Depending on the environment a young seedling encounters, the developmental program following seed germination could be skotomorphogenesis in the dark or photomorphogenesis in the light. Light signals are interpreted by a repertoire of photoreceptors followed by sophisticated gene expression networks, eventually resulting in developmental changes. The expression and functions of photoreceptors and key signaling molecules are highly coordinated and regulated at multiple levels of the central dogma in molecular biology. Light activates gene expression through the actions of positive transcriptional regulators and the relaxation of chromatin by histone acetylation. Small regulatory RNAs help attenuate the expression of light-responsive genes. Alternative splicing, protein phosphorylation/dephosphorylation, the formation of diverse transcriptional complexes, and selective protein degradation all contribute to proteome diversity and change the functions of individual proteins.


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Literature Cited

  1. Ahmad M, Jarillo JA, Smirnova O, Cashmore AR. 1.  1998. The CRY1 blue light photoreceptor of Arabidopsis interacts with phytochrome A in vitro. Mol. Cell 1:939–48 [Google Scholar]
  2. Al-Sady B, Ni W, Kircher S, Schäfer E, Quail PH. 2.  2006. Photoactivated phytochrome induces rapid PIF3 phosphorylation prior to proteasome-mediated degradation. Mol. Cell 23:439–46 [Google Scholar]
  3. Bae G, Choi G. 3.  2008. Decoding of light signals by plant phytochromes and their interacting proteins. Annu. Rev. Plant Biol. 59:281–311 [Google Scholar]
  4. Ballesteros ML, Bolle C, Lois LM, Moore JM, Vielle-Calzada JP. 4.  et al. 2001. LAF1, a MYB transcription activator for phytochrome A signaling. Genes Dev. 15:2613–25 [Google Scholar]
  5. Benhamed M, Bertrand C, Servet C, Zhou DX. 5.  2006. Arabidopsis GCN5, HD1, and TAF1/HAF2 interact to regulate histone acetylation required for light-responsive gene expression. Plant Cell 18:2893–903 [Google Scholar]
  6. Benhamed M, Martin-Magniette ML, Taconnat L, Bitton F, Servet C. 6.  et al. 2008. Genome-scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5. Plant J. 56:493–504 [Google Scholar]
  7. Bertrand C, Benhamed M, Li YF, Ayadi M, Lemonnier G. 7.  et al. 2005. Arabidopsis HAF2 gene encoding TATA-binding protein (TBP)-associated factor TAF1, is required to integrate light signals to regulate gene expression and growth. J. Biol. Chem. 280:1465–73 [Google Scholar]
  8. Beyer A, Hollunder J, Nasheuer HP, Wilhelm T. 8.  2004. Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale. Mol. Cell. Proteomics 3:1083–92 [Google Scholar]
  9. Bolle C, Koncz C, Chua NH. 9.  2000. PAT1, a new member of the GRAS family, is involved in phytochrome A signal transduction. Genes Dev. 14:1269–78 [Google Scholar]
  10. Bourbousse C, Ahmed I, Roudier F, Zabulon G, Blondet E. 10.  et al. 2012. Histone H2B monoubiquitination facilitates the rapid modulation of gene expression during Arabidopsis photomorphogenesis. PLoS Genet. 8:e1002825 [Google Scholar]
  11. Bowler C, Botto J, Deng XW. 11.  2013. Photomorphogenesis, B-box transcription factors, and the legacy of Magnus Holm. Plant Cell 25:1192–95 [Google Scholar]
  12. Branco-Price C, Kaiser KA, Jang CJ, Larive CK, Bailey-Serres J. 12.  2008. Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana. Plant J. 56:743–55 [Google Scholar]
  13. Branco-Price C, Kawaguchi R, Ferreira RB, Bailey-Serres J. 13.  2005. Genome-wide analysis of transcript abundance and translation in Arabidopsis seedlings subjected to oxygen deprivation. Ann. Bot. 96:647–60 [Google Scholar]
  14. Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, Dunoyer P, Yamamoto YY. 14.  et al. 2008. Widespread translational inhibition by plant miRNAs and siRNAs. Science 320:1185–90 [Google Scholar]
  15. Brodersen P, Voinnet O. 15.  2006. The diversity of RNA silencing pathways in plants. Trends Genet. 22:268–80 [Google Scholar]
  16. Bu Q, Zhu L, Dennis MD, Yu L, Lu SX. 16.  et al. 2011. Phosphorylation by CK2 enhances the rapid light-induced degradation of phytochrome interacting factor 1 in Arabidopsis. J. Biol. Chem. 286:12066–74 [Google Scholar]
  17. Castillon A, Shen H, Huq E. 17.  2007. Phytochrome Interacting Factors: central players in phytochrome-mediated light signaling networks. Trends Plant Sci. 12:514–21 [Google Scholar]
  18. Chang CS, Li YH, Chen LT, Chen WC, Hsieh WP. 18.  et al. 2008. LZF1, a HY5-regulated transcriptional factor, functions in Arabidopsis de-etiolation. Plant J. 54:205–19 [Google Scholar]
  19. Chang CS, Maloof JN, Wu SH. 19.  2011. COP1-mediated degradation of BBX22/LZF1 optimizes seedling development in Arabidopsis. Plant Physiol. 156:228–39 [Google Scholar]
  20. Charron JB, He H, Elling AA, Deng XW. 20.  2009. Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis. Plant Cell 21:3732–48 [Google Scholar]
  21. Chattopadhyay S, Ang LH, Puente P, Deng XW, Wei N. 21.  1998. Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression. Plant Cell 10:673–83 [Google Scholar]
  22. Chaves I, Pokorny R, Byrdin M, Hoang N, Ritz T. 22.  et al. 2011. The cryptochromes: blue light photoreceptors in plants and animals. Annu. Rev. Plant Biol. 62:335–64 [Google Scholar]
  23. Chen M. 23.  2008. Phytochrome nuclear body: an emerging model to study interphase nuclear dynamics and signaling. Curr. Opin. Plant Biol. 11:503–8 [Google Scholar]
  24. Chory J. 24.  2010. Light signal transduction: an infinite spectrum of possibilities. Plant J. 61:982–91 [Google Scholar]
  25. Chua YL, Brown AP, Gray JC. 25.  2001. Targeted histone acetylation and altered nuclease accessibility over short regions of the pea plastocyanin gene. Plant Cell 13:599–612 [Google Scholar]
  26. Chua YL, Watson LA, Gray JC. 26.  2003. The transcriptional enhancer of the pea plastocyanin gene associates with the nuclear matrix and regulates gene expression through histone acetylation. Plant Cell 15:1468–79 [Google Scholar]
  27. Colon-Carmona A, Chen DL, Yeh KC, Abel S. 27.  2000. Aux/IAA proteins are phosphorylated by phytochrome in vitro. Plant Physiol. 124:1728–38 [Google Scholar]
  28. Datta S, Hettiarachchi C, Johansson H, Holm M. 28.  2007. SALT TOLERANCE HOMOLOG2, a B-box protein in Arabidopsis that activates transcription and positively regulates light-mediated development. Plant Cell 19:3242–55 [Google Scholar]
  29. Datta S, Hettiarachchi GHCM, Deng XW, Holm M. 29.  2006. Arabidopsis CONSTANS-LIKE3 is a positive regulator of red light signaling and root growth. Plant Cell 18:70–84 [Google Scholar]
  30. Datta S, Johansson H, Hettiarachchi C, Irigoyen ML, Desai M. 30.  et al. 2008. LZF1/SALT TOLERANCE HOMOLOG3, an Arabidopsis B-box protein involved in light-dependent development and gene expression, undergoes COP1-mediated ubiquitination. Plant Cell 20:2324–38 [Google Scholar]
  31. Deng XW, Caspar T, Quail PH. 31.  1991. cop1: a regulatory locus involved in light-controlled development and gene expression in Arabidopsis. Genes Dev. 5:1172–82 [Google Scholar]
  32. Dickey LF, Petracek ME, Nguyen TT, Hansen ER, Thompson WF. 32.  1998. Light regulation of Fed-1 mRNA requires an element in the 5′ untranslated region and correlates with differential polyribosome association. Plant Cell 10:475–84 [Google Scholar]
  33. Dieterle M, Zhou YC, Schäfer E, Funk M, Kretsch T. 33.  2001. EID1, an F-box protein involved in phytochrome A-specific light signaling. Genes Dev. 15:939–44 [Google Scholar]
  34. Fairchild CD, Schumaker MA, Quail PH. 34.  2000. HFR1 encodes an atypical bHLH protein that acts in phytochrome A signal transduction. Genes Dev. 14:2377–91 [Google Scholar]
  35. Fan XY, Sun Y, Cao DM, Bai MY, Luo XM. 35.  et al. 2012. BZS1, a B-box protein, promotes photomorphogenesis downstream of both brassinosteroid and light signaling pathways. Mol. Plant 5:591–600 [Google Scholar]
  36. Fankhauser C, Chen M. 36.  2008. Transposing phytochrome into the nucleus. Trends Plant Sci. 13:596–601 [Google Scholar]
  37. Fankhauser C, Yeh KC, Lagarias JC, Zhang H, Elich TD, Chory J. 37.  1999. PKS1, a substrate phosphorylated by phytochrome that modulates light signaling in Arabidopsis. Science 284:1539–41 [Google Scholar]
  38. Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW. 38.  et al. 2010. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res. 20:45–58 [Google Scholar]
  39. Gangappa SN, Holm M, Botto JF. 39.  2013. Molecular interactions of BBX24 and BBX25 with HYH, HY5 HOMOLOG, to modulate Arabidopsis seedling development. Plant Signal. Behav. 8:e25208 [Google Scholar]
  40. Genoud T, Schweizer F, Tscheuschler A, Debrieux D, Casal JJ. 40.  et al. 2008. FHY1 mediates nuclear import of the light-activated phytochrome A photoreceptor. PLoS Genet. 4:e1000143 [Google Scholar]
  41. Gong W, He K, Covington M, Dinesh-Kumar SP, Snyder M. 41.  et al. 2008. The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors. Mol. Plant 1:27–41 [Google Scholar]
  42. Guo L, Zhou J, Elling AA, Charron JB, Deng XW. 42.  2008. Histone modifications and expression of light-regulated genes in Arabidopsis are cooperatively influenced by changing light conditions. Plant Physiol. 147:2070–83 [Google Scholar]
  43. Hao Y, Oh E, Choi G, Liang Z, Wang ZY. 43.  2012. Interactions between HLH and bHLH factors modulate light-regulated plant development. Mol. Plant 5:688–97 [Google Scholar]
  44. Hardtke CS, Gohda K, Osterlund MT, Oyama T, Okada K, Deng XW. 44.  2000. HY5 stability and activity in Arabidopsis is regulated by phosphorylation in its COP1 binding domain. EMBO J. 19:4997–5006 [Google Scholar]
  45. Harmon FG, Kay SA. 45.  2003. The F box protein AFR is a positive regulator of phytochrome A-mediated light signaling. Curr. Biol. 13:2091–96 [Google Scholar]
  46. Hiltbrunner A, Tscheuschler A, Viczian A, Kunkel T, Kircher S, Schäfer E. 46.  2006. FHY1 and FHL act together to mediate nuclear accumulation of the phytochrome A photoreceptor. Plant Cell Physiol. 47:1023–34 [Google Scholar]
  47. Holm M, Ma LG, Qu LJ, Deng XW. 47.  2002. Two interacting bZIP proteins are direct targets of COP1-mediated control of light-dependent gene expression in Arabidopsis. Genes Dev. 16:1247–59 [Google Scholar]
  48. Hong SY, Seo PJ, Ryu JY, Cho SH, Woo JC, Park CM. 48.  2013. A competitive peptide inhibitor KIDARI negatively regulates HFR1 by forming nonfunctional heterodimers in Arabidopsis photomorphogenesis. Mol. Cells 35:25–31 [Google Scholar]
  49. Hornitschek P, Lorrain S, Zoete V, Michielin O, Fankhauser C. 49.  2009. Inhibition of the shade avoidance response by formation of non-DNA binding bHLH heterodimers. EMBO J. 28:3893–902 [Google Scholar]
  50. Hsieh WP, Hsieh HL, Wu SH. 50.  2012. Arabidopsis bZIP16 transcription factor integrates light and hormone signaling pathways to regulate early seedling development. Plant Cell 24:3997–4011 [Google Scholar]
  51. Hu W, Su YS, Lagarias JC. 51.  2009. A light-independent allele of phytochrome B faithfully recapitulates photomorphogenic transcriptional networks. Mol. Plant 2:166–82 [Google Scholar]
  52. Hudson ME, Lisch DR, Quail PH. 52.  2003. The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway. Plant J. 34:453–71 [Google Scholar]
  53. Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 53.  2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324:218–23 [Google Scholar]
  54. Jang IC, Chung PJ, Hemmes H, Jung C, Chua NH. 54.  2011. Rapid and reversible light-mediated chromatin modifications of Arabidopsis phytochrome A locus. Plant Cell 23:459–70 [Google Scholar]
  55. Jang IC, Henriques R, Seo HS, Nagatani A, Chua NH. 55.  2010. Arabidopsis PHYTOCHROME INTERACTING FACTOR proteins promote phytochrome B polyubiquitination by COP1 E3 ligase in the nucleus. Plant Cell 22:2370–83 [Google Scholar]
  56. Jang IC, Yang JY, Seo HS, Chua NH. 56.  2005. HFR1 is targeted by COP1 E3 ligase for post-translational proteolysis during phytochrome A signaling. Genes Dev. 19:593–602 [Google Scholar]
  57. Jeong J, Choi G. 57.  2013. Phytochrome-interacting factors have both shared and distinct biological roles. Mol. Cells 35:371–80 [Google Scholar]
  58. Jiao Y, Yang H, Ma L, Sun N, Yu H. 58.  et al. 2003. A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development. Plant Physiol. 133:1480–93 [Google Scholar]
  59. Jing Y, Zhang D, Wang X, Tang W, Wang W. 59.  et al. 2013. Arabidopsis chromatin remodeling factor PICKLE interacts with transcription factor HY5 to regulate hypocotyl cell elongation. Plant Cell 25:242–56 [Google Scholar]
  60. Jones-Rhoades MW, Bartel DP, Bartel B. 60.  2006. MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant Biol. 57:19–53 [Google Scholar]
  61. Juntawong P, Bailey-Serres J. 61.  2012. Dynamic light regulation of translation status in Arabidopsis thaliana. Front. Plant Sci. 3:66 [Google Scholar]
  62. Kaiserli E, Jenkins GI. 62.  2007. UV-B promotes rapid nuclear translocation of the Arabidopsis UV-B specific signaling component UVR8 and activates its function in the nucleus. Plant Cell 19:2662–73 [Google Scholar]
  63. Kami C, Lorrain S, Hornitschek P, Fankhauser C. 63.  2010. Light-regulated plant growth and development. Curr. Top. Dev. Biol. 91:29–66 [Google Scholar]
  64. Kawaguchi R, Girke T, Bray EA, Bailey-Serres J. 64.  2004. Differential mRNA translation contributes to gene regulation under non-stress and dehydration stress conditions in Arabidopsis thaliana. Plant J. 38:823–39 [Google Scholar]
  65. Khanna R, Kronmiller B, Maszle DR, Coupland G, Holm M. 65.  et al. 2009. The Arabidopsis B-box zinc finger family. Plant Cell 21:3416–20 [Google Scholar]
  66. Kim BH, Cai X, Vaughn JN, von Arnim AG. 66.  2007. On the functions of the h subunit of eukaryotic initiation factor 3 in late stages of translation initiation. Genome Biol. 8:R60 [Google Scholar]
  67. Kim DH, Kang JG, Yang SS, Chung KS, Song PS, Park CM. 67.  2002. A phytochrome-associated protein phosphatase 2A modulates light signals in flowering time control in Arabidopsis. Plant Cell 14:3043–56 [Google Scholar]
  68. Kim JI, Shen Y, Han YJ, Park JE, Kirchenbauer D. 68.  et al. 2004. Phytochrome phosphorylation modulates light signaling by influencing the protein-protein interaction. Plant Cell 16:2629–40 [Google Scholar]
  69. Kim TH, Kim BH, Yahalom A, Chamovitz DA, von Arnim AG. 69.  2004. Translational regulation via 5′ mRNA leader sequences revealed by mutational analysis of the Arabidopsis translation initiation factor subunit eIF3h. Plant Cell 16:3341–56 [Google Scholar]
  70. Kouzarides T. 70.  2007. Chromatin modifications and their function. Cell 128:693–705 [Google Scholar]
  71. Lapko VN, Jiang XY, Smith DL, Song PS. 71.  1999. Mass spectrometric characterization of oat phytochrome A: isoforms and posttranslational modifications. Protein Sci. 8:1032–44 [Google Scholar]
  72. Lau OS, Deng XW. 72.  2010. Plant hormone signaling lightens up: integrators of light and hormones. Curr. Opin. Plant Biol. 13:571–77 [Google Scholar]
  73. Lau OS, Deng XW. 73.  2012. The photomorphogenic repressors COP1 and DET1: 20 years later. Trends Plant Sci. 17:584–93 [Google Scholar]
  74. Lazarova GI, Kerckhoffs LH, Brandstädter J, Matsui M, Kendrick RE. 74.  et al. 1998. Molecular analysis of PHYA in wild-type and phytochrome A-deficient mutants of tomato. Plant J. 14:653–62 [Google Scholar]
  75. Lazarova GI, Kubota T, Frances S, Peters JL, Hughes MJ. 75.  et al. 1998. Characterization of tomato PHYB1 and identification of molecular defects in four mutant alleles. Plant Mol. Biol. 38:1137–46 [Google Scholar]
  76. Leivar P, Quail PH. 76.  2011. PIFs: pivotal components in a cellular signaling hub. Trends Plant Sci. 16:19–28 [Google Scholar]
  77. Leivar P, Tepperman JM, Cohn MM, Monte E, Al-Sady B. 77.  et al. 2012. Dynamic antagonism between phytochromes and PIF family basic helix-loop-helix factors induces selective reciprocal responses to light and shade in a rapidly responsive transcriptional network in Arabidopsis. Plant Cell 24:1398–419 [Google Scholar]
  78. Li J, Li G, Gao S, Martinez C, He G. 78.  et al. 2010. Arabidopsis transcription factor ELONGATED HYPOCOTYL5 plays a role in the feedback regulation of phytochrome A signaling. Plant Cell 22:3634–49 [Google Scholar]
  79. Li JF, Chung HS, Niu Y, Bush J, McCormack M, Sheen J. 79.  2013. Comprehensive protein-based artificial microRNA screens for effective gene silencing in plants. Plant Cell 25:1507–22 [Google Scholar]
  80. Li S, Liu L, Zhuang X, Yu Y, Liu X. 80.  et al. 2013. MicroRNAs inhibit the translation of target mRNAs on the endoplasmic reticulum in Arabidopsis. Cell 153:562–74 [Google Scholar]
  81. Liu B, Zuo Z, Liu H, Liu X, Lin C. 81.  2011. Arabidopsis cryptochrome 1 interacts with SPA1 to suppress COP1 activity in response to blue light. Genes Dev. 25:1029–34 [Google Scholar]
  82. Liu MJ, Wu SH, Chen HM, Wu SH. 82.  2012. Widespread translational control contributes to the regulation of Arabidopsis photomorphogenesis. Mol. Syst. Biol. 8:566 [Google Scholar]
  83. Liu MJ, Wu SH, Wu JF, Lin WD, Wu YC. 83.  et al. 2013. Translational landscape of photomorphogenic Arabidopsis. Plant Cell 25:3699–710 [Google Scholar]
  84. Liu X, Chen CY, Wang KC, Luo M, Tai R. 84.  et al. 2013. PHYTOCHROME INTERACTING FACTOR3 associates with the histone deacetylase HDA15 in repression of chlorophyll biosynthesis and photosynthesis in etiolated Arabidopsis seedlings. Plant Cell 25:1258–73 [Google Scholar]
  85. Lorrain S, Genoud T, Fankhauser C. 85.  2006. Let there be light in the nucleus!. Curr. Opin. Plant Biol. 9:509–14 [Google Scholar]
  86. Losi A, Gärtner W. 86.  2012. The evolution of flavin-binding photoreceptors: an ancient chromophore serving trendy blue-light sensors. Annu. Rev. Plant Biol. 63:49–72 [Google Scholar]
  87. Luo XM, Lin WH, Zhu S, Zhu JY, Sun Y. 87.  et al. 2010. Integration of light- and brassinosteroid-signaling pathways by a GATA transcription factor in Arabidopsis. Dev. Cell 19:872–83 [Google Scholar]
  88. Ma L, Gao Y, Qu L, Chen Z, Li J. 88.  et al. 2002. Genomic evidence for COP1 as a repressor of light-regulated gene expression and development in Arabidopsis. Plant Cell 14:2383–98 [Google Scholar]
  89. Ma L, Li J, Qu L, Hager J, Chen Z. 89.  et al. 2001. Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways. Plant Cell 13:2589–607 [Google Scholar]
  90. Mallappa C, Yadav V, Negi P, Chattopadhyay S. 90.  2006. A basic leucine zipper transcription factor, G-box-binding factor 1, regulates blue light-mediated photomorphogenic growth in Arabidopsis. J. Biol. Chem. 281:22190–99 [Google Scholar]
  91. Mallory AC, Vaucheret H. 91.  2006. Functions of microRNAs and related small RNAs in plants. Nat. Genet. 38:Suppl.S31–36 [Google Scholar]
  92. Marquez Y, Brown JW, Simpson C, Barta A, Kalyna M. 92.  2012. Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res. 22:1184–95 [Google Scholar]
  93. Marrocco K, Zhou Y, Bury E, Dieterle M, Funk M. 93.  et al. 2006. Functional analysis of EID1, an F-box protein involved in phytochrome A-dependent light signal transduction. Plant J. 45:423–38 [Google Scholar]
  94. Matsuura H, Ishibashi Y, Shinmyo A, Kanaya S, Kato K. 94.  2010. Genome-wide analyses of early translational responses to elevated temperature and high salinity in Arabidopsis thaliana. Plant Cell Physiol. 51:448–62 [Google Scholar]
  95. McKim SM, Durnford DG. 95.  2006. Translational regulation of light-harvesting complex expression during photoacclimation to high-light in Chlamydomonas reinhardtii. Plant Physiol. Biochem. 44:857–65 [Google Scholar]
  96. Moglich A, Yang X, Ayers RA, Moffat K. 96.  2010. Structure and function of plant photoreceptors. Annu. Rev. Plant Biol. 61:21–47 [Google Scholar]
  97. Ni M, Tepperman JM, Quail PH. 97.  1998. PIF3, a phytochrome-interacting factor necessary for normal photoinduced signal transduction, is a novel basic helix-loop-helix protein. Cell 95:657–67 [Google Scholar]
  98. Nicolai M, Roncato MA, Canoy AS, Rouquie D, Sarda X. 98.  et al. 2006. Large-scale analysis of mRNA translation states during sucrose starvation in Arabidopsis cells identifies cell proliferation and chromatin structure as targets of translational control. Plant Physiol. 141:663–73 [Google Scholar]
  99. Offermann S, Danker T, Dreymuller D, Kalamajka R, Topsch S. 99.  et al. 2006. Illumination is necessary and sufficient to induce histone acetylation independent of transcriptional activity at the C4-specific phosphoenolpyruvate carboxylase promoter in maize. Plant Physiol. 141:1078–88 [Google Scholar]
  100. Offermann S, Dreesen B, Horst I, Danker T, Jaskiewicz M, Peterhansel C. 100.  2008. Developmental and environmental signals induce distinct histone acetylation profiles on distal and proximal promoter elements of the C4-Pepc gene in maize. Genetics 179:1891–901 [Google Scholar]
  101. Osterlund MT, Hardtke CS, Wei N, Deng XW. 101.  2000. Targeted destabilization of HY5 during light-regulated development of Arabidopsis. Nature 405:462–66 [Google Scholar]
  102. Oyama T, Shimura Y, Okada K. 102.  1997. The Arabidopsis HY5 gene encodes a bZIP protein that regulates stimulus-induced development of root and hypocotyl. Genes Dev. 11:2983–95 [Google Scholar]
  103. Paik I, Yang S, Choi G. 103.  2012. Phytochrome regulates translation of mRNA in the cytosol. Proc. Natl. Acad. Sci. USA 109:1335–40 [Google Scholar]
  104. Park E, Park J, Kim J, Nagatani A, Lagarias JC, Choi G. 104.  2012. Phytochrome B inhibits binding of phytochrome-interacting factors to their target promoters. Plant J. 72:537–46 [Google Scholar]
  105. Park HJ, Ding L, Dai M, Lin R, Wang H. 105.  2008. Multisite phosphorylation of Arabidopsis HFR1 by casein kinase II and a plausible role in regulating its degradation rate. J. Biol. Chem. 283:23264–73 [Google Scholar]
  106. Park MJ, Seo PJ, Park CM. 106.  2012. CCA1 alternative splicing as a way of linking the circadian clock to temperature response in Arabidopsis. Plant Signal. Behav. 7:1194–96 [Google Scholar]
  107. Penfield S, Josse EM, Halliday KJ. 107.  2010. A role for an alternative splice variant of PIF6 in the control of Arabidopsis primary seed dormancy. Plant Mol. Biol. 73:89–95 [Google Scholar]
  108. Petracek ME, Dickey LF, Huber SC, Thompson WF. 108.  1997. Light-regulated changes in abundance and polyribosome association of ferredoxin mRNA are dependent on photosynthesis. Plant Cell 9:2291–300 [Google Scholar]
  109. Phee BK, Kim JI, Shin DH, Yoo J, Park KJ. 109.  et al. 2008. A novel protein phosphatase indirectly regulates phytochrome-interacting factor 3 via phytochrome. Biochem. J. 415:247–55 [Google Scholar]
  110. Piques M, Schulze WX, Hohne M, Usadel B, Gibon Y. 110.  et al. 2009. Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis. Mol. Syst. Biol. 5:314 [Google Scholar]
  111. Rizzini L, Favory JJ, Cloix C, Faggionato D, O'Hara A. 111.  et al. 2011. Perception of UV-B by the Arabidopsis UVR8 protein. Science 332:103–6 [Google Scholar]
  112. Roy B, Vaughn JN, Kim BH, Zhou F, Gilchrist MA, Von Arnim AG. 112.  2010. The h subunit of eIF3 promotes reinitiation competence during translation of mRNAs harboring upstream open reading frames. RNA 16:748–61 [Google Scholar]
  113. Ryu JS, Kim JI, Kunkel T, Kim BC, Cho DS. 113.  et al. 2005. Phytochrome-specific type 5 phosphatase controls light signal flux by enhancing phytochrome stability and affinity for a signal transducer. Cell 120:395–406 [Google Scholar]
  114. Saijo Y, Zhu D, Li J, Rubio V, Zhou Z. 114.  et al. 2008. Arabidopsis COP1/SPA1 complex and FHY1/FHY3 associate with distinct phosphorylated forms of phytochrome A in balancing light signaling. Mol. Cell 31:607–13 [Google Scholar]
  115. Schindler U, Menkens AE, Beckmann H, Ecker JR, Cashmore AR. 115.  1992. Heterodimerization between light-regulated and ubiquitously expressed Arabidopsis GBF bZIP proteins. EMBO J. 11:1261–73 [Google Scholar]
  116. Seo HS, Watanabe E, Tokutomi S, Nagatani A, Chua NH. 116.  2004. Photoreceptor ubiquitination by COP1 E3 ligase desensitizes phytochrome A signaling. Genes Dev. 18:617–22 [Google Scholar]
  117. Seo HS, Yang JY, Ishikawa M, Bolle C, Ballesteros ML, Chua NH. 117.  2003. LAF1 ubiquitination by COP1 controls photomorphogenesis and is stimulated by SPA1. Nature 423:995–99 [Google Scholar]
  118. Seo PJ, Park MJ, Lim MH, Kim SG, Lee M. 118.  et al. 2012. A self-regulatory circuit of CIRCADIAN CLOCK-ASSOCIATED1 underlies the circadian clock regulation of temperature responses in Arabidopsis. Plant Cell 24:2427–42 [Google Scholar]
  119. Shaikhali J, Norén L, de Dios Barajas-López J, Srivastava V, König J. 119.  et al. 2012. Redox-mediated mechanisms regulate DNA binding activity of the G-group of basic region leucine zipper (bZIP) transcription factors in Arabidopsis. J. Biol. Chem. 287:27510–25 [Google Scholar]
  120. Shen H, Cao K, Wang X. 120.  2008. AtbZIP16 and AtbZIP68, two new members of GBFs, can interact with other G group bZIPs in Arabidopsis thaliana. BMB Rep. 41:132–38 [Google Scholar]
  121. Shen H, Luong P, Huq E. 121.  2007. The F-box protein MAX2 functions as a positive regulator of photomorphogenesis in Arabidopsis. Plant Physiol. 145:1471–83 [Google Scholar]
  122. Shen H, Moon J, Huq E. 122.  2005. PIF1 is regulated by light-mediated degradation through the ubiquitin-26S proteasome pathway to optimize photomorphogenesis of seedlings in Arabidopsis. Plant J. 44:1023–35 [Google Scholar]
  123. Shen Y, Zhou Z, Feng S, Li J, Tan-Wilson A. 123.  et al. 2009. Phytochrome A mediates rapid red light-induced phosphorylation of Arabidopsis FAR-RED ELONGATED HYPOCOTYL1 in a low fluence response. Plant Cell 21:494–506 [Google Scholar]
  124. Sherameti I, Nakamura M, Yamamoto YY, Pfannschmidt T, Obokata J, Oelmüller R. 124.  2002. Polyribosome loading of spinach mRNAs for photosystem I subunits is controlled by photosynthetic electron transport. Plant J. 32:631–39 [Google Scholar]
  125. Shikata H, Shibata M, Ushijima T, Nakashima M, Kong SG. 125.  et al. 2012. The RS domain of Arabidopsis splicing factor RRC1 is required for phytochrome B signal transduction. Plant J. 70:727–38 [Google Scholar]
  126. Sibout R, Sukumar P, Hettiarachchi C, Holm M, Muday GK, Hardtke CS. 126.  2006. Opposite root growth phenotypes of hy5 versus hy5 hyh mutants correlate with increased constitutive auxin signaling. PLoS Genet. 2:e202 [Google Scholar]
  127. Simpson CG, Fuller J, Maronova M, Kalyna M, Davidson D. 127.  et al. 2008. Monitoring changes in alternative precursor messenger RNA splicing in multiple gene transcripts. Plant J. 53:1035–48 [Google Scholar]
  128. Sorin C, Bussell JD, Camus I, Ljung K, Kowalczyk M. 128.  et al. 2005. Auxin and light control of adventitious rooting in Arabidopsis require ARGONAUTE1. Plant Cell 17:1343–59 [Google Scholar]
  129. Sormani R, Delannoy E, Lageix S, Bitton F, Lanet E. 129.  et al. 2011. Sublethal cadmium intoxication in Arabidopsis thaliana impacts translation at multiple levels. Plant Cell Physiol. 52:436–47 [Google Scholar]
  130. Tepperman JM, Hudson ME, Khanna R, Zhu T, Chang SH. 130.  et al. 2004. Expression profiling of phyB mutant demonstrates substantial contribution of other phytochromes to red-light-regulated gene expression during seedling de-etiolation. Plant J. 38:725–39 [Google Scholar]
  131. Tepperman JM, Zhu T, Chang HS, Wang X, Quail PH. 131.  2001. Multiple transcription-factor genes are early targets of phytochrome A signaling. Proc. Natl. Acad. Sci. USA 98:9437–42 [Google Scholar]
  132. Tessadori F, van Zanten M, Pavlova P, Clifton R, Pontvianne F. 132.  et al. 2009. Phytochrome B and histone deacetylase 6 control light-induced chromatin compaction in Arabidopsis thaliana. PLoS Genet. 5:e1000638 [Google Scholar]
  133. Tian Q, Stepaniants SB, Mao M, Weng L, Feetham MC. 133.  et al. 2004. Integrated genomic and proteomic analyses of gene expression in mammalian cells. Mol. Cell. Proteomics 3:960–69 [Google Scholar]
  134. Van Buskirk EK, Decker PV, Chen M. 134.  2012. Photobodies in light signaling. Plant Physiol. 158:52–60 [Google Scholar]
  135. von Arnim AG, Deng XW. 135.  1994. Light inactivation of Arabidopsis photomorphogenic repressor COP1 involves a cell-specific regulation of its nucleocytoplasmic partitioning. Cell 79:1035–45 [Google Scholar]
  136. Wang X, Wu F, Xie Q, Wang H, Wang Y. 136.  et al. 2012. SKIP is a component of the spliceosome linking alternative splicing and the circadian clock in Arabidopsis. Plant Cell 24:3278–95 [Google Scholar]
  137. Wang ZY, Bai MY, Oh E, Zhu JY. 137.  2012. Brassinosteroid signaling network and regulation of photomorphogenesis. Annu. Rev. Genet. 46:701–24 [Google Scholar]
  138. Wu G, Spalding EP. 138.  2007. Separate functions for nuclear and cytoplasmic cryptochrome 1 during photomorphogenesis of Arabidopsis seedlings. Proc. Natl. Acad. Sci. USA 104:18813–18 [Google Scholar]
  139. Wu HP, Su YS, Chen HC, Chen YR, Wu CC. 139.  et al. 2014. Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella. Genome Biol. 15:R10 [Google Scholar]
  140. Yadav V, Mallappa C, Gangappa SN, Bhatia S, Chattopadhyay S. 140.  2005. A basic helix-loop-helix transcription factor in Arabidopsis, MYC2, acts as a repressor of blue light-mediated photomorphogenic growth. Plant Cell 17:1953–66 [Google Scholar]
  141. Yahalom A, Kim TH, Roy B, Singer R, von Arnim AG, Chamovitz DA. 141.  2008. Arabidopsis eIF3e is regulated by the COP9 signalosome and has an impact on development and protein translation. Plant J. 53:300–11 [Google Scholar]
  142. Yan H, Marquardt K, Indorf M, Jutt D, Kircher S. 142.  et al. 2011. Nuclear localization and interaction with COP1 are required for STO/BBX24 function during photomorphogenesis. Plant Physiol. 156:1772–82 [Google Scholar]
  143. Yeh KC, Lagarias JC. 143.  1998. Eukaryotic phytochromes: light-regulated serine/threonine protein kinases with histidine kinase ancestry. Proc. Natl. Acad. Sci. USA 95:13976–81 [Google Scholar]
  144. Yeh KC, Wu SH, Murphy JT, Lagarias JC. 144.  1997. A cyanobacterial phytochrome two-component light sensory system. Science 277:1505–8 [Google Scholar]
  145. Yu X, Klejnot J, Zhao X, Shalitin D, Maymon M. 145.  et al. 2007. Arabidopsis cryptochrome 2 completes its posttranslational life cycle in the nucleus. Plant Cell 19:3146–56 [Google Scholar]
  146. Zhang H, He H, Wang X, Wang X, Yang X. 146.  et al. 2011. Genome-wide mapping of the HY5-mediated gene networks in Arabidopsis that involve both transcriptional and post-transcriptional regulation. Plant J. 65:346–58 [Google Scholar]
  147. Zhang Y, Mayba O, Pfeiffer A, Shi H, Tepperman JM. 147.  et al. 2013. A quartet of PIF bHLH factors provides a transcriptionally centered signaling hub that regulates seedling morphogenesis through differential expression-patterning of shared target genes in Arabidopsis. PLoS Genet. 9:e1003244 [Google Scholar]
  148. Zhou DX, Kim YJ, Li YF, Carol P, Mache R. 148.  1998. COP1b, an isoform of COP1 generated by alternative splicing, has a negative effect on COP1 function in regulating light-dependent seedling development in Arabidopsis. Mol. Gen. Genet. 257:387–91 [Google Scholar]

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