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Plant Research Projects in Riken Institutes Research Projects in Riken Institutes Project Research Projects in Riken Institutess in Riken Inst Research Projects in Riken Institutesit Research Projects in Riken Institutesut Research Projects in Riken Instituteses Kiyot Research Projects in Riken Institutesaka Okada Minami Mat Research Projects in Riken Institutessui Mot Research Projects in Riken Institutesoaki Seki Plant Research Projects in Riken Institutes Genomic Research Projects in Riken Instituteses in Japan Minist Research Projects in Riken Institutesry of Education and Technology (MIXT) Educat Research Projects in Riken Institutesion and Tech Projects in Riken Institutesnology (MIXT) Nat Research Projects in Riken Institutesional Universit Research Projects in Riken Institutesies Nat Research Projects in Riken Institutesional Inst Research Projects in Riken Institutesit Research Projects in Riken Institutesut Research Projects in Riken Instituteses NI f Education and Technology (MIXT)or Basic Biology in Okazaki NI of Education and Technology (MIXT) Genet Research Projects in Riken Institutesics in Mish Projects in Riken Institutesima Riken Inst Research Projects in Riken Institutesit Research Projects in Riken Institutesut Research Projects in Riken Instituteses Plant Research Projects in Riken Institutes Science Cent Research Projects in Riken Instituteser Genomics Science Cent Research Projects in Riken Instituteser Bioresource Cent Research Projects in Riken Instituteser Minist Research Projects in Riken Institutesry of Education and Technology (MIXT) Agricult Research Projects in Riken Institutesure Nat Research Projects in Riken Institutesional Inst Research Projects in Riken Institutesit Research Projects in Riken Institutesut Research Projects in Riken Institutese of Education and Technology (MIXT) Agrobiological Inst Research Projects in Riken Institutesit Research Projects in Riken Institutesut Research Projects in Riken Institutese Rice genomics providing f Education and Technology (MIXT)unds t Research Projects in Riken Instituteso research Projects in Riken Institutesers at Research Projects in Riken Institutes Nat Research Projects in Riken Institutesional Universit Research Projects in Riken Institutesies and Inst Research Projects in Riken Institutesit Research Projects in Riken Institutesut Research Projects in Riken Instituteses Minist Research Projects in Riken Institutesry of Education and Technology (MIXT) Indust Research Projects in Riken Institutesry Arabidopsis met Research Projects in Riken Institutesabolome analysis, genomics of genomics of Education and Technology (MIXT) Lot Research Projects in Riken Institutesus japonicus providing f Education and Technology (MIXT)unds t Research Projects in Riken Instituteso research Projects in Riken Institutesers at Research Projects in Riken Institutes Nat Research Projects in Riken Institutesional Universit Research Projects in Riken Institutesies and Inst Research Projects in Riken Institutesit Research Projects in Riken Institutesut Research Projects in Riken Instituteses Regional Government Research Projects in Riken Institutes Ch Projects in Riken Institutesiba Kazusa DNA Research Projects in Riken Institutes Inst Research Projects in Riken Institutesit Research Projects in Riken Institutesut Research Projects in Riken Institutese Okayama RIBS Collect Research Projects in Riken Institutesion of Education and Technology (MIXT) Arabidopsis t Research Projects in Riken Institutesagged lines, genomics of Genome sequencing of Education and Technology (MIXT) Lot Research Projects in Riken Institutesus japonicus Privat Research Projects in Riken Institutese Organizat Research Projects in Riken Institutesion privat Research Projects in Riken Institutese universit Research Projects in Riken Institutesies companies

Plant Research Projects in Riken Institutes Science Cent Research Projects in Riken Instituteser Genomics Science Cent Research Projects in Riken Instituteser NMR f Education and Technology (MIXT)acilit Research Projects in Riken Institutesies Riken Yokoh Projects in Riken Institutesama Campus Genomic Funct Research Projects in Riken Institutesion Research Projects in Riken Institutes Group Group direct Research Projects in Riken Institutesor: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Kiyot Research Projects in Riken Institutesaka Okada (Kyot Research Projects in Riken Instituteso Univ. and Riken PSC) and Riken PSC) Forward genet Research Projects in Riken Institutesics-based analyses of Education and Technology (MIXT) Arabidopsis Laborat Research Projects in Riken Institutesory f Education and Technology (MIXT)or Int Research Projects in Riken Instituteserdisciplinary Analysis of Education and Technology (MIXT) Plant Research Projects in Riken Institutes Development Research Projects in Riken Institutes Team leader: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Takuji Wada Cell dif Education and Technology (MIXT)f Education and Technology (MIXT)erent Research Projects in Riken Institutesiat Research Projects in Riken Institutesion of Education and Technology (MIXT) epidermal cells root Research Projects in Riken Institutes h Projects in Riken Institutesair development Research Projects in Riken Institutes, genomics of t Research Projects in Riken Institutesr ich Projects in Riken Institutesome development Research Projects in Riken Institutes, genomics of int Research Projects in Riken Institutesercelllular signaling, genomics of et Research Projects in Riken Institutesc. and Riken PSC) Laborat Research Projects in Riken Institutesory f Education and Technology (MIXT)or Genet Research Projects in Riken Institutesic Regulat Research Projects in Riken Institutesory Syst Research Projects in Riken Institutesems Team leader: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Tat Research Projects in Riken Institutessuya Sakai Signaling mech Projects in Riken Institutesanism by environment Research Projects in Riken Institutesal cues ph Projects in Riken Institutesot Research Projects in Riken Institutesot Research Projects in Riken Institutesropism, genomics of c h Projects in Riken Institutesloroplast Research Projects in Riken Institutes relocat Research Projects in Riken Institutesion, genomics of mech Projects in Riken Institutesanosensing, genomics of et Research Projects in Riken Institutesc. and Riken PSC) Expressed Protein Catalog Expressed Gene Catalog Morph Projects in Riken Institutesogenesis Research Projects in Riken Institutes Group Group direct Research Projects in Riken Institutesor: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Hiroo Fukuda (Univ. and Riken PSC) Tokyo and Riken PSC) Laborat Research Projects in Riken Institutesory f Education and Technology (MIXT)or Gene Regulat Research Projects in Riken Institutesion Team leader: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Taku Demura Novel Culture Systems

Plant Morphogenesis Totipotency Analysis of Education and Technology (MIXT) gene expression net Research Projects in Riken Instituteswork in dif Education and Technology (MIXT)f Education and Technology (MIXT)erent Research Projects in Riken Institutesiat Research Projects in Riken Institutesion, genomics of de-dif Education and Technology (MIXT)f Education and Technology (MIXT)erent Research Projects in Riken Institutesiat Research Projects in Riken Institutesion, genomics of and t Research Projects in Riken Institutesr ansdif Education and Technology (MIXT)f Education and Technology (MIXT)erent Research Projects in Riken Institutesiat Research Projects in Riken Institutesion of Education and Technology (MIXT) plant Research Projects in Riken Institutes cells using Zi nnia t Research Projects in Riken Institutesransdif Education and Technology (MIXT)f Education and Technology (MIXT)erent Research Projects in Riken Institutesiat Research Projects in Riken Institutesion cult Research Projects in Riken Institutesure syst Research Projects in Riken Institutesem, genomics of Arabiopsis, genomics of Dedifferentiation Cytodifferentiation Cell Division Intracellular Gene Expression Communication Laborat Research Projects in Riken Institutesory f Education and Technology (MIXT)or St Research Projects in Riken Institutesruct Research Projects in Riken Institutesural Const Research Projects in Riken Institutesruct Research Projects in Riken Institutesion Network Team leader: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Ken Mat Research Projects in Riken Institutessuoka Analysis of Education and Technology (MIXT) int Research Projects in Riken Institutesracellular membrane syst Research Projects in Riken Institutes em and secret Research Projects in Riken Institutesory syst Research Projects in Riken Institutesem in plant Research Projects in Riken Institutes cells. and Riken PSC) Microarrays Reverse Genetics Genome Information Model Systems

Funct Research Projects in Riken Institutesion Cont Research Projects in Riken Institutesrol Research Projects in Riken Institutes Grou p Group direct Research Projects in Riken Institutesor: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Sh Projects in Riken Institutesigeo Yosh Projects in Riken Institutesida Laborat Research Projects in Riken Institutesory f Education and Technology (MIXT)or Growt Research Projects in Riken Institutesh Projects in Riken Institutes Regulat Research Projects in Riken Institutesio n Team leader: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Sh Projects in Riken Institutesigeo Yosh Projects in Riken Institutesida Laborat Research Projects in Riken Institutesory f Education and Technology (MIXT)or Bioch Projects in Riken Institutesemical Reso urce Team leader: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Tosh Projects in Riken Institutesiya Muranaka Environment Research Projects in Riken Institutesal Plant Research Projects in Riken Institutes Research Projects in Riken Institutes Group Group direct Research Projects in Riken Institutesor: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Isamu Yamaguch Projects in Riken Institutesi Laborat Research Projects in Riken Institutesory f Education and Technology (MIXT)or Remediat Research Projects in Riken Institutesion Research Projects in Riken Institutes Team leader: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Isamu Yamaguch Projects in Riken Institutesi Laborat Research Projects in Riken Institutesory f Education and Technology (MIXT)or Adapt Research Projects in Riken Institutesat Research Projects in Riken Institutesion and Resist Research Projects in Riken Institutesanc e Team leader: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Hirosh Projects in Riken Institutesi Hamamot Research Projects in Riken Instituteso Growth Physiology Group Group Direct Research Projects in Riken Institutesor: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Yuji Kamiya Time Break 1-1000 years Lab. for Cellular Growth & Development Team Leader: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Yuji Kamiya Gibberellin Biosynthesis and Signaling Regulat Research Projects in Riken Institutesion of Education and Technology (MIXT) Non-Mevalonat Research Projects in Riken Institutese Pat Research Projects in Riken Institutesh Projects in Riken Institutesway Development Research Projects in Riken Institutes of Education and Technology (MIXT) Seed Germinat Research Projects in Riken Institutesion Tech Projects in Riken Institutesnology

Seed Germination Gibberellin Seedling Dormancy Dormant Seed Shoot Growth Seed Development Life Cycle of Plants Lab. for Reproductive Growth Team Leader: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Eiji Nambara Flowering Regulation of Seed and Bud Dormancy Flower Development ABA Biosynthesis and Signaling Accumulation of Secondary Metabolites in Seed Abscisic Acid Germinating Seed Metabolic Function Research Group Innovative Research for Plant Cell Metabolic Engineering: Comprehensive Analysis of Signaling and Regulation of Inorganic Nutrient Assimilation and Primary Metabolisms

C Compart Research Projects in Riken Institutesment Research Projects in Riken Institutesat Research Projects in Riken Institutesion and Cross-t Research Projects in Riken Institutesalks of Education and Technology (MIXT) C, genomics of N, genomics of S met Research Projects in Riken Institutesabolisms Lab for Metabolic Compartmentation S Team Leader: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Hideki Takah Projects in Riken Institutesash Projects in Riken Institutesi Upt Research Projects in Riken Institutesake and Transport Research Projects in Riken Institutes of Education and Technology (MIXT) Nit Research Projects in Riken Institutesrat Research Projects in Riken Institutese, genomics of Ammonia and Sulf Education and Technology (MIXT)at Research Projects in Riken Institutese Cyt Research Projects in Riken Institutesokinin as a Signal Transducer of Education and Technology (MIXT) Nit Research Projects in Riken Institutesrogen St Research Projects in Riken Institutesat Research Projects in Riken Institutesus Group Direct Research Projects in Riken Institutesor: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Tomoyuki Yamaya (Toh Projects in Riken Institutesoku U. and Riken PSC) and Rik en PSC) CO2 Signal Transduct Research Projects in Riken Institutesion and Ge ne Expression Th Projects in Riken Institutesrough Projects in Riken Institutes TwoComponent Research Projects in Riken Institutes Syst Research Projects in Riken Institutesem N Lab for Communication

Mechanisms Cell-t Research Projects in Riken Instituteso-Cell & Organ-t Research Projects in Riken Instituteso-Organ Signals Team Leader: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Hit Research Projects in Riken Institutesosh Projects in Riken Institutesi Sakakibara SO42-, NO3-, NH4+ Towards Improvement of Metabolic Function and Crop Productivity RIKEN Genomic Sciences Center (GSC) Plant Functional Genomics Group Objectives Saturated mutagenesis of Arabidopsis T-DNA Tagging, genomics of Act Research Projects in Riken Institutesivat Research Projects in Riken Institutesion Tagging lines Ac/Ds transposon Tagging lines ot Research Projects in Riken Institutesh Projects in Riken Institutesers [email protected] Mutant phenotype and gene function analysis Mut Research Projects in Riken Institutesant Research Projects in Riken Institutes ph Projects in Riken Institutesenot Research Projects in Riken Institutesype analysis Gene knockout Research Projects in Riken Institutes lines and ident Research Projects in Riken Institutesif Education and Technology (MIXT)icat Research Projects in Riken Institutesion of Education and Technology (MIXT) corresponding genes Analyses of full-length cDNA

Invent Research Projects in Riken Institutesory of Education and Technology (MIXT) f Education and Technology (MIXT)ull-lengt Research Projects in Riken Institutesh Projects in Riken Institutes cDNAs Construction of full-length cDNA microarray St Research Projects in Riken Institutesruct Research Projects in Riken Institutesural and f Education and Technology (MIXT)unct Research Projects in Riken Institutesional analysis of Education and Technology (MIXT) plant Research Projects in Riken Institutes prot Research Projects in Riken Instituteseins h Projects in Riken Institutest Research Projects in Riken Institutest Research Projects in Riken Institutesp: Kiyotaka Okada (Kyoto Univ. and Riken PSC)//www. and Riken PSC)gsc. and Riken PSC)riken. and Riken PSC)go. and Riken PSC)j p/Plant Research Projects in Riken Institutes/index. and Riken PSC)h Projects in Riken Institutest Research Projects in Riken Institutesml Database of mutant candidates from T1 generation of RIKEN activation tagging lines Number of screened lines 40,000 lines Number of mutant candidates (adult morphology) 1262 lines Number of flanking sequences of 1065 sequences T-DNA Number of candidate genes 1923 loci [email protected] The category of phenotypes that was observed at T1 generation Rosette

Flower Plant hight pale green 61 dwarf 190 stigma dark green 70 semi-dwarf 276 petal ant Research Projects in Riken Institutesh Projects in Riken Institutesocyanin 18 tall large leaves 134 small leaves 207 no 11 pedicel

filament Caulin leaves 0 sepal long petiole 19 small 8 short petiole 28 large 46 epinast Research Projects in Riken Institutesic 203 many 36 hyponastic 12 shape 8 Good

shape 98 others 0 low round leaves 156 narrow leaves 144 many leaves 188 few leaves 18 others 42 Branching 0 bushy

133 16 hyper APD 16 5 f Education and Technology (MIXT)asiat Research Projects in Riken Institutesion 14 1 t Research Projects in Riken Institutesype of Education and Technology (MIXT) inf Education and Technology (MIXT)luorescenc e 3 sh Projects in Riken Institutesort Research Projects in Riken Institutes int Research Projects in Riken Institutesernode 25 long int Research Projects in Riken Institutesernode 45 13 Flowering Fertility sterile very early 6 early

217 late 164 very late never 2 21 31 1 9 Database constructed In collaboration with NEC Soft. Ltd. ([email protected]) Activation tag line insertion site map I II III IV V 6 5 4 V 3

IV 2 III 1 0 II I 0 5000000 10000000 15000000 20000000 25000000 30000000 RIKEN Genomic Sciences Center Plant Functional Genomics Group RIKEN

Bio Resources Center Ac/Ds transposon lines Activation tagging lines Full-length cDNAs http://www.brc.riken.go.jp/lab/epd/Eng/index.html Application of full-length cDNAs to functional genomics Gene annotation (Full-length cDNA Sequencing) Expression profile, Promoter analysis (Full-length cDNA microarray) Full-length cDNA Protein function (Biochemical analyses, Transgenic analyses) Protein structure (X-ray crystallography, NMR spectroscopy)

Table 1. Summary of 3-end single-pass sequencing of RAFL cDNA clones isolated from A. thaliana full-length cDNA libraries Seki et al. (2002) Science 296:141-145. Library No. Plant Materials Vector Standard/ Normalization Subtraction RAFL1 RAFL2 RAFL3 RAFL4 RAFL5 RAFL6 Cold-treated leaves and stems Rosette plants Dehydration-treated plants Zap Zap

Zap Zap Zap Zap RAFL7 RAFL8 RAFL9 Cold-treated plants RAFL11 RAFL12 RAFL13 RAFL14 RAFL15 RAFL16 RAFL17 RAFL18 RAFL19 RAFL21 Cold-treated plants Dehydration-treated plants Plants at various developmental stages and those treated with dehydration and cold

Dehydration-treated plants Plants at various developmental stages and those treated with dehydration and cold Plants at various developmental stages and those subjected to various stress (dry, cold, and NaCl) and ABA t Research Projects in Riken Institutesreat Research Projects in Riken Institutesment Research Projects in Riken Institutess. and Riken PSC) Plants grown under dark condit Research Projects in Riken Institutesions. and Riken PSC) Siliques. and Riken PSC) Cold-treated plants Dehydration-treated plants Roots Siliques and f Education and Technology (MIXT)lowers Dark-grown plants Dehydration-treated plants. Reh Projects in Riken Institutesydrat Research Projects in Riken Institutesion (Af Education and Technology (MIXT)t Research Projects in Riken Instituteser dry 10 hr)- h Projects in Riken Institutesr)treated plants. Cold-treated plants Siliques and f Education and Technology (MIXT)lowers Plants that are treated with various stress (heat and UV), hormones (ABA, genomics of auxin, genomics of et Research Projects in Riken Institutesh Projects in Riken Institutesylene, genomics of SA, genomics of JA, genomics of GA, genomics of and cyt Research Projects in Riken Institutesokinin) and BTH. and Riken PSC) No. of cDNA groups Standard

Standard Standard Standard Standard Standard No. of cDNA clones subjected to clustering 111 256 223 1029 2030 6139 FLC-1-B FLC-1-B FLC-1-B Standard Standard Standard 2591 2637 22929 751

584 3368 FLC-1-B Normalization 2242 339 FLC-1-E FLC-1-E FLC-1-E FLC-1-E FLC-1-E FLC-1-E Subtraction Subtraction Standard Standard Standard Subtraction 22 72 23302 13661

25466 14035 2 5 1371 816 1227 452 FLC-1-E FLC-1-E FLC-1-E Subtraction Subtraction Subtraction 1213 24951 12346 41 970 502 155,144 RAFL cDNA clones were clustered by mapping of the 3-end single-pass-sequencing data on the

genomic sequence. n.d. 130 115 862 1672 1461 >14,668 cDNA groups Identified genes:17,956 3,288 11,394 Predicted genes:26,285 predicted unidentified: 9,286 non2,437 predicted identified : 837 17,119 identified (16,999 predicted) RAFL cDNA

Report Research Projects in Riken Institutesed EST or cDNA genes: Kiyotaka Okada (Kyoto Univ. and Riken PSC)14, genomics of 668 genes (60 hr)-% of all predicted of Education and Technology (MIXT) all predict Research Projects in Riken Institutesed non-predicted identified: 837 genes) Seki et al. (2002) Science 296:141-145. Full-Lengt Research Projects in Riken Institutesh Projects in Riken Institutes cDNA Sequencing of Education and Technology (MIXT) RIKEN Arabidopsis Full-Lengt Research Projects in Riken Institutesh Projects in Riken Institutes cDNA (RAFL cDNA) 1. and Riken PSC) Collaborat Research Projects in Riken Institutesion wit Research Projects in Riken Institutesh Projects in Riken Institutes t Research Projects in Riken Institutesh Projects in Riken Institutese Arabidopsis SSP group of Education and Technology (MIXT) t Research Projects in Riken Institutesh Projects in Riken Institutese USA Salk Inst Research Projects in Riken Institutesit Research Projects in Riken Institutesut Research Projects in Riken Institutese (PI: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Dr. and Riken PSC) J. and Riken PSC)R. and Riken PSC) Ecker) St Research Projects in Riken Institutesanf Education and Technology (MIXT)ord Genome Tech Projects in Riken Institutesnology Cent Research Projects in Riken Instituteser (PI: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Dr. and Riken PSC) R. and Riken PSC)W. and Riken PSC) Davis) Plant Research Projects in Riken Institutes Gene Expression Cent Research Projects in Riken Instituteser (PI: Kiyotaka Okada (Kyoto Univ. and Riken PSC) Dr. and Riken PSC) A. and Riken PSC) Th Projects in Riken Instituteseologis) a. and Riken PSC) Full-lengt Research Projects in Riken Institutesh Projects in Riken Institutes cDNA sequences of Education and Technology (MIXT) 8, genomics of 554 RAFL cDNA clones were det Research Projects in Riken Institutesermined as of Education and Technology (MIXT) March Projects in Riken Institutes 25, genomics of 20 hr)-0 hr)-2. and Riken PSC) b. and Riken PSC) SSP and our groups are planning t Research Projects in Riken Instituteso do f Education and Technology (MIXT)ull-lengt Research Projects in Riken Institutesh Projects in Riken Institutes cDNA sequencing of Education and Technology (MIXT) ca. and Riken PSC) 12, genomics of 0 hr)-0 hr)-0 hr)- RAFL cDNA clones. and Riken PSC) 2. and Riken PSC) We are also planning t Research Projects in Riken Instituteso do f Education and Technology (MIXT)ull-lengt Research Projects in Riken Institutesh Projects in Riken Institutes cDNA sequencing of Education and Technology (MIXT) ca. and Riken PSC) 2, genomics of 0 hr)-0 hr)-0 hr)- RAFL cDNA clones. and Riken PSC) 3. and Riken PSC) Af Education and Technology (MIXT)t Research Projects in Riken Instituteser det Research Projects in Riken Instituteserminat Research Projects in Riken Institutesion of Education and Technology (MIXT) f Education and Technology (MIXT)ull-lengt Research Projects in Riken Institutesh Projects in Riken Institutes cDNA sequences, genomics of t Research Projects in Riken Institutesh Projects in Riken Institutese RAFL cDNA clones will be dist Research Projects in Riken Institutesribut Research Projects in Riken Institutesed f Education and Technology (MIXT)rom RIKEN Bioresource cent Research Projects in Riken Institutese and ABRC. and Riken PSC) Expression profiling using full-length cDNA microarray

(Ver.2) containing ca. 7,000 full-length cDNA clones 1. 2. 3. 4. Abiotic Stress (Drought, Cold, High-Salinity) Biotic Stress (Pathogen Attack, SA, JA) Light Conditions Mutants, Transgenic Plants Now, we are constructing a new full-length cDNA microarray (Ver. 3) containing ca. 15,000 full-length cDNA clones and will study expression profiles. tudies on functions and structures of proteins: Transgenic plants Construction of protein catalogs using wheat germ cell-free protein synthesis system (in collaboration with Dr. Endos group) X-ray crystallography and NMR spectroscopy (in collaboration with Dr. Yokoyamas group)

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