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Volumn 27, Issue , 2015, Pages 141-147

Advances in understanding cis regulation of the plant gene with an emphasis on comparative genomics

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 84938689427     PISSN: 13695266     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbi.2015.07.001     Document Type: Review
Times cited : (18)

References (51)
  • 1
    • 0037819447 scopus 로고    scopus 로고
    • Transcription regulation and animal diversity
    • Levine M., Tjian R. Transcription regulation and animal diversity. Nature 2003, 424:147-151.
    • (2003) Nature , vol.424 , pp. 147-151
    • Levine, M.1    Tjian, R.2
  • 2
    • 77149139820 scopus 로고    scopus 로고
    • Enhancers: the abundance and function of regulatory sequences beyond promoters
    • Bulger M., Groudine M. Enhancers: the abundance and function of regulatory sequences beyond promoters. Dev Biol 2010, 339:250-257.
    • (2010) Dev Biol , vol.339 , pp. 250-257
    • Bulger, M.1    Groudine, M.2
  • 3
    • 84862174850 scopus 로고    scopus 로고
    • Transcriptional repression via antilooping in the Drosophila embryo
    • Chopra V.S., Kong N., Levine M. Transcriptional repression via antilooping in the Drosophila embryo. Proc Natl Acad Sci U S A 2012, 109:9460-9464.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 9460-9464
    • Chopra, V.S.1    Kong, N.2    Levine, M.3
  • 4
    • 68449092480 scopus 로고    scopus 로고
    • Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C)
    • Louwers M., Splinter E., van Driel R., de Laat W., Stam M. Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C). Nat Protoc 2009, 4:1216-1229.
    • (2009) Nat Protoc , vol.4 , pp. 1216-1229
    • Louwers, M.1    Splinter, E.2    van Driel, R.3    de Laat, W.4    Stam, M.5
  • 5
    • 66449105851 scopus 로고    scopus 로고
    • Tissue- and expression level-specific chromatin looping at maize b1 epialleles
    • Louwers M., Bader R., Haring M., van Driel R., de Laat W., Stam M. Tissue- and expression level-specific chromatin looping at maize b1 epialleles. Plant Cell 2009, 21:832-842.
    • (2009) Plant Cell , vol.21 , pp. 832-842
    • Louwers, M.1    Bader, R.2    Haring, M.3    van Driel, R.4    de Laat, W.5    Stam, M.6
  • 6
    • 84899154279 scopus 로고    scopus 로고
    • A distal CCAAT/NUCLEAR FACTOR Y complex promotes chromatin looping at the FLOWERING LOCUS T promoter and regulates the timing of flowering in Arabidopsis
    • Cao S., Kumimoto R.W., Gnesutta N., Calogero A.M., Mantovani R., Holt B.F. A distal CCAAT/NUCLEAR FACTOR Y complex promotes chromatin looping at the FLOWERING LOCUS T promoter and regulates the timing of flowering in Arabidopsis. Plant Cell 2014, 26:1009-1017.
    • (2014) Plant Cell , vol.26 , pp. 1009-1017
    • Cao, S.1    Kumimoto, R.W.2    Gnesutta, N.3    Calogero, A.M.4    Mantovani, R.5    Holt, B.F.6
  • 7
    • 84905591635 scopus 로고    scopus 로고
    • Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop
    • Ariel F., Jegu T., Latrasse D., Romero-Barrios N., Christ A., Benhamed M., Crespi M. Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop. Mol Cell 2014, 55:383-396.
    • (2014) Mol Cell , vol.55 , pp. 383-396
    • Ariel, F.1    Jegu, T.2    Latrasse, D.3    Romero-Barrios, N.4    Christ, A.5    Benhamed, M.6    Crespi, M.7
  • 8
    • 71749120382 scopus 로고    scopus 로고
    • Finding distal regulatory elements in the human genome
    • Heintzman N.D., Ren B. Finding distal regulatory elements in the human genome. Curr Opin Genet Dev 2009, 19:541-549.
    • (2009) Curr Opin Genet Dev , vol.19 , pp. 541-549
    • Heintzman, N.D.1    Ren, B.2
  • 9
    • 77958107370 scopus 로고    scopus 로고
    • Insulators as mediators of intra- and inter-chromosomal interactions: a common evolutionary theme
    • Ong C.-T., Corces V.G. Insulators as mediators of intra- and inter-chromosomal interactions: a common evolutionary theme. J Biol 2009, 8:73.
    • (2009) J Biol , vol.8 , pp. 73
    • Ong, C.-T.1    Corces, V.G.2
  • 11
    • 43549114120 scopus 로고    scopus 로고
    • Direct repression of KNOX loci by the ASYMMETRIC LEAVES1 complex of Arabidopsis
    • Guo M., Thomas J., Collins G., Timmermans M.C. Direct repression of KNOX loci by the ASYMMETRIC LEAVES1 complex of Arabidopsis. Plant Cell 2008, 20:48-58.
    • (2008) Plant Cell , vol.20 , pp. 48-58
    • Guo, M.1    Thomas, J.2    Collins, G.3    Timmermans, M.C.4
  • 12
    • 84875313702 scopus 로고    scopus 로고
    • The ASYMMETRIC LEAVES complex maintains repression of KNOX homeobox genes via direct recruitment of Polycomb-repressive complex2
    • Lodha M., Marco C.F., Timmermans M.C. The ASYMMETRIC LEAVES complex maintains repression of KNOX homeobox genes via direct recruitment of Polycomb-repressive complex2. Genes Dev 2013, 27:596-601.
    • (2013) Genes Dev , vol.27 , pp. 596-601
    • Lodha, M.1    Marco, C.F.2    Timmermans, M.C.3
  • 13
    • 84988711068 scopus 로고    scopus 로고
    • Trihelix transcription factor GT-4 mediates salt tolerance via interaction with TEM2 in Arabidopsis
    • Wang X.H., Li Q.T., Chen H.W., Zhang W.K., Ma B., Chen S.Y., Zhang J.S. Trihelix transcription factor GT-4 mediates salt tolerance via interaction with TEM2 in Arabidopsis. BMC Plant Biol 2014, 14:339.
    • (2014) BMC Plant Biol , vol.14 , pp. 339
    • Wang, X.H.1    Li, Q.T.2    Chen, H.W.3    Zhang, W.K.4    Ma, B.5    Chen, S.Y.6    Zhang, J.S.7
  • 14
    • 84893110293 scopus 로고    scopus 로고
    • Timing mechanism dependent on cell division is invoked by Polycomb eviction in plant stem cells
    • Sun B., Looi L.S., Guo S., He Z., Gan E.S., Huang J., Xu Y., Wee W.Y., Ito T. Timing mechanism dependent on cell division is invoked by Polycomb eviction in plant stem cells. Science 2014, 343:1248559.
    • (2014) Science , vol.343 , pp. 1248559
    • Sun, B.1    Looi, L.S.2    Guo, S.3    He, Z.4    Gan, E.S.5    Huang, J.6    Xu, Y.7    Wee, W.Y.8    Ito, T.9
  • 15
    • 84927770026 scopus 로고    scopus 로고
    • Genome-wide characterization of cis-acting DNA targets reveals the transcriptional regulatory framework of Opaque2 in maize
    • Li C., Qiao Z., Qi W., Wang Q., Yuan Y., Yang X., Tang Y., Mei B., Lv Y., Zhao H., et al. Genome-wide characterization of cis-acting DNA targets reveals the transcriptional regulatory framework of Opaque2 in maize. Plant Cell 2015, 27:532-545.
    • (2015) Plant Cell , vol.27 , pp. 532-545
    • Li, C.1    Qiao, Z.2    Qi, W.3    Wang, Q.4    Yuan, Y.5    Yang, X.6    Tang, Y.7    Mei, B.8    Lv, Y.9    Zhao, H.10
  • 17
    • 84912124204 scopus 로고    scopus 로고
    • A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana
    • Heyndrickx K.S., Van de Velde J., Wang C., Weigel D., Vandepoele K. A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana. Plant Cell 2014, 26:3894-3910.
    • (2014) Plant Cell , vol.26 , pp. 3894-3910
    • Heyndrickx, K.S.1    Van de Velde, J.2    Wang, C.3    Weigel, D.4    Vandepoele, K.5
  • 19
    • 84887478181 scopus 로고    scopus 로고
    • Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins
    • Teytelman L., Thurtle D.M., Rine J., van Oudenaarden A. Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins. Proc Natl Acad Sci U S A 2013, 110:18602-18607.
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 18602-18607
    • Teytelman, L.1    Thurtle, D.M.2    Rine, J.3    van Oudenaarden, A.4
  • 20
    • 84929315761 scopus 로고    scopus 로고
    • Combinatorial complexity in a transcriptionally centered signaling hub in Arabidopsis
    • Pfeiffer A., Shi H., Tepperman J.M., Zhang Y., Quail P.H. Combinatorial complexity in a transcriptionally centered signaling hub in Arabidopsis. Mol Plant 2014, 7:1598-1618.
    • (2014) Mol Plant , vol.7 , pp. 1598-1618
    • Pfeiffer, A.1    Shi, H.2    Tepperman, J.M.3    Zhang, Y.4    Quail, P.H.5
  • 21
    • 80054728495 scopus 로고    scopus 로고
    • Animal transcription networks as highly connected, quantitative continua
    • Biggin M.D. Animal transcription networks as highly connected, quantitative continua. Dev Cell 2011, 21:611-626.
    • (2011) Dev Cell , vol.21 , pp. 611-626
    • Biggin, M.D.1
  • 22
    • 84865249952 scopus 로고    scopus 로고
    • Transcription factors: from enhancer binding to developmental control
    • Spitz F., Furlong E.E. Transcription factors: from enhancer binding to developmental control. Nat Rev Genet 2012, 13:613-626.
    • (2012) Nat Rev Genet , vol.13 , pp. 613-626
    • Spitz, F.1    Furlong, E.E.2
  • 28
    • 84878440106 scopus 로고    scopus 로고
    • Genome-wide prediction of nucleosome occupancy in maize reveals plant chromatin structural features at genes and other elements at multiple scales
    • Fincher J.A., Vera D.L., Hughes D.D., McGinnis K.M., Dennis J.H., Bass H.W. Genome-wide prediction of nucleosome occupancy in maize reveals plant chromatin structural features at genes and other elements at multiple scales. Plant Physiol 2013, 162:1127-1141.
    • (2013) Plant Physiol , vol.162 , pp. 1127-1141
    • Fincher, J.A.1    Vera, D.L.2    Hughes, D.D.3    McGinnis, K.M.4    Dennis, J.H.5    Bass, H.W.6
  • 31
    • 84865331447 scopus 로고    scopus 로고
    • Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis
    • Zhang W., Zhang T., Wu Y., Jiang J. Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis. Plant Cell 2012, 24:2719-2731.
    • (2012) Plant Cell , vol.24 , pp. 2719-2731
    • Zhang, W.1    Zhang, T.2    Wu, Y.3    Jiang, J.4
  • 34
    • 78651081445 scopus 로고    scopus 로고
    • The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana
    • Deal R.B., Henikoff S. The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana. Nat Protoc 2011, 6:56-68.
    • (2011) Nat Protoc , vol.6 , pp. 56-68
    • Deal, R.B.1    Henikoff, S.2
  • 36
    • 79953231729 scopus 로고    scopus 로고
    • AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana
    • baq034
    • Bulow L., Brill Y., Hehl R. AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana. Database (Oxford) 2010, 2010:baq034.
    • (2010) Database (Oxford) , vol.2010
    • Bulow, L.1    Brill, Y.2    Hehl, R.3
  • 39
    • 84899149304 scopus 로고    scopus 로고
    • Automated conserved noncoding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses
    • Turco G., Schnable J., Pedersen B., Freeling M. Automated conserved noncoding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses. Front Plant Genet Genom 2013, 4:170-180.
    • (2013) Front Plant Genet Genom , vol.4 , pp. 170-180
    • Turco, G.1    Schnable, J.2    Pedersen, B.3    Freeling, M.4
  • 40
    • 84907307297 scopus 로고    scopus 로고
    • Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis
    • Van de Velde J., Heyndrickx K.S., Vandepoele K. Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis. Plant Cell 2014, 26:2729-2745.
    • (2014) Plant Cell , vol.26 , pp. 2729-2745
    • Van de Velde, J.1    Heyndrickx, K.S.2    Vandepoele, K.3
  • 41
    • 84899140736 scopus 로고    scopus 로고
    • The most deeply conserved noncoding sequences in plants serve similar functions to those in vertebrates despite large differences in evolutionary rates
    • Burgess D., Freeling M. The most deeply conserved noncoding sequences in plants serve similar functions to those in vertebrates despite large differences in evolutionary rates. Plant Cell 2014, 26:946-961.
    • (2014) Plant Cell , vol.26 , pp. 946-961
    • Burgess, D.1    Freeling, M.2
  • 43
    • 79952744855 scopus 로고    scopus 로고
    • Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss
    • Schnable J.C., Springer N.M., Freeling M. Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc Natl Acad Sci U S A 2011, 108:4069-4074.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 4069-4074
    • Schnable, J.C.1    Springer, N.M.2    Freeling, M.3
  • 45
    • 84859890589 scopus 로고    scopus 로고
    • Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants
    • Freeling M., Woodhouse M.R., Subramaniam S., Turco G., Lisch D., Schnable J.C. Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants. Curr Opin Plant Biol 2012, 15:131-139.
    • (2012) Curr Opin Plant Biol , vol.15 , pp. 131-139
    • Freeling, M.1    Woodhouse, M.R.2    Subramaniam, S.3    Turco, G.4    Lisch, D.5    Schnable, J.C.6
  • 46
    • 68149144366 scopus 로고    scopus 로고
    • Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression
    • Hollister J.D., Gaut B.S. Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res 2009, 19:1419-1428.
    • (2009) Genome Res , vol.19 , pp. 1419-1428
    • Hollister, J.D.1    Gaut, B.S.2
  • 47
    • 79952303685 scopus 로고    scopus 로고
    • Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata
    • Hollister J.D., Smith L.M., Guo Y.L., Ott F., Weigel D., Gaut B.S. Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc Natl Acad Sci U S A 2011, 108:2322-2327.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 2322-2327
    • Hollister, J.D.1    Smith, L.M.2    Guo, Y.L.3    Ott, F.4    Weigel, D.5    Gaut, B.S.6
  • 49
    • 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. Nat Rev Genet 2014, 15:394-408.
    • (2014) Nat Rev Genet , vol.15 , pp. 394-408
    • Matzke, M.A.1    Mosher, R.A.2
  • 50
    • 84896288527 scopus 로고    scopus 로고
    • Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice
    • Wei L., Gu L., Song X., Cui X., Lu Z., Zhou M., Wang L., Hu F., Zhai J., Meyers B.C., et al. Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice. Proc Natl Acad Sci U S A 2014, 111:3877-3882.
    • (2014) Proc Natl Acad Sci U S A , vol.111 , pp. 3877-3882
    • Wei, L.1    Gu, L.2    Song, X.3    Cui, X.4    Lu, Z.5    Zhou, M.6    Wang, L.7    Hu, F.8    Zhai, J.9    Meyers, B.C.10
  • 51
    • 84930926129 scopus 로고    scopus 로고
    • A solution to the C-value paradox and the function of junk DNA: the genome balance hypothesis
    • Freeling M., Xu J., Woodhouse M., Lisch D. A solution to the C-value paradox and the function of junk DNA: the genome balance hypothesis. Mol Plant 2015, 8:899-910.
    • (2015) Mol Plant , vol.8 , pp. 899-910
    • Freeling, M.1    Xu, J.2    Woodhouse, M.3    Lisch, D.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.