Kessler F, Schnell D: Chloroplast biogenesis: diversity and regulation of the protein import apparatus. Curr Opin Cell Biol. 2009, 21: 494-500.
Article
PubMed
CAS
Google Scholar
Leister D: Chloroplast research in the genomic age. Trends Genet. 2003, 19: 47-56.
Article
PubMed
CAS
Google Scholar
Pogson BJ, Albrecht V: Genetic dissection of chloroplast biogenesis and development: an overview. Plant Physiol. 2011
Google Scholar
Waters MT, Langdale JA: The making of a chloroplast. EMBO J. 2009, 28: 2861-2873.
Article
PubMed
CAS
PubMed Central
Google Scholar
Wei N, Deng XW: The role of the COP/DET/FUS genes in light control of Arabidopsis seedling development. Plant Physiol. 1996, 112: 871-878.
Article
PubMed
CAS
PubMed Central
Google Scholar
Chory J, Peto CA: Mutations in the DET1 gene affect cell-type-specific expression of light-regulated genes and chloroplast development in Arabidopsis. Proc Natl Acad Sci USA. 1990, 87: 8776-8780.
Article
PubMed
CAS
PubMed Central
Google Scholar
Stephenson PG, Fankhauser C, Terry MJ: PIF3 is a repressor of chloroplast development. Proc Natl Acad Sci USA. 2009, 106: 7654-7659.
Article
PubMed
CAS
PubMed Central
Google Scholar
Oyama T, Shimura Y, Okada K: The Arabidopsis HY5 gene encodes a bZIP protein that regulates stimulus-induced development of root and hypocotyl. Genes Dev. 1997, 11: 2983-2995.
Article
PubMed
CAS
PubMed Central
Google Scholar
Chattopadhyay S, Ang LH, Puente P, Deng XW, Wei N: Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression. Plant Cell. 1998, 10: 673-683.
Article
PubMed
CAS
PubMed Central
Google Scholar
Saijo Y, Sullivan JA, Wang H, Yang J, Shen Y, Rubio V, Ma L, Hoecker U, Deng XW: The COP1-SPA1 interaction defines a critical step in phytochrome A-mediated regulation of HY5 activity. Genes Dev. 2003, 17: 2642-2647.
Article
PubMed
CAS
PubMed Central
Google Scholar
Lau OS, Deng XW: Plant hormone signaling lightens up: integrators of light and hormones. Curr Opin Plant Biol. 2010, 13 (5): 571-577.
Article
PubMed
CAS
Google Scholar
Ang LH, Chattopadhyay S, Wei N, Oyama T, Okada K, Batschauer A, Deng XW: Molecular interaction between COP1 and HY5 defines a regulatory switch for light control of Arabidopsis development. Mol Cell. 1998, 1: 213-222.
Article
PubMed
CAS
Google Scholar
Robertson EJ, Pyke KA, Leech RM: arc6, an extreme chloroplast division mutant of Arabidopsis also alters proplastid proliferation and morphology in shoot and root apices. J Cell Sci. 1995, 108: 2937-2944.
PubMed
CAS
Google Scholar
Lu S, Van EJ, Zhou X, Lopez AB, O'Halloran DM, Cosman KM, Conlin BJ, Paolillo DJ, Garvin DF, Vrebalov J, et al: The cauliflower Or gene encodes a DnaJ cysteine-rich domain-containing protein that mediates high levels of beta-carotene accumulation. Plant Cell. 2006, 18: 3594-3605.
Article
PubMed
CAS
PubMed Central
Google Scholar
Paolillo DJ, Garvin DF, Parthasarathy MV: The chromoplasts of Or mutants of cauliflower (Brassica oleracea L. var. botrytis). Protoplasma. 2004, 224: 245-253.
Article
PubMed
Google Scholar
Wu JA, Zhang YL, Zhang HQ, Huang H, Folta KM, Lu JA: Whole genome wide expression profiles of Vitis amurensis grape responding to downy mildew by using Solexa sequencing technology. BMC Plant Biol. 2010, 10:
Google Scholar
Joung JG, Corbett AM, Fellman SM, Tieman DM, Klee HJ, Giovannoni JJ, Fei Z: Plant MetGenMAP: an integrative analysis system for plant systems biology. Plant Physiol. 2009, 151: 1758-1768.
Article
PubMed
CAS
PubMed Central
Google Scholar
Larkin RM, Alonso JM, Ecker JR, Chory J: GUN4, a regulator of chlorophyll synthesis and intracellular signaling. Science. 2003, 299: 902-906.
Article
PubMed
CAS
Google Scholar
Mochizuki N, Brusslan JA, Larkin R, Nagatani A, Chory J: Arabidopsis genomes uncoupled 5 (GUN5) mutant reveals the involvement of Mg-chelatase H subunit in plastid-to-nucleus signal transduction. Proc Natl Acad Sci USA. 2001, 98: 2053-2058.
Article
PubMed
CAS
PubMed Central
Google Scholar
Latijnhouwers M, Xu XM, Moller SG: Arabidopsis stromal 70-kDa heat shock proteins are essential for chloroplast development. Planta. 2010, 232: 567-578.
Article
PubMed
CAS
Google Scholar
Shimada H, Mochizuki M, Ogura K, Froehlich JE, Osteryoung KW, Shirano Y, Shibata D, Masuda S, Mori K, Takamiya KI: Arabidopsis cotyledon-specific chloroplast biogenesis factor CYO1 is a protein disulfide isomerase. Plant Cell. 2007, 19: 3157-3169.
Article
PubMed
CAS
PubMed Central
Google Scholar
Tsuchiya T, Ohta H, Okawa K, Iwamatsu A, Shimada H, Masuda T, Takamiya Ki: Cloning of chlorophyllase, the key enzyme in chlorophyll degradation: Finding of a lipase motif and the induction by methyl jasmonate. Proc Natl Acad Sci USA. 1999, 96: 15362-15367.
Article
PubMed
CAS
PubMed Central
Google Scholar
Wei N, Chamovitz DA, Deng XW: Arabidopsis COP9 is a component of a novel signaling complex mediating light control of development. Cell. 1994, 78: 117-124.
Article
PubMed
CAS
Google Scholar
Hoecker U, Quail PH: The phytochrome A-specific signaling intermediate SPA1 interacts directly with COP1, a constitutive repressor of light signaling in Arabidopsis. J Biol Chem. 2001, 276: 38173-38178.
PubMed
CAS
Google Scholar
Hoecker U, Tepperman JM, Quail PH: SPA1, a WD-repeat protein specific to phytochrome A signal transduction. Science. 1999, 284: 496-499.
Article
PubMed
CAS
Google Scholar
Zhang HY, He H, Wang XC, Wang XF, Yang XZ, Li L, Deng XW: Genome-wide mapping of the HY5-mediated genenetworks in Arabidopsis that involve both transcriptional and post-transcriptional regulation. Plant J. 2011, 65: 346-358.
Article
PubMed
CAS
Google Scholar
Lee J, He K, Stolc V, Lee H, Figueroa P, Gao Y, Tongprasit W, Zhao HY, Lee I, Deng X: Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. Plant Cell. 2007, 19: 731-749.
Article
PubMed
CAS
PubMed Central
Google Scholar
Li J, Li G, Gao S, Martinez C, He G, Zhou Z, Huang X, Lee JH, Zhang H, Shen Y, et al: Arabidopsis transcription factor ELONGATED HYPOCOTYL5 plays a role in the feedback regulation of phytochrome a signaling. Plant Cell. 2010, 22: 3634-3649.
Article
PubMed
CAS
PubMed Central
Google Scholar
Hurd PJ, Nelson CJ: Advantages of next-generation sequencing versus the microarray in epigenetic research. Brief Funct Genomics. 2009, 8: 174-183.
Article
CAS
Google Scholar
Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M, et al: Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotech. 2000, 18: 630-634.
Article
CAS
Google Scholar
Li P, Ponnala L, Gandotra N, Wang L, Si Y, Tausta SL, Kebrom TH, Provart N, Patel R, Myers CR, et al: The developmental dynamics of the maize leaf transcriptome. Nat Genet. 2010, 42: 1060-1067.
Article
PubMed
CAS
Google Scholar
Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, et al: Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet. 2010, 42: 961-967.
Article
PubMed
CAS
Google Scholar
Mullet JE: Chloroplast development and gene expression. Annu Rev Plant Physiol Plant Mol Biol. 1988, 39: 475-502.
Article
CAS
Google Scholar
Matsui M, Stoop CD, von Arnim AG, Wei N, Deng XW: Arabidopsis COP1 protein specifically interacts in vitro with a cytoskeleton-associated protein, CIP1. Proc Natl Acad Sci USA. 1995, 92: 4239-4243.
Article
PubMed
CAS
PubMed Central
Google Scholar
Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10:
Google Scholar
Birol I, Jackman SD, Nielsen CB, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE, et al: De novo transcriptome assembly with ABySS. Bioinformatics. 2009, 25: 2872-2877.
Article
PubMed
CAS
Google Scholar
Mortazavi A, Williams BA, Mccue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Med. 2008, 5: 621-628.
CAS
Google Scholar
Stekel DJ, Git Y, Falciani F: The comparison of gene expression from multiple cDNA libraries. Genome Res. 2000, 10: 2055-2061.
Article
PubMed
CAS
PubMed Central
Google Scholar
Benjamini Y, Hochberg Y: Controlling the false discovery rate - a practical and powerful approach to multiple testing. J R Stat Soc Ser B. 1995, 57: 289-300.
Google Scholar
Karp PD, Paley S, Romero P: The pathway tools software. Bioinformatics. 2002, 18: S225-S232.
Article
PubMed
Google Scholar
Arnon DI: Copper enzymes in isolated chloroplasts. Polyphenoloxidase in Beta Vulgaris. Plant Physiol. 1949, 24: 1-15.
Article
PubMed
CAS
PubMed Central
Google Scholar