메뉴 건너뛰기




Volumn 25, Issue 8, 2015, Pages 1182-1195

Determinants of nucleosome positioning and their influence on plant gene expression

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE I; JASMONIC ACID; CYCLOPENTANE DERIVATIVE; NUCLEOSOME; OXYLIPIN; PLANT DNA;

EID: 84938826120     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.188680.114     Document Type: Article
Times cited : (59)

References (77)
  • 2
    • 0028385745 scopus 로고
    • The 5′-region of Arabidopsis thaliana cor15a has cis-acting elements that confer cold-, drought- and ABA-regulated gene expression
    • Baker SS, Wilhelm KS, Thomashow MF. 1994. The 5′-region of Arabidopsis thaliana cor15a has cis-acting elements that confer cold-, drought- and ABA-regulated gene expression. Plant Mol Biol 24: 701-713.
    • (1994) Plant Mol Biol , vol.24 , pp. 701-713
    • Baker, S.S.1    Wilhelm, K.S.2    Thomashow, M.F.3
  • 4
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc 57: 289-300.
    • (1995) J R Stat Soc , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 5
    • 84924863892 scopus 로고    scopus 로고
    • A key general stress response motif is regulated non-uniformly by CAMTA transcription factors
    • Benn G, Wang CQ, Hicks DR, Stein J, Guthrie C, Dehesh K. 2014. A key general stress response motif is regulated non-uniformly by CAMTA transcription factors. Plant J 80: 82-92.
    • (2014) Plant J , vol.80 , pp. 82-92
    • Benn, G.1    Wang, C.Q.2    Hicks, D.R.3    Stein, J.4    Guthrie, C.5    Dehesh, K.6
  • 6
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: A flexible trimmer for Illumina sequence data
    • Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120.
    • (2014) Bioinformatics , vol.30 , pp. 2114-2120
    • Bolger, A.M.1    Lohse, M.2    Usadel, B.3
  • 7
    • 3042741883 scopus 로고    scopus 로고
    • Conserved MYC transcription factors play a key role in jasmonate signaling both in tomato and Arabidopsis
    • Boter M, Ruíz-Rivero O, Abdeen A, Prat S. 2004. Conserved MYC transcription factors play a key role in jasmonate signaling both in tomato and Arabidopsis. Genes Dev 18: 1577-1591.
    • (2004) Genes Dev , vol.18 , pp. 1577-1591
    • Boter, M.1    Ruíz-Rivero, O.2    Abdeen, A.3    Prat, S.4
  • 8
    • 54949147307 scopus 로고    scopus 로고
    • F-Seq: A feature density estimator for high-throughput sequence tags
    • Boyle AP, Guinney J, Crawford GE, Furey TS. 2008. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 24: 2537-2538.
    • (2008) Bioinformatics , vol.24 , pp. 2537-2538
    • Boyle, A.P.1    Guinney, J.2    Crawford, G.E.3    Furey, T.S.4
  • 9
    • 84891703149 scopus 로고    scopus 로고
    • Activator control of nucleosome occupancy in activation and repression of transcription
    • Bryant GO, Prabhu V, Floer M, Wang X, Spagna D, Schreiber D, Ptashne M. 2008. Activator control of nucleosome occupancy in activation and repression of transcription. PLoS Biol 6: 2928-2939.
    • (2008) PLoS Biol , vol.6 , pp. 2928-2939
    • Bryant, G.O.1    Prabhu, V.2    Floer, M.3    Wang, X.4    Spagna, D.5    Schreiber, D.6    Ptashne, M.7
  • 14
    • 0028121490 scopus 로고
    • Arabidopsis mutants selected for resistance to the phytotoxin coronatine are male sterile, insensitive to methyl jasmonate, and resistant to a bacterial pathogen
    • Feys B, Benedetti CE, Penfold CN, Turner JG. 1994. Arabidopsis mutants selected for resistance to the phytotoxin coronatine are male sterile, insensitive to methyl jasmonate, and resistant to a bacterial pathogen. Plant Cell 6: 751-759.
    • (1994) Plant Cell , vol.6 , pp. 751-759
    • Feys, B.1    Benedetti, C.E.2    Penfold, C.N.3    Turner, J.G.4
  • 15
    • 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 JA, Vera DL, Hughes DD, McGinnis KM, Dennis JH, Bass HW. 2013. Genome-wide prediction of nucleosome occupancy in maize reveals plant chromatin structural features at genes and other elements at multiple scales. Plant Physiol 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
  • 18
    • 79953126490 scopus 로고    scopus 로고
    • Improved protein-binding microarrays for the identification of DNA-binding specificities of transcription factors
    • Godoy M, Franco-Zorrilla JM, Pérez-Pérez J, Oliveros JC, Lorenzo O, Solano R. 2011. Improved protein-binding microarrays for the identification of DNA-binding specificities of transcription factors. Plant J 66: 700-711.
    • (2011) Plant J , vol.66 , pp. 700-711
    • Godoy, M.1    Franco-Zorrilla, J.M.2    Pérez-Pérez, J.3    Oliveros, J.C.4    Lorenzo, O.5    Solano, R.6
  • 19
    • 25144442704 scopus 로고    scopus 로고
    • TAMO: A flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs
    • Gordon DB, Nekludova L, McCallum S, Fraenkel E. 2005. TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs. Bioinformatics 21: 3164-3165.
    • (2005) Bioinformatics , vol.21 , pp. 3164-3165
    • Gordon, D.B.1    Nekludova, L.2    McCallum, S.3    Fraenkel, E.4
  • 20
    • 84864059329 scopus 로고    scopus 로고
    • In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae
    • Gossett AJ, Lieb JD. 2012. In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae. PLoS Genet 8: e1002771.
    • (2012) PLoS Genet , vol.8 , pp. e1002771
    • Gossett, A.J.1    Lieb, J.D.2
  • 21
    • 0023899769 scopus 로고
    • Nuclease hypersensitive sites in chromatin
    • Gross DS, Garrard WT. 1988. Nuclease hypersensitive sites in chromatin. Annu Rev Biochem 57: 159-197.
    • (1988) Annu Rev Biochem , vol.57 , pp. 159-197
    • Gross, D.S.1    Garrard, W.T.2
  • 22
    • 78049440475 scopus 로고    scopus 로고
    • Chromatin landscape dictates HSF binding to target DNA elements
    • Guertin MJ, Lis JT. 2010. Chromatin landscape dictates HSF binding to target DNA elements. PLoS Genet 6: e1001114.
    • (2010) PLoS Genet , vol.6 , pp. e1001114
    • Guertin, M.J.1    Lis, J.T.2
  • 25
    • 84912124204 scopus 로고    scopus 로고
    • A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana
    • Heyndrickx KS, Van de Velde J, Wang C, Weigel D, Vandepoele K. 2014. A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana. Plant Cell 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
  • 27
    • 77957725616 scopus 로고    scopus 로고
    • Ubiquitin ligase-coupled receptors extend their reach to jasmonate
    • Howe GA. 2010. Ubiquitin ligase-coupled receptors extend their reach to jasmonate. Plant Physiol 154: 471-474.
    • (2010) Plant Physiol , vol.154 , pp. 471-474
    • Howe, G.A.1
  • 28
    • 84901980324 scopus 로고    scopus 로고
    • Mechanisms underlying nucleosome positioning in vivo
    • Hughes AL, Rando OJ. 2014. Mechanisms underlying nucleosome positioning in vivo. Annu Rev Biophys 43: 41-63.
    • (2014) Annu Rev Biophys , vol.43 , pp. 41-63
    • Hughes, A.L.1    Rando, O.J.2
  • 29
    • 84867371116 scopus 로고    scopus 로고
    • A functional evolutionary approach to identify determinants of nucleosome positioning: A unifying model for establishing the genome-wide pattern
    • Hughes AL, Jin Y, Rando OJ, Struhl K. 2012. A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern. Mol Cell 48: 5-15.
    • (2012) Mol Cell , vol.48 , pp. 5-15
    • Hughes, A.L.1    Jin, Y.2    Rando, O.J.3    Struhl, K.4
  • 30
    • 34447092534 scopus 로고    scopus 로고
    • Expression of the ASYMMETRIC LEAVES2 gene in the adaxial domain of Arabidopsis leaves represses cell proliferation in this domain and is critical for the development of properly expanded leaves
    • Iwakawa H, Iwasaki M, Kojima S, Ueno Y, Soma T, Tanaka H, Semiarti E, Machida Y, Machida C. 2007. Expression of the ASYMMETRIC LEAVES2 gene in the adaxial domain of Arabidopsis leaves represses cell proliferation in this domain and is critical for the development of properly expanded leaves. Plant J 51: 173-184.
    • (2007) Plant J , vol.51 , pp. 173-184
    • Iwakawa, H.1    Iwasaki, M.2    Kojima, S.3    Ueno, Y.4    Soma, T.5    Tanaka, H.6    Semiarti, E.7    Machida, Y.8    Machida, C.9
  • 34
    • 48049085446 scopus 로고    scopus 로고
    • Jasmonate signaling: A conserved mechanism of hormone sensing
    • Katsir L, Chung HS, Koo AJ, Howe GA. 2008. Jasmonate signaling: a conserved mechanism of hormone sensing. Curr Opin Plant Biol 11: 428-435.
    • (2008) Curr Opin Plant Biol , vol.11 , pp. 428-435
    • Katsir, L.1    Chung, H.S.2    Koo, A.J.3    Howe, G.A.4
  • 35
    • 65949090511 scopus 로고    scopus 로고
    • Target genes of the MADS transcription factor SEPALLATA3: Integration of developmental and hormonal pathways in the Arabidopsis flower
    • Kaufmann K, Muiño JM, Jauregui R, Airoldi CA, Smaczniak C, Krajewski P, Angenent GC. 2009. Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower. PLoS Biol 7: e1000090.
    • (2009) PLoS Biol , vol.7 , pp. e1000090
    • Kaufmann, K.1    Muiño, J.M.2    Jauregui, R.3    Airoldi, C.A.4    Smaczniak, C.5    Krajewski, P.6    Angenent, G.C.7
  • 36
    • 70350516781 scopus 로고    scopus 로고
    • The wound hormone jasmonate
    • Koo AJ, Howe GA. 2009. The wound hormone jasmonate. Phytochemistry 70: 1571-1580.
    • (2009) Phytochemistry , vol.70 , pp. 1571-1580
    • Koo, A.J.1    Howe, G.A.2
  • 37
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memoryefficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
    • (2009) Genome Biol , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 39
    • 84900474003 scopus 로고    scopus 로고
    • ISWI proteins participate in the genome-wide nucleosome distribution in Arabidopsis
    • Li G, Liu S, Wang J, He J, Huang H, Zhang Y, Xu L. 2014. ISWI proteins participate in the genome-wide nucleosome distribution in Arabidopsis. Plant J 78: 706-714.
    • (2014) Plant J , vol.78 , pp. 706-714
    • Li, G.1    Liu, S.2    Wang, J.3    He, J.4    Huang, H.5    Zhang, Y.6    Xu, L.7
  • 40
    • 77955944154 scopus 로고    scopus 로고
    • Overexpression of AHL20 negatively regulates defenses in Arabidopsis
    • Lu H, Zou Y, Feng N. 2010. Overexpression of AHL20 negatively regulates defenses in Arabidopsis. J Integr Plant Biol 52: 801-808.
    • (2010) J Integr Plant Biol , vol.52 , pp. 801-808
    • Lu, H.1    Zou, Y.2    Feng, N.3
  • 41
    • 79953044960 scopus 로고    scopus 로고
    • Genome-wide transcription factor binding: Beyond direct target regulation
    • MacQuarrie KL, Fong AP, Morse RH, Tapscott SJ. 2011. Genome-wide transcription factor binding: beyond direct target regulation. Trends Genet 27: 141-148.
    • (2011) Trends Genet , vol.27 , pp. 141-148
    • MacQuarrie, K.L.1    Fong, A.P.2    Morse, R.H.3    Tapscott, S.J.4
  • 42
    • 0024740034 scopus 로고
    • Abscisic acid-responsive sequences from the em gene of wheat
    • Marcotte WR Jr, Russell SH, Quatrano RS. 1989. Abscisic acid-responsive sequences from the Em gene of wheat. Plant Cell 1: 969-976.
    • (1989) Plant Cell , vol.1 , pp. 969-976
    • Marcotte, W.R.1    Russell, S.H.2    Quatrano, R.S.3
  • 43
    • 73449098946 scopus 로고    scopus 로고
    • TCP genes: A family snapshot ten years later
    • Martín-Trillo M, Cubas P. 2010. TCP genes: a family snapshot ten years later. Trends Plant Sci 15: 31-39.
    • (2010) Trends Plant Sci , vol.15 , pp. 31-39
    • Martín-Trillo, M.1    Cubas, P.2
  • 45
    • 84908420287 scopus 로고    scopus 로고
    • Identification of target genes of the bZIP transcription factor OsTGAP1, whose overexpression causes elicitor-induced hyperaccumulation of diterpenoid phytoalexins in rice cells
    • Miyamoto K, Matsumoto T, Okada A, Komiyama K, Chujo T, Yoshikawa H, Nojiri H, Yamane H, Okada K. 2014. Identification of target genes of the bZIP transcription factor OsTGAP1, whose overexpression causes elicitor-induced hyperaccumulation of diterpenoid phytoalexins in rice cells. PLoS One 9: e105823.
    • (2014) PLoS One , vol.9 , pp. e105823
    • Miyamoto, K.1    Matsumoto, T.2    Okada, A.3    Komiyama, K.4    Chujo, T.5    Yoshikawa, H.6    Nojiri, H.7    Yamane, H.8    Okada, K.9
  • 46
    • 0025098288 scopus 로고
    • Nuclear proteins bind conserved elements in the abscisic acid-responsive promoter of a rice rab gene
    • Mundy J, Yamaguchi-Shinozaki K, Chua NH. 1990. Nuclear proteins bind conserved elements in the abscisic acid-responsive promoter of a rice rab gene. Proc Natl Acad Sci 87: 1406-1410.
    • (1990) Proc Natl Acad Sci , vol.87 , pp. 1406-1410
    • Mundy, J.1    Yamaguchi-Shinozaki, K.2    Chua, N.H.3
  • 49
    • 84863304598 scopus 로고    scopus 로고
    • R Foundation for Statistical Computing, Vienna, Austria
    • R Core Team. 2014. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.Rproject.org/.
    • (2014) R: A Language and Environment for Statistical Computing
  • 51
    • 0037992395 scopus 로고    scopus 로고
    • The structure of DNA in the nucleosome core
    • Richmond TJ, Davey CA. 2003. The structure of DNA in the nucleosome core. Nature 423: 145-150.
    • (2003) Nature , vol.423 , pp. 145-150
    • Richmond, T.J.1    Davey, C.A.2
  • 52
    • 77956858986 scopus 로고    scopus 로고
    • The GATA-type transcription factors GNC and GNL/CGA1 repress gibberellin signaling downstream from della proteins and phytochrome-interacting factors
    • Richter R, Behringer C, Müller IK, Schwechheimer C. 2010. The GATA-type transcription factors GNC and GNL/CGA1 repress gibberellin signaling downstream from DELLA proteins and PHYTOCHROME-INTERACTING FACTORS. Genes Dev 24: 2093-2104.
    • (2010) Genes Dev , vol.24 , pp. 2093-2104
    • Richter, R.1    Behringer, C.2    Müller, I.K.3    Schwechheimer, C.4
  • 53
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: A bioconductor package for differential expression analysis of digital gene expression data
    • Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 55
    • 84880126285 scopus 로고    scopus 로고
    • Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNASeq
    • Shamimuzzaman M, Vodkin L. 2013. Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNASeq. BMC Genomics 14: 477.
    • (2013) BMC Genomics , vol.14 , pp. 477
    • Shamimuzzaman, M.1    Vodkin, L.2
  • 58
    • 84875196326 scopus 로고    scopus 로고
    • Determinants of nucleosome positioning
    • Struhl K, Segal E. 2013. Determinants of nucleosome positioning. Nat Struct Mol Biol 20: 267-273.
    • (2013) Nat Struct Mol Biol , vol.20 , pp. 267-273
    • Struhl, K.1    Segal, E.2
  • 60
    • 84922589001 scopus 로고    scopus 로고
    • DNase footprint signatures are dictated by factor dynamics and DNA sequence
    • Sung MH, Guertin MJ, Baek S, Hager GL. 2014. DNase footprint signatures are dictated by factor dynamics and DNA sequence. Mol Cell 56: 275-285.
    • (2014) Mol Cell , vol.56 , pp. 275-285
    • Sung, M.H.1    Guertin, M.J.2    Baek, S.3    Hager, G.L.4
  • 62
    • 0042421751 scopus 로고    scopus 로고
    • The Arabidopsis basic/helix-loop-helix transcription factor family
    • Toledo-Ortiz G, Huq E, Quail PH. 2003. The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell 15: 1749-1770.
    • (2003) Plant Cell , vol.15 , pp. 1749-1770
    • Toledo-Ortiz, G.1    Huq, E.2    Quail, P.H.3
  • 63
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 68
    • 84894651254 scopus 로고    scopus 로고
    • Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH
    • Vierstra J, Wang H, John S, Sandstrom R, Stamatoyannopoulos JA. 2014. Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH. Nat Methods 11: 66-72.
    • (2014) Nat Methods , vol.11 , pp. 66-72
    • Vierstra, J.1    Wang, H.2    John, S.3    Sandstrom, R.4    Stamatoyannopoulos, J.A.5
  • 69
    • 34447129612 scopus 로고    scopus 로고
    • Identification of a bipartite jasmonate-responsive promoter element in the Catharanthus roseus ORCA3 transcription factor gene that interacts specifically with AT-Hook DNA-binding proteins
    • Vom Endt D, Soares e Silva M, Kijne JW, Pasquali G, Memelink J. 2007. Identification of a bipartite jasmonate-responsive promoter element in the Catharanthus roseus ORCA3 transcription factor gene that interacts specifically with AT-Hook DNA-binding proteins. Plant Physiol 144: 1680-1689.
    • (2007) Plant Physiol , vol.144 , pp. 1680-1689
    • Vom Endt, D.1    Soares-E-Silva, M.2    Kijne, J.W.3    Pasquali, G.4    Memelink, J.5
  • 72
    • 0024712231 scopus 로고
    • Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data
    • Wolfe KH, Gouy M, Yang YW, Sharp PM, Li WH. 1989. Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc Natl Acad Sci 86: 6201-6205.
    • (1989) Proc Natl Acad Sci , vol.86 , pp. 6201-6205
    • Wolfe, K.H.1    Gouy, M.2    Yang, Y.W.3    Sharp, P.M.4    Li, W.H.5
  • 73
    • 84901611019 scopus 로고    scopus 로고
    • Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice
    • Wu Y, Zhang W, Jiang J. 2014. Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice. PLoS Genet 10: e1004378.
    • (2014) PLoS Genet , vol.10 , pp. e1004378
    • Wu, Y.1    Zhang, W.2    Jiang, J.3
  • 75
    • 79956316470 scopus 로고    scopus 로고
    • A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome
    • Zhang Z, Wippo CJ, Wal M, Ward E, Korber P, Pugh BF. 2011. A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science 332: 977-980.
    • (2011) Science , vol.332 , pp. 977-980
    • Zhang, Z.1    Wippo, C.J.2    Wal, M.3    Ward, E.4    Korber, P.5    Pugh, B.F.6
  • 76
    • 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. 2012. Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis. Plant Cell 24: 2719-2731.
    • (2012) Plant Cell , vol.24 , pp. 2719-2731
    • Zhang, W.1    Zhang, T.2    Wu, Y.3    Jiang, J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.