nature Genetics , vol.44 , pp. 825-830
    • Segura, V.1    Vilhjálmsson, B.J.2    Platt, A.3    Korte, A.4    Seren, Ü.5    Long, Q.6    Nordborg, M.7
  • 34
    • 84912120604 scopus 로고    scopus 로고
    • Evolution of DNA methylation patterns in the brassicaceae is driven by differences in genome organization
    • Seymour DK, Koenig D, Hagmann J, Becker C, Weigel D. 2014. Evolution of DNA methylation patterns in the brassicaceae is driven by differences in genome organization. PLOS Genetics 10:e1004785. doi: 10.1371/journal. pgen.1004785.
    • (2014) PLOS Genetics , vol.10
    • Seymour, D.K.1    Koenig, D.2    Hagmann, J.3    Becker, C.4    Weigel, D.5
  • 35
    • 84919682702 scopus 로고    scopus 로고
    • Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonality
    • Shen X, De Jonge J, Forsberg SK, Pettersson ME, Sheng Z, Hennig L, Carlborg Ö. 2014. Natural CMT2 variation is associated with genome-wide methylation changes and temperature seasonality. PLOS Genetics 10:e1004842. doi: 10.1371/journal.pgen.1004842.
    • (2014) PLOS Genetics , vol.10
    • Shen, X.1    De Jonge, J.2    Forsberg, S.K.3    Pettersson, M.E.4    Sheng, Z.5    Hennig, L.6    Carlborg, Ö.7
  • 36
    • 85090878417 scopus 로고    scopus 로고
    • LDheatmap: An r function for graphical display of pairwise linkage disequilibria between single nucleotide polymorphisms
    • Shin JH, Blay S, McNeney B, Graham J. 2006. LDheatmap: An r function for graphical display of pairwise linkage disequilibria between single nucleotide polymorphisms. Journal of Statistical Software 16.
    • (2006) Journal of Statistical Software , pp. 16
    • Shin, J.H.1    Blay, S.2    McNeney, B.3    Graham, J.4
  • 39
    • 84872614860 scopus 로고    scopus 로고
    • Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome
    • Stroud H, Greenberg MV, Feng S, Bernatavichute YV, Jacobsen SE. 2013. Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 152:352-364. doi: 10.1016/j.cell.2012. 10.054.
    • (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
  • 40
    • 84861062626 scopus 로고    scopus 로고
    • Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly
    • Takuno S, Gaut BS. 2012. Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly. Molecular Biology and Evolution 29:219-227. doi: 10.1093/molbev/msr188.
    • (2012) Molecular Biology and Evolution , vol.29 , pp. 219-227
    • Takuno, S.1    Gaut, B.S.2
  • 43
    • 68949141599 scopus 로고    scopus 로고
    • BSMAP: Whole genome bisulfite sequence MAPping program
    • Xi Y, Li W. 2009. BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics 10:232. doi: 10.1186/1471-2105-10-232.
    • (2009) BMC Bioinformatics , vol.10 , pp. 232
    • Xi, Y.1    Li, W.2
  • 44
    • 84875741680 scopus 로고    scopus 로고
    • The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin
    • Zemach A, Kim MY, Hsieh PH, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153:193-205. doi: 10.1016/j.cell.2013.02.033.
    • (2013) Cell , vol.153 , pp. 193-205
    • Zemach, A.1    Kim, M.Y.2    Hsieh, P.H.3    Coleman-Derr, D.4    Eshed-Williams, L.5    Thao, K.6    Harmer, S.L.7    Zilberman, D.8
  • 45
  • 47
    • 33845880624 scopus 로고    scopus 로고
    • Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
    • Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. 2007. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genetics 39: 61-69. doi: 10.1038/ng1929.
    • (2007) Nature Genetics , vol.39 , pp. 61-69
    • Zilberman, D.1    Gehring, M.2    Tran, R.K.3    Ballinger, T.4    Henikoff, S.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.