메뉴 건너뛰기




Volumn 55, Issue 3, 2014, Pages 383-396

Noncoding transcription by alternative rna polymerases dynamically regulates an auxin-driven chromatin loop

Author keywords

[No Author keywords available]

Indexed keywords

AUXIN; LIKE HETEROCHROMATIN PROTEIN 1; LONG UNTRANSLATED RNA; POLYCOMB GROUP PROTEIN; POLYCOMB REPRESSIVE COMPLEX 2; RNA POLYMERASE; RNA POLYMERASE II; RNA POLYMERASE V; UNCLASSIFIED DRUG; VEGETABLE PROTEIN;

EID: 84905591635     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2014.06.011     Document Type: Article
Times cited : (314)

References (48)
  • 3
    • 0034752569 scopus 로고    scopus 로고
    • The PINOID protein kinase regulates organ development in Arabidopsis by enhancing polar auxin transport
    • Benjamins R., Quint A., Weijers D., Hooykaas P., Offringa R. The PINOID protein kinase regulates organ development in Arabidopsis by enhancing polar auxin transport. Development 2001, 128:4057-4067.
    • (2001) Development , vol.128 , pp. 4057-4067
    • Benjamins, R.1    Quint, A.2    Weijers, D.3    Hooykaas, P.4    Offringa, R.5
  • 4
    • 84875165863 scopus 로고    scopus 로고
    • Epigenetic programming and reprogramming during development
    • Cantone I., Fisher A.G. Epigenetic programming and reprogramming during development. Nat. Struct. Mol. Biol. 2013, 20:282-289.
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 282-289
    • Cantone, I.1    Fisher, A.G.2
  • 5
    • 84875200698 scopus 로고    scopus 로고
    • Functional implications of genome topology
    • Cavalli G., Misteli T. Functional implications of genome topology. Nat. Struct. Mol. Biol. 2013, 20:290-299.
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 290-299
    • Cavalli, G.1    Misteli, T.2
  • 6
    • 80054756754 scopus 로고    scopus 로고
    • Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions
    • Chu C., Qu K., Zhong F.L., Artandi S.E., Chang H.Y. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol. Cell 2011, 44:667-678.
    • (2011) Mol. Cell , vol.44 , pp. 667-678
    • Chu, C.1    Qu, K.2    Zhong, F.L.3    Artandi, S.E.4    Chang, H.Y.5
  • 7
    • 84872855164 scopus 로고    scopus 로고
    • A gene loop containing the floral repressor FLC is disrupted in the early phase of vernalization
    • Crevillén P., Sonmez C., Wu Z., Dean C. A gene loop containing the floral repressor FLC is disrupted in the early phase of vernalization. EMBO J. 2013, 32:140-148.
    • (2013) EMBO J. , vol.32 , pp. 140-148
    • Crevillén, P.1    Sonmez, C.2    Wu, Z.3    Dean, C.4
  • 8
    • 32644481938 scopus 로고    scopus 로고
    • Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis
    • Czechowski T., Stitt M., Altmann T., Udvardi M.K., Scheible W.R. Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol. 2005, 139:5-17.
    • (2005) Plant Physiol. , vol.139 , pp. 5-17
    • Czechowski, T.1    Stitt, M.2    Altmann, T.3    Udvardi, M.K.4    Scheible, W.R.5
  • 9
    • 84861976397 scopus 로고    scopus 로고
    • Polycomb: a paradigm for genome organization from one to three dimensions
    • Delest A., Sexton T., Cavalli G. Polycomb: a paradigm for genome organization from one to three dimensions. Curr. Opin. Cell Biol. 2012, 24:405-414.
    • (2012) Curr. Opin. Cell Biol. , vol.24 , pp. 405-414
    • Delest, A.1    Sexton, T.2    Cavalli, G.3
  • 10
    • 78349272804 scopus 로고    scopus 로고
    • Histone depletion facilitates chromatin loops on the kilobasepair scale
    • Diesinger P.M., Kunkel S., Langowski J., Heermann D.W. Histone depletion facilitates chromatin loops on the kilobasepair scale. Biophys. J. 2010, 99:2995-3001.
    • (2010) Biophys. J. , vol.99 , pp. 2995-3001
    • Diesinger, P.M.1    Kunkel, S.2    Langowski, J.3    Heermann, D.W.4
  • 11
    • 84860362829 scopus 로고    scopus 로고
    • Active chromatin and noncoding RNAs: an intimate relationship
    • Flynn R.A., Chang H.Y. Active chromatin and noncoding RNAs: an intimate relationship. Curr. Opin. Genet. Dev. 2012, 22:172-178.
    • (2012) Curr. Opin. Genet. Dev. , vol.22 , pp. 172-178
    • Flynn, R.A.1    Chang, H.Y.2
  • 13
    • 0035207613 scopus 로고    scopus 로고
    • Mutations in LIKE HETEROCHROMATIN PROTEIN 1 affect flowering time and plant architecture in Arabidopsis
    • Gaudin V., Libault M., Pouteau S., Juul T., Zhao G., Lefebvre D., Grandjean O. Mutations in LIKE HETEROCHROMATIN PROTEIN 1 affect flowering time and plant architecture in Arabidopsis. Development 2001, 128:4847-4858.
    • (2001) Development , vol.128 , pp. 4847-4858
    • Gaudin, V.1    Libault, M.2    Pouteau, S.3    Juul, T.4    Zhao, G.5    Lefebvre, D.6    Grandjean, O.7
  • 14
    • 23744483843 scopus 로고    scopus 로고
    • Profiling histone modification patterns in plants using genomic tiling microarrays
    • Gendrel A.-V., Lippman Z., Martienssen R., Colot V. Profiling histone modification patterns in plants using genomic tiling microarrays. Nat. Methods 2005, 2:213-218.
    • (2005) Nat. Methods , vol.2 , pp. 213-218
    • Gendrel, A.-V.1    Lippman, Z.2    Martienssen, R.3    Colot, V.4
  • 15
    • 69449097106 scopus 로고    scopus 로고
    • Diversity of Polycomb group complexes in plants: same rules, different players?
    • Hennig L., Derkacheva M. Diversity of Polycomb group complexes in plants: same rules, different players?. Trends Genet. 2009, 25:414-423.
    • (2009) Trends Genet. , vol.25 , pp. 414-423
    • Hennig, L.1    Derkacheva, M.2
  • 17
    • 84897062460 scopus 로고    scopus 로고
    • The BAF60 subunit of the SWI/SNF chromatin-remodeling complex directly controls the formation of a gene loop at FLOWERING LOCUS C in Arabidopsis
    • Jégu T., Latrasse D., Delarue M., Hirt H., Domenichini S., Ariel F., Crespi M., Bergounioux C., Raynaud C., Benhamed M. The BAF60 subunit of the SWI/SNF chromatin-remodeling complex directly controls the formation of a gene loop at FLOWERING LOCUS C in Arabidopsis. Plant Cell 2014, 26:538-551.
    • (2014) Plant Cell , vol.26 , pp. 538-551
    • Jégu, T.1    Latrasse, D.2    Delarue, M.3    Hirt, H.4    Domenichini, S.5    Ariel, F.6    Crespi, M.7    Bergounioux, C.8    Raynaud, C.9    Benhamed, M.10
  • 18
    • 84875605101 scopus 로고    scopus 로고
    • CLASP-mediated cortical microtubule organization guides PIN polarization axis
    • Kakar K., Zhang H., Scheres B., Dhonukshe P. CLASP-mediated cortical microtubule organization guides PIN polarization axis. Nature 2013, 495:529-533.
    • (2013) Nature , vol.495 , pp. 529-533
    • Kakar, K.1    Zhang, H.2    Scheres, B.3    Dhonukshe, P.4
  • 20
    • 52949113419 scopus 로고    scopus 로고
    • RNAi, heterochromatin and the cell cycle
    • Kloc A., Martienssen R. RNAi, heterochromatin and the cell cycle. Trends Genet. 2008, 24:511-517.
    • (2008) Trends Genet. , vol.24 , pp. 511-517
    • Kloc, A.1    Martienssen, R.2
  • 21
    • 84874368349 scopus 로고    scopus 로고
    • Activating RNAs associate with Mediator to enhance chromatin architecture and transcription
    • Lai F., Orom U.A., Cesaroni M., Beringer M., Taatjes D.J., Blobel G.A., Shiekhattar R. Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature 2013, 494:497-501.
    • (2013) Nature , vol.494 , pp. 497-501
    • Lai, F.1    Orom, U.A.2    Cesaroni, M.3    Beringer, M.4    Taatjes, D.J.5    Blobel, G.A.6    Shiekhattar, R.7
  • 22
    • 34848825691 scopus 로고    scopus 로고
    • Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex
    • Lanzuolo C., Roure V., Dekker J., Bantignies F., Orlando V. Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex. Nat. Cell Biol. 2007, 9:1167-1174.
    • (2007) Nat. Cell Biol. , vol.9 , pp. 1167-1174
    • Lanzuolo, C.1    Roure, V.2    Dekker, J.3    Bantignies, F.4    Orlando, V.5
  • 23
    • 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. Nat. Rev. Genet. 2010, 11:204-220.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 204-220
    • Law, J.A.1    Jacobsen, S.E.2
  • 25
    • 84871910383 scopus 로고    scopus 로고
    • Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis
    • Liu J., Jung C., Xu J., Wang H., Deng S., Bernad L., Arenas-Huertero C., Chua N.-H. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 2012, 24:4333-4345.
    • (2012) Plant Cell , vol.24 , pp. 4333-4345
    • Liu, J.1    Jung, C.2    Xu, J.3    Wang, H.4    Deng, S.5    Bernad, L.6    Arenas-Huertero, C.7    Chua, N.-H.8
  • 26
    • 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
  • 27
    • 84875183056 scopus 로고    scopus 로고
    • Structure and function of long noncoding RNAs in epigenetic regulation
    • Mercer T.R., Mattick J.S. Structure and function of long noncoding RNAs in epigenetic regulation. Nat. Struct. Mol. Biol. 2013, 20:300-307.
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 300-307
    • Mercer, T.R.1    Mattick, J.S.2
  • 28
    • 77956527844 scopus 로고    scopus 로고
    • Oscillating gene expression determines competence for periodic Arabidopsis root branching
    • Moreno-Risueno M.A., Van Norman J.M., Moreno A., Zhang J., Ahnert S.E., Benfey P.N. Oscillating gene expression determines competence for periodic Arabidopsis root branching. Science 2010, 329:1306-1311.
    • (2010) Science , vol.329 , pp. 1306-1311
    • Moreno-Risueno, M.A.1    Van Norman, J.M.2    Moreno, A.3    Zhang, J.4    Ahnert, S.E.5    Benfey, P.N.6
  • 29
    • 28544433646 scopus 로고    scopus 로고
    • The Arabidopsis heterochromatin protein1 homolog (TERMINAL FLOWER2) silences genes within the euchromatic region but not genes positioned in heterochromatin
    • Nakahigashi K., Jasencakova Z., Schubert I., Goto K. The Arabidopsis heterochromatin protein1 homolog (TERMINAL FLOWER2) silences genes within the euchromatic region but not genes positioned in heterochromatin. Plant Cell Physiol. 2005, 46:1747-1756.
    • (2005) Plant Cell Physiol. , vol.46 , pp. 1747-1756
    • Nakahigashi, K.1    Jasencakova, Z.2    Schubert, I.3    Goto, K.4
  • 30
    • 45549098196 scopus 로고    scopus 로고
    • Intersection of the RNA interference and X-inactivation pathways
    • Ogawa Y., Sun B.K., Lee J.T. Intersection of the RNA interference and X-inactivation pathways. Science 2008, 320:1336-1341.
    • (2008) Science , vol.320 , pp. 1336-1341
    • Ogawa, Y.1    Sun, B.K.2    Lee, J.T.3
  • 31
    • 80052815461 scopus 로고    scopus 로고
    • Noncoding RNAs and enhancers: complications of a long-distance relationship
    • Orom U.A., Shiekhattar R. Noncoding RNAs and enhancers: complications of a long-distance relationship. Trends Genet. 2011, 27:433-439.
    • (2011) Trends Genet. , vol.27 , pp. 433-439
    • Orom, U.A.1    Shiekhattar, R.2
  • 33
    • 77951996967 scopus 로고    scopus 로고
    • VisuaLRTC: a new view on lateral root initiation by combining specific transcriptome data sets
    • Parizot B., De Rybel B., Beeckman T. VisuaLRTC: a new view on lateral root initiation by combining specific transcriptome data sets. Plant Physiol. 2010, 153:34-40.
    • (2010) Plant Physiol. , vol.153 , pp. 34-40
    • Parizot, B.1    De Rybel, B.2    Beeckman, T.3
  • 34
    • 73449102588 scopus 로고    scopus 로고
    • Heterochromatin protein 1 (HP1a) positively regulates euchromatic gene expression through RNA transcript association and interaction with hnRNPs in Drosophila
    • Piacentini L., Fanti L., Negri R., Del Vescovo V., Fatica A., Altieri F., Pimpinelli S. Heterochromatin protein 1 (HP1a) positively regulates euchromatic gene expression through RNA transcript association and interaction with hnRNPs in Drosophila. PLoS Genet. 2009, 5:e1000670.
    • (2009) PLoS Genet. , vol.5
    • Piacentini, L.1    Fanti, L.2    Negri, R.3    Del Vescovo, V.4    Fatica, A.5    Altieri, F.6    Pimpinelli, S.7
  • 35
    • 84861904178 scopus 로고    scopus 로고
    • Genome regulation by long noncoding RNAs
    • Rinn J.L., Chang H.Y. Genome regulation by long noncoding RNAs. Annu. Rev. Biochem. 2012, 81:145-166.
    • (2012) Annu. Rev. Biochem. , vol.81 , pp. 145-166
    • Rinn, J.L.1    Chang, H.Y.2
  • 37
    • 84861733509 scopus 로고    scopus 로고
    • Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA
    • Simon J.M., Giresi P.G., Davis I.J., Lieb J.D. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nat. Protoc. 2012, 7:256-267.
    • (2012) Nat. Protoc. , vol.7 , pp. 256-267
    • Simon, J.M.1    Giresi, P.G.2    Davis, I.J.3    Lieb, J.D.4
  • 38
    • 66649116809 scopus 로고    scopus 로고
    • PINOID kinase regulates root gravitropism through modulation of PIN2-dependent basipetal auxin transport in Arabidopsis
    • Sukumar P., Edwards K.S., Rahman A., Delong A., Muday G.K. PINOID kinase regulates root gravitropism through modulation of PIN2-dependent basipetal auxin transport in Arabidopsis. Plant Physiol. 2009, 150:722-735.
    • (2009) Plant Physiol. , vol.150 , pp. 722-735
    • Sukumar, P.1    Edwards, K.S.2    Rahman, A.3    Delong, A.4    Muday, G.K.5
  • 39
    • 42449140588 scopus 로고    scopus 로고
    • Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene
    • Tan-Wong S.M., French J.D., Proudfoot N.J., Brown M.A. Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene. Proc. Natl. Acad. Sci. USA 2008, 105:5160-5165.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 5160-5165
    • Tan-Wong, S.M.1    French, J.D.2    Proudfoot, N.J.3    Brown, M.A.4
  • 41
    • 0036923833 scopus 로고    scopus 로고
    • Looping and interaction between hypersensitive sites in the active beta-globin locus
    • Tolhuis B., Palstra R.J., Splinter E., Grosveld F., de Laat W. Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol. Cell 2002, 10:1453-1465.
    • (2002) Mol. Cell , vol.10 , pp. 1453-1465
    • Tolhuis, B.1    Palstra, R.J.2    Splinter, E.3    Grosveld, F.4    de Laat, W.5
  • 44
    • 55449131096 scopus 로고    scopus 로고
    • Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes
    • Wierzbicki A.T., Haag J.R., Pikaard C.S. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 2008, 135:635-648.
    • (2008) Cell , vol.135 , pp. 635-648
    • Wierzbicki, A.T.1    Haag, J.R.2    Pikaard, C.S.3
  • 45
    • 79960484375 scopus 로고    scopus 로고
    • Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation
    • Wutz A. Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation. Nat. Rev. Genet. 2011, 12:542-553.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 542-553
    • Wutz, A.1
  • 47
    • 77953096072 scopus 로고    scopus 로고
    • Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by Polycomb CBX7 in transcriptional silencing of INK4a
    • Yap K.L., Li S., Muñoz-Cabello A.M., Raguz S., Zeng L., Mujtaba S., Gil J., Walsh M.J., Zhou M.M. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by Polycomb CBX7 in transcriptional silencing of INK4a. Mol. Cell 2010, 38:662-674.
    • (2010) Mol. Cell , vol.38 , pp. 662-674
    • Yap, K.L.1    Li, S.2    Muñoz-Cabello, A.M.3    Raguz, S.4    Zeng, L.5    Mujtaba, S.6    Gil, J.7    Walsh, M.J.8    Zhou, M.M.9
  • 48
    • 72849124237 scopus 로고    scopus 로고
    • Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis
    • Zheng B., Wang Z., Li S., Yu B., Liu J.-Y., Chen X. Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis. Genes Dev. 2009, 23:2850-2860.
    • (2009) Genes Dev. , vol.23 , pp. 2850-2860
    • Zheng, B.1    Wang, Z.2    Li, S.3    Yu, B.4    Liu, J.-Y.5    Chen, X.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.