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Transcriptome and epigenome analyses of vernalization in Arabidopsis thaliana
dc.contributor.authorXi, Yanpeng
dc.contributor.authorPark, Sung‐rye
dc.contributor.authorKim, Dong‐hwan
dc.contributor.authorKim, Eun‐deok
dc.contributor.authorSung, Sibum
dc.date.accessioned2020-09-02T15:01:26Z
dc.date.availableWITHHELD_12_MONTHS
dc.date.available2020-09-02T15:01:26Z
dc.date.issued2020-08
dc.identifier.citationXi, Yanpeng; Park, Sung‐rye ; Kim, Dong‐hwan ; Kim, Eun‐deok ; Sung, Sibum (2020). "Transcriptome and epigenome analyses of vernalization in Arabidopsis thaliana." The Plant Journal 103(4): 1490-1502.
dc.identifier.issn0960-7412
dc.identifier.issn1365-313X
dc.identifier.urihttps://hdl.handle.net/2027.42/156480
dc.publisherWiley Periodicals, Inc.
dc.subject.othervernalization
dc.subject.othertranscriptome
dc.subject.otherArabidopsis
dc.subject.otherChIP- seq
dc.subject.otherRNA- seq
dc.subject.otherhistone modification
dc.titleTranscriptome and epigenome analyses of vernalization in Arabidopsis thaliana
dc.typeArticle
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelNatural Resources and Environment
dc.subject.hlbtoplevelScience
dc.description.peerreviewedPeer Reviewed
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/156480/2/tpj14817_am.pdfen_US
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/156480/1/tpj14817.pdfen_US
dc.identifier.doi10.1111/tpj.14817
dc.identifier.sourceThe Plant Journal
dc.identifier.citedreferenceSung, S., He, Y., Eshoo, T.W., Tamada, Y., Johnson, L., Nakahigashi, K., Goto, K., Jacobsen, S.E. and Amasino, R.M. ( 2006 ) Epigenetic maintenance of the vernalized state in Arabidopsis thaliana requires LIKE HETEROCHROMATIN PROTEIN 1. Nat. Genet. 38, 706 - 710.
dc.identifier.citedreferenceSearle, I., He, Y., Turck, F., Vincent, C., Fornara, F., Krober, S., Amasino, R.A. and Coupland, G. ( 2006 ) The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis. Genes Dev. 20, 898 - 912.
dc.identifier.citedreferenceSheldon, C.C., Hills, M.J., Lister, C., Dean, C., Dennis, E.S. and Peacock, W.J. ( 2008 ) Resetting of FLOWERING LOCUS C expression after epigenetic repression by vernalization. Proc. Natl Acad. Sci. USA, 105, 2214 - 2219.
dc.identifier.citedreferenceSheldon, C.C., Rouse, D.T., Finnegan, E.J., Peacock, W.J. and Dennis, E.S. ( 2000 ) The molecular basis of vernalization: the central role of FLOWERING LOCUS C (FLC). Proc. Natl Acad. Sci. USA, 97, 3753 - 3758.
dc.identifier.citedreferenceShindo, C., Aranzana, M.J., Lister, C., Baxter, C., Nicholls, C., Nordborg, M. and Dean, C. ( 2005 ) Role of FRIGIDA and FLOWERING LOCUS C in determining variation in flowering time of Arabidopsis. Plant Physiol. 138, 1163 - 1173.
dc.identifier.citedreferenceStreet, I.H., Shah, P.K., Smith, A.M., Avery, N. and Neff, M.M. ( 2008 ) The AT- hook- containing proteins SOB3/AHL29 and ESC/AHL27 are negative modulators of hypocotyl growth in Arabidopsis. Plant J. 54, 1 - 14.
dc.identifier.citedreferenceSun, M., Qi, X., Hou, L., Xu, X., Zhu, Z. and Li, M. ( 2015 ) Gene expression analysis of Pak Choi in response to vernalization. PLoS ONE, 10, e0141446.
dc.identifier.citedreferenceSung, S. and Amasino, R.M. ( 2004 ) Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature, 427, 159 - 164.
dc.identifier.citedreferenceSung, S. and Amasino, R.M. ( 2006 ) Molecular genetic studies of the memory of winter. J. Exp. Bot. 57, 3369 - 3377.
dc.identifier.citedreferenceSwiezewski, S., Liu, F., Magusin, A. and Dean, C. ( 2009 ) Cold- induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature, 462, 799 - 802.
dc.identifier.citedreferenceTamada, Y., Yun, J.Y., Woo, S.C. and Amasino, R.M. ( 2009 ) ARABIDOPSIS TRITHORAX- RELATED7 is required for methylation of lysine 4 of histone H3 and for transcriptional activation of FLOWERING LOCUS C. Plant Cell, 21, 3257 - 3269.
dc.identifier.citedreferenceVastenhouw, N.L. and Schier, A.F. ( 2012 ) Bivalent histone modifications in early embryogenesis. Curr. Opin. Cell Biol. 24, 374 - 386.
dc.identifier.citedreferenceVoigt, P., Tee, W.W. and Reinberg, D. ( 2013 ) A double take on bivalent promoters. Genes Dev. 27, 1318 - 1338.
dc.identifier.citedreferenceWagner, E.J. and Carpenter, P.B. ( 2012 ) Understanding the language of Lys36 methylation at histone H3. Nat. Rev. Mol. Cell Biol. 13, 115 - 126.
dc.identifier.citedreferenceWerner, J.D., Borevitz, J.O., Uhlenhaut, N.H., Ecker, J.R., Chory, J. and Weigel, D. ( 2005 ) FRIGIDA- independent variation in flowering time of natural Arabidopsis thaliana accessions. Genetics, 170, 1197 - 1207.
dc.identifier.citedreferenceWhittaker, C. and Dean, C. ( 2017 ) The FLC locus: a platform for discoveries in epigenetics and adaptation. Annu. Rev. Cell Dev. Biol. 33, 555 - 575.
dc.identifier.citedreferenceXiao, C., Chen, F., Yu, X., Lin, C. and Fu, Y.F. ( 2009 ) Over- expression of an AT- hook gene, AHL22, delays flowering and inhibits the elongation of the hypocotyl in Arabidopsis thaliana. Plant Mol. Biol. 71, 39 - 50.
dc.identifier.citedreferenceXu, Y., Gan, E.S., He, Y. and Ito, T. ( 2013 ) Flowering and genome integrity control by a nuclear matrix protein in Arabidopsis. Nucleus, 4, 274 - 276.
dc.identifier.citedreferenceYang, C.Y., Hsu, F.C., Li, J.P., Wang, N.N. and Shih, M.C. ( 2011 ) The AP2/ERF transcription factor AtERF73/HRE1 modulates ethylene responses during hypoxia in Arabidopsis. Plant Physiol. 156, 202 - 212.
dc.identifier.citedreferenceYuan, W., Luo, X., Li, Z., Yang, W., Wang, Y., Liu, R., Du, J. and He, Y. ( 2016 ) A cis cold memory element and a trans epigenome reader mediate Polycomb silencing of FLC by vernalization in Arabidopsis. Nat. Genet. 48, 1527 - 1534.
dc.identifier.citedreferenceYun, J., Kim, Y.S., Jung, J.H., Seo, P.J. and Park, C.M. ( 2012 ) The AT- hook motif- containing protein AHL22 regulates flowering initiation by modifying FLOWERING LOCUS T chromatin in Arabidopsis. J. Biol. Chem. 287, 15307 - 15316.
dc.identifier.citedreferenceZaidi, S.K., Frietze, S.E., Gordon, J.A. et al. ( 2017 ) Bivalent epigenetic control of oncofetal gene expression in cancer. Mol. Cell Biol. 37, https://doi.org/10.1128/MCB.00352- 17.
dc.identifier.citedreferenceZhao, J., Favero, D.S., Peng, H. and Neff, M.M. ( 2013 ) Arabidopsis thaliana AHL family modulates hypocotyl growth redundantly by interacting with each other via the PPC/DUF296 domain. Proc. Natl Acad. Sci. USA, 110, E4688 - E4697.
dc.identifier.citedreferenceZhao, J., Favero, D.S., Qiu, J., Roalson, E.H. and Neff, M.M. ( 2014 ) Insights into the evolution and diversification of the AT- hook Motif Nuclear Localized gene family in land plants. BMC Plant Biol. 14, 266.
dc.identifier.citedreferenceBond, D.M., Wilson, I.W., Dennis, E.S., Pogson, B.J. and Jean Finnegan, E. ( 2009 ) VERNALIZATION INSENSITIVE 3 (VIN3) is required for the response of Arabidopsis thaliana seedlings exposed to low oxygen conditions. Plant J. 59, 576 - 587.
dc.identifier.citedreferenceChen, M. and Penfield, S. ( 2018 ) Feedback regulation of COOLAIR expression controls seed dormancy and flowering time. Science, 360, 1014 - 1017.
dc.identifier.citedreferenceChoi, K., Kim, S., Kim, S.Y., Kim, M., Hyun, Y., Lee, H., Choe, S., Kim, S.G., Michaels, S. and Lee, I. ( 2005 ) SUPPRESSOR OF FRIGIDA3 encodes a nuclear ACTIN- RELATED PROTEIN6 required for floral repression in Arabidopsis. Plant Cell, 17, 2647 - 2660.
dc.identifier.citedreferenceCoustham, V., Li, P., Strange, A., Lister, C., Song, J. and Dean, C. ( 2012 ) Quantitative modulation of polycomb silencing underlies natural variation in vernalization. Science, 337, 584 - 587.
dc.identifier.citedreferenceCrevillen, P., Sonmez, C., Wu, Z. and Dean, C. ( 2013 ) A gene loop containing the floral repressor FLC is disrupted in the early phase of vernalization. EMBO J. 32, 140 - 148.
dc.identifier.citedreferenceCsorba, T., Questa, J.I., Sun, Q. and Dean, C. ( 2014 ) Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization. Proc. Natl Acad. Sci. USA, 111, 16160 - 16165.
dc.identifier.citedreferenceDe Lucia, F., Crevillen, P., Jones, A.M., Greb, T. and Dean, C. ( 2008 ) A PHD- polycomb repressive complex 2 triggers the epigenetic silencing of FLC during vernalization. Proc. Natl Acad. Sci. USA, 105, 16831 - 16836.
dc.identifier.citedreferenceGasch, P., Fundinger, M., Muller, J.T., Lee, T., Bailey- Serres, J. and Mustroph, A. ( 2016 ) Redundant ERF- VII transcription factors bind to an evolutionarily conserved cis- motif to regulate hypoxia- responsive gene expression in Arabidopsis. Plant Cell, 28, 160 - 180.
dc.identifier.citedreferenceGeraldo, N., Baurle, I., Kidou, S., Hu, X. and Dean, C. ( 2009 ) FRIGIDA delays flowering in Arabidopsis via a cotranscriptional mechanism involving direct interaction with the nuclear cap- binding complex. Plant Physiol. 150, 1611 - 1618.
dc.identifier.citedreferenceGibbs, D.J., Tedds, H.M., Labandera, A.M. et al. ( 2018 ) Oxygen- dependent proteolysis regulates the stability of angiosperm polycomb repressive complex 2 subunit VERNALIZATION 2. Nat. Commun. 9, 5438.
dc.identifier.citedreferenceGu, X., Le, C., Wang, Y., Li, Z., Jiang, D. and He, Y. ( 2013 ) Arabidopsis FLC clade members form flowering- repressor complexes coordinating responses to endogenous and environmental cues. Nat. Commun. 4, 1947.
dc.identifier.citedreferenceHarikumar, A. and Meshorer, E. ( 2015 ) Chromatin remodeling and bivalent histone modifications in embryonic stem cells. EMBO Rep. 16, 1609 - 1619.
dc.identifier.citedreferenceHelliwell, C.A., Wood, C.C., Robertson, M., James Peacock, W. and Dennis, E.S. ( 2006 ) The Arabidopsis FLC protein interacts directly in vivo with SOC1 and FT chromatin and is part of a high- molecular- weight protein complex. Plant J. 46, 183 - 192.
dc.identifier.citedreferenceHeo, J.B. and Sung, S. ( 2011 ) Vernalization- mediated epigenetic silencing by a long intronic noncoding RNA. Science, 331, 76 - 79.
dc.identifier.citedreferenceHepworth, S.R., Valverde, F., Ravenscroft, D., Mouradov, A. and Coupland, G. ( 2002 ) Antagonistic regulation of flowering- time gene SOC1 by CONSTANS and FLC via separate promoter motifs. Embo J. 21, 4327 - 4337.
dc.identifier.citedreferenceHu, X., Kong, X., Wang, C. et al. ( 2014 ) Proteasome- mediated degradation of FRIGIDA modulates flowering time in Arabidopsis during vernalization. Plant Cell, 26, 4763 - 4781.
dc.identifier.citedreferenceJiang, D., Gu, X. and He, Y. ( 2009 ) Establishment of the winter- annual growth habit via FRIGIDA- mediated histone methylation at FLOWERING LOCUS C in Arabidopsis. Plant Cell, 21, 1733 - 1746.
dc.identifier.citedreferenceJohanson, U., West, J., Lister, C., Michaels, S., Amasino, R. and Dean, C. ( 2000 ) Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science, 290, 344 - 347.
dc.identifier.citedreferenceKim, D.H. and Sung, S. ( 2017 ) Vernalization- triggered intragenic chromatin loop formation by long noncoding RNAs. Dev. Cell, 40, 302 - 312.e4.
dc.identifier.citedreferenceKim, D.H., Zografos, B.R. and Sung, S. ( 2010 ) Mechanisms underlying vernalization- mediated VIN3 induction in Arabidopsis. Plant Signal Behav. 5, 1457 - 1459.
dc.identifier.citedreferenceKim, S., Choi, K., Park, C., Hwang, H.J. and Lee, I. ( 2006 ) SUPPRESSOR OF FRIGIDA4, encoding a C2H2- Type zinc finger protein, represses flowering by transcriptional activation of Arabidopsis FLOWERING LOCUS C. Plant Cell, 18, 2985 - 2998.
dc.identifier.citedreferenceKim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S. and Amasino, R. ( 2005 ) Establishment of the vernalization- responsive, winter- annual habit in Arabidopsis requires a putative histone H3 methyl transferase. Plant Cell, 17, 3301 - 3310.
dc.identifier.citedreferenceLee, J. and Lee, I. ( 2010 ) Regulation and function of SOC1, a flowering pathway integrator. J. Exp. Bot. 61, 2247 - 2254.
dc.identifier.citedreferenceLi, Z., Jiang, D. and He, Y. ( 2018 ) FRIGIDA establishes a local chromosomal environment for FLOWERING LOCUS C mRNA production. Nat. Plants, 4, 836 - 846.
dc.identifier.citedreferenceLim, P.O., Kim, Y., Breeze, E. et al. ( 2007 ) Overexpression of a chromatin architecture- controlling AT- hook protein extends leaf longevity and increases the post- harvest storage life of plants. Plant J. 52, 1140 - 1153.
dc.identifier.citedreferenceLiu, C., Wang, C., Wang, G., Becker, C., Zaidem, M. and Weigel, D. ( 2016 ) Genome- wide analysis of chromatin packing in Arabidopsis thaliana at single- gene resolution. Genome Res. 26, 1057 - 1068.
dc.identifier.citedreferenceLuo, X., Chen, T., Zeng, X., He, D. and He, Y. ( 2019 ) Feedback Regulation of FLC by FLOWERING LOCUS T (FT) and FD through a 5’ FLC Promoter Region in Arabidopsis. Mol. Plant 12, 285 - 288.
dc.identifier.citedreferenceMichaels, S.D. and Amasino, R.M. ( 1999 ) FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell, 11, 949 - 956.
dc.identifier.citedreferenceMichaels, S.D., Himelblau, E., Kim, S.Y., Schomburg, F.M. and Amasino, R.M. ( 2005 ) Integration of flowering signals in winter- annual Arabidopsis. Plant Physiol. 137, 149 - 156.
dc.identifier.citedreferenceMoon, J., Suh, S.S., Lee, H., Choi, K.R., Hong, C.B., Paek, N.C., Kim, S.G. and Lee, I. ( 2003 ) The SOC1 MADS- box gene integrates vernalization and gibberellin signals for flowering in Arabidopsis. Plant J. 35, 613 - 623.
dc.identifier.citedreferenceMylne, J.S., Barrett, L., Tessadori, F., Mesnage, S., Johnson, L., Bernatavichute, Y.V., Jacobsen, S.E., Fransz, P. and Dean, C. ( 2006 ) LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN1, is required for epigenetic silencing of FLC. Proc. Natl Acad. Sci. USA, 103, 5012 - 5017.
dc.identifier.citedreferenceNg, K.H., Yu, H. and Ito, T. ( 2009 ) AGAMOUS controls GIANT KILLER, a multifunctional chromatin modifier in reproductive organ patterning and differentiation. PLoS Biol, 7, e1000251.
dc.identifier.citedreferenceOquist, G. and Huner, N.P. ( 2003 ) Photosynthesis of overwintering evergreen plants. Annu. Rev. Plant Biol. 54, 329 - 355.
dc.identifier.citedreferenceQuesta, J.I., Song, J., Geraldo, N., An, H. and Dean, C. ( 2016 ) Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization. Science, 353, 485 - 488.
dc.identifier.citedreferenceRosa, S., De Lucia, F., Mylne, J.S., Zhu, D., Ohmido, N., Pendle, A., Kato, N., Shaw, P. and Dean, C. ( 2013 ) Physical clustering of FLC alleles during Polycomb- mediated epigenetic silencing in vernalization. Genes Dev. 27, 1845 - 1850.
dc.identifier.citedreferenceSakoe, H. and Chiba, S. ( 1978 ) Dynamic- programming algorithm optimization for spoken word recognition. IEEE Trans. Acoust. Speech Signal Proc. 26, 43 - 49.
dc.identifier.citedreferenceSchmitz, R.J., Hong, L., Michaels, S. and Amasino, R.M. ( 2005 ) FRIGIDA- ESSENTIAL 1 interacts genetically with FRIGIDA and FRIGIDA- LIKE 1 to promote the winter- annual habit of Arabidopsis thaliana. Development, 132, 5471 - 5478.
dc.owningcollnameInterdisciplinary and Peer-Reviewed


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