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  • Alon, U. (2003) Biological networks: the tinkerer as an engineer. Science, 301, 18661867.
  • Botto, J.F. and Smith, H. (2002) Differential genetic variation in adaptive strategies to a common environmental signal in Arabidopsis accession: phytochrome-mediated shade avoidance. Plant, Cell Environ. 25, 5363.
  • Bou-Torrent, J., Roig-Villanova, I. and Martinez-Garcia, J.F. (2008) Light signaling: back to space. Trends Plant Sci. 13, 108114.
  • Bou-Torrent, J., Salla-Martret, M., Brandt, R., Musielak, T., Palauqui, J.C., Martinez-Garcia, J.F. and Wenkel, S. (2012) ATHB4 and HAT3, two class II HD–ZIP transcription factors, control leaf development in Arabidopsis. Plant Signal. Behav. 7, 13821387.
  • Bracha-Drori, K., Shichrur, K., Katz, A., Oliva, M., Angelovici, R., Yalovsky, S. and Ohad, N. (2004) Detection of protein–protein interactions in plants using bimolecular fluorescence complementation. Plant J. 40, 419427.
  • Carabelli, M., Morelli, G., Whitelam, G. and Ruberti, I. (1996) Twilight-zone and canopy shade induction of the Athb–2 homeobox gene in green plants. Proc. Natl Acad. Sci. USA, 93, 35303535.
  • Carabelli, M., Possenti, M., Sessa, G., Ciolfi, A., Sassi, M., Morelli, G. and Ruberti, I. (2007) Canopy shade causes a rapid and transient arrest in leaf development through auxin-induced cytokinin oxidase activity. Genes Dev. 21, 18631868.
  • Carretero-Paulet, L., Galstyan, A., Roig-Villanova, I., Martinez-Garcia, J.F., Bilbao-Castro, J.R. and Robertson, D.L. (2010) Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae. Plant Physiol. 153, 13981412.
  • Casal, J.J. (2012) Shade avoidance. Arabidopsis Book, 10, e0157.
  • Casal, J.J., Fankhauser, C., Coupland, G. and Blazquez, M.A. (2004) Signalling for developmental plasticity. Trends Plant Sci. 9, 309314.
  • Chandler, J.W., Cole, M., Flier, A. and Werr, W. (2009) BIM1, a bHLH protein involved in brassinosteroid signalling, controls Arabidopsis embryonic patterning via interaction with DORNROSCHEN and DORNROSCHEN-LIKE. Plant Mol. Biol. 69, 5768.
  • Ciarbelli, A.R., Ciolfi, A., Salvucci, S., Ruzza, V., Possenti, M., Carabelli, M., Fruscalzo, A., Sessa, G., Morelli, G. and Ruberti, I. (2008) The Arabidopsis homeodomain-leucine zipper II gene family: diversity and redundancy. Plant Mol. Biol. 68, 465478.
  • Clack, T., Mathews, S. and Sharrock, R.A. (1994) The phytochrome apoprotein family in Arabidopsis is encoded by five genes: the sequences and expression of PHYD and PHYE. Plant Mol. Biol. 25, 413427.
  • Crawford, B.C. and Yanofsky, M.F. (2011) HALF FILLED promotes reproductive tract development and fertilization efficiency in Arabidopsis thaliana. Development, 138, 29993009.
  • Crocco, C.D., Holm, M., Yanovsky, M.J. and Botto, J.F. (2010) AtBBX21 and COP1 genetically interact in the regulation of shade avoidance. Plant J. 64, 551562.
  • Devlin, P.F., Yanovsky, M.J. and Kay, S.A. (2003) A genomic analysis of the shade avoidance response in Arabidopsis. Plant Physiol. 133, 16171629.
  • Djakovic-Petrovic, T., de Wit, M., Voesenek, L.A. and Pierik, R. (2007) DELLA protein function in growth responses to canopy signals. Plant J. 51, 117126.
  • Faigon-Soverna, A., Harmon, F.G., Storani, L., Karayekov, E., Staneloni, R.J., Gassmann, W., Mas, P., Casal, J.J., Kay, S.A. and Yanovsky, M.J. (2006) A constitutive shade-avoidance mutant implicates TIR–NBS–LRR proteins in Arabidopsis photomorphogenic development. Plant Cell, 18, 29192928.
  • Friedrichsen, D.M., Nemhauser, J., Muramitsu, T., Maloof, J.N., Alonso, J., Ecker, J.R., Furuya, M. and Chory, J. (2002) Three redundant brassinosteroid early response genes encode putative bHLH transcription factors required for normal growth. Genetics, 162, 14451456.
  • Galstyan, A., Cifuentes-Esquivel, N., Bou-Torrent, J. and Martinez-Garcia, J.F. (2011) The shade avoidance syndrome in Arabidopsis: a fundamental role for atypical basic helix-loop-helix proteins as transcriptional cofactors. Plant J. 66, 258267.
  • Galstyan, A., Bou-Torrent, J., Roig-Villanova, I. and Martinez-Garcia, J.F. (2012) A dual mechanism controls nuclear localization in the atypical basic-helix-loop-helix protein PAR1 of Arabidopsis thaliana. Mol. Plant, 5, 669677.
  • Halliday, K.J., Martinez-Garcia, J.F. and Josse, E.M. (2009) Integration of light and auxin signaling. Cold Spring Harb. Perspect. Biol. 1, a001586.
  • Hao, Y., Oh, E., Choi, G., Liang, Z. and Wang, Z.Y. (2012) Interactions between HLH and bHLH factors modulate light-regulated plant development. Mol. Plant 5, 688697.
  • Hartwell, L.H., Hopfield, J.J., Leibler, S. and Murray, A.W. (1999) From molecular to modular cell biology. Nature, 402, C47C52.
  • Heim, M.A., Jakoby, M., Werber, M., Martin, C., Weisshaar, B. and Bailey, P.C. (2003) The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol. Biol. Evol. 20, 735747.
  • Hornitschek, P., Lorrain, S., Zoete, V., Michielin, O. and Fankhauser, C. (2009) Inhibition of the shade avoidance response by formation of non-DNA binding bHLH heterodimers. EMBO J. 28, 38933902.
  • Hornitschek, P., Kohnen, M.V., Lorrain, S., et al. (2012) Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling. Plant J. 71, 699711.
  • Hruz, T., Laule, O., Szabo, G., Wessendorp, F., Bleuler, S., Oertle, L., Widmayer, P., Gruissem, W. and Zimmermann, P. (2008) Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Adv. Bioinformatics, 2008, 420747.
  • Josse, E.M., Gan, Y., Bou-Torrent, J., et al. (2011) A DELLA in disguise: SPATULA restrains the growth of the developing Arabidopsis seedling. Plant Cell, 23, 13371351.
  • Keuskamp, D.H., Sasidharan, R. and Pierik, R. (2010) Physiological regulation and functional significance of shade avoidance responses to neighbors. Plant Signal. Behav. 5, 655662.
  • Kozuka, T., Kobayashi, J., Horiguchi, G., Demura, T., Sakakibara, H., Tsukaya, H. and Nagatani, A. (2010) Involvement of auxin and brassinosteroid in the regulation of petiole elongation under the shade. Plant Physiol. 153, 16081618.
  • Leivar, P. and Quail, P.H. (2011) PIFs: pivotal components in a cellular signaling hub. Trends Plant Sci. 16, 1928.
  • Leivar, P., Tepperman, J.M., Cohn, M.M., Monte, E., Al–Sady, B., Erickson, E. and Quail, P.H. (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, 13981419.
  • Li, L., Ljung, K., Breton, G. et al. (2012) Linking photoreceptor excitation to changes in plant architecture. Genes Dev. 26, 785790.
  • Lorrain, S., Allen, T., Duek, P.D., Whitelam, G.C. and Fankhauser, C. (2008) Phytochrome-mediated inhibition of shade avoidance involves degradation of growth-promoting bHLH transcription factors. Plant J. 53, 312323.
  • Martinez-Garcia, J.F. and Quail, P.H. (1999) The HMG–I/Y protein PF1 stimulates binding of the transcriptional activator GT–2 to the PHYA gene promoter. Plant J. 18, 173183.
  • Martinez-Garcia, J.F., Huq, E. and Quail, P.H. (2000) Direct targeting of light signals to a promoter element-bound transcription factor. Science, 288, 859863.
  • Martinez-Garcia, J.F., Virgos-Soler, A. and Prat, S. (2002) Control of photoperiod-regulated tuberization in potato by the Arabidopsis flowering-time gene CONSTANS. Proc. Natl Acad. Sci. USA, 99, 1521115216.
  • Martinez-Garcia, J.F., Galstyan, A., Salla-Martret, M., Cifuentes-Esquivel, N., Gallemí, M. and Bou-Torrent, J. (2010) Regulatory components of shade avoidance syndrome. Adv. Bot. Res. 53, 65116.
  • Nemhauser, J.L. (2008) Dawning of a new era: photomorphogenesis as an integrated molecular network. Curr. Opin. Plant Biol. 11, 48.
  • Poppenberger, B., Rozhon, W., Khan, M., Husar, S., Adam, G., Luschnig, C., Fujioka, S. and Sieberer, T. (2011) CESTA, a positive regulator of brassinosteroid biosynthesis. EMBO J. 30, 11491161.
  • Prigge, M.J., Otsuga, D., Alonso, J.M., Ecker, J.R., Drews, G.N. and Clark, S.E. (2005) Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development. Plant Cell, 17, 6176.
  • Reymond, M.C., Brunoud, G., Chauvet, A., Martinez-Garcia, J.F., Martin-Magniette, M.L., Moneger, F. and Scutt, C.P. (2012) A light-regulated genetic module was recruited to carpel development in Arabidopsis following a structural change to SPATULA. Plant Cell, 24, 28122825.
  • Roig-Villanova, I., Bou, J., Sorin, C., Devlin, P.F. and Martinez-Garcia, J.F. (2006) Identification of primary target genes of phytochrome signaling. Early transcriptional control during shade avoidance responses in Arabidopsis. Plant Physiol. 141, 8596.
  • Roig-Villanova, I., Bou-Torrent, J., Galstyan, A., Carretero-Paulet, L., Portoles, S., Rodriguez-Concepcion, M. and Martinez-Garcia, J.F. (2007) Interaction of shade avoidance and auxin responses: a role for two novel atypical bHLH proteins. EMBO J. 26, 47564767.
  • Ruberti, I., Sessa, G., Ciolfi, A., Possenti, M., Carabelli, M. and Morelli, G. (2012) Plant adaptation to dynamically changing environment: the shade avoidance response. Biotechnol. Adv. 30, 10471058.
  • Salter, M.G., Franklin, K.A. and Whitelam, G.C. (2003) Gating of the rapid shade-avoidance response by the circadian clock in plants. Nature, 426, 680683.
  • Santner, A. and Estelle, M. (2009) Recent advances and emerging trends in plant hormone signalling. Nature, 459, 10711078.
  • Sasidharan, R., Chinnappa, C.C., Staal, M., Elzenga, J.T., Yokoyama, R., Nishitani, K., Voesenek, L.A. and Pierik, R. (2010) Light quality-mediated petiole elongation in Arabidopsis during shade avoidance involves cell wall modification by xyloglucan endotransglucosylase/hydrolases. Plant Physiol. 154, 978990.
  • Sessa, G., Carabelli, M., Sassi, M., Ciolfi, A., Possenti, M., Mittempergher, F., Becker, J., Morelli, G. and Ruberti, I. (2005) A dynamic balance between gene activation and repression regulates the shade avoidance response in Arabidopsis. Genes Dev. 19, 28112815.
  • Sharrock, R.A. and Quail, P.H. (1989) Novel phytochrome sequences in Arabidopsis thaliana: structure, evolution, and differential expression of a plant regulatory photoreceptor family. Genes Dev. 3, 17451757.
  • Sorin, C., Salla-Martret, M., Bou-Torrent, J., Roig-Villanova, I. and Martinez-Garcia, J.F. (2009) ATHB4, a regulator of shade avoidance, modulates hormone response in Arabidopsis seedlings. Plant J. 59, 266277.
  • Steindler, C., Matteucci, A., Sessa, G., Weimar, T., Ohgishi, M., Aoyama, T., Morelli, G. and Ruberti, I. (1999) Shade avoidance responses are mediated by the ATHB–2 HD–zip protein, a negative regulator of gene expression. Development, 126, 42354245.
  • Talbert, P.B., Adler, H.T., Parks, D.W. and Comai, L. (1995) The REVOLUTA gene is necessary for apical meristem development and for limiting cell divisions in the leaves and stems of Arabidopsis thaliana. Development, 121, 27232735.
  • Tao, Y., Ferrer, J.L., Ljung, K. et al. (2008) Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants. Cell, 133, 164176.
  • Toledo-Ortiz, G., Huq, E. and Quail, P.H. (2003) The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell, 15, 17491770.
  • Toledo-Ortiz, G., Huq, E. and Rodriguez-Concepcion, M. (2010) Direct regulation of phytoene synthase gene expression and carotenoid biosynthesis by phytochrome-interacting factors. Proc. Natl Acad. Sci. USA, 107, 1162611631.
  • Turchi, L., Carabelli, M., Ruzza, V. et al. (2013) Arabidopsis HD–Zip II transcription factors control apical embryo development and meristem function. Development, 140, 21182129.
  • Vert, G., Nemhauser, J.L., Geldner, N., Hong, F. and Chory, J. (2005) Molecular mechanisms of steroid hormone signaling in plants. Annu. Rev. Cell Dev. Biol. 21, 177201.
  • Walhout, A.J.M. (2011) What does biologically meaningful mean? A perspective on gene regulatory network validation. Genome Biol. 12, 109.
  • Wang, H., Zhu, Y., Fujioka, S., Asami, T. and Li, J. (2009) Regulation of Arabidopsis brassinosteroid signaling by atypical basic helix-loop-helix proteins. Plant Cell, 21, 37813791.
  • Yin, Y., Vafeados, D., Tao, Y., Yoshida, S., Asami, T. and Chory, J. (2005) A new class of transcription factors mediates brassinosteroid-regulated gene expression in Arabidopsis. Cell, 120, 249259.
  • Zhang, Y., Mayba, O., Pfeiffer, A., Shi, H., Tepperman, J.M., Speed, T.P. and Quail, P.H. (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.