Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Science 31 October 2003:
Vol. 302. no. 5646, pp. 842 - 846
DOI: 10.1126/science.1088305
Prev | Table of Contents | Next

Research Articles

Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome

Kayoko Yamada,1* Jun Lim,2* Joseph M. Dale,1 Huaming Chen,2,3 Paul Shinn,2,3 Curtis J. Palm,4 Audrey M. Southwick,4 Hank C. Wu,1 Christopher Kim,2,3 Michelle Nguyen,4 Paul Pham,1 Rosa Cheuk,2,3 George Karlin-Newmann,4 Shirley X. Liu,1 Bao Lam,4 Hitomi Sakano,1 Troy Wu,4 Guixia Yu,1 Molly Miranda,4 Hong L. Quach,1 Matthew Tripp,4 Charlie H. Chang,1 Jeong M. Lee,1 Mitsue Toriumi,1 Marie M. H. Chan,1 Carolyn C. Tang,1 Courtney S. Onodera,1 Justine M. Deng,1 Kenji Akiyama,5 Yasser Ansari,2 Takahiro Arakawa,6 Jenny Banh,1 Fumika Banno,1 Leah Bowser,4 Shelise Brooks,3 Piero Carninci,6,7 Qimin Chao,3 Nathan Choy,2 Akiko Enju,5 Andrew D. Goldsmith,1 Mani Gurjal,4 Nancy F. Hansen,4 Yoshihide Hayashizaki,6,7 Chanda Johnson-Hopson,3 Vickie W. Hsuan,1 Kei Iida,5 Meagan Karnes,2 Shehnaz Khan,3 Eric Koesema,2 Junko Ishida,5 Paul X. Jiang,1 Ted Jones,4 Jun Kawai,6,7 Asako Kamiya,5 Cristina Meyers,2 Maiko Nakajima,5 Mari Narusaka,5 Motoaki Seki,5,8 Tetsuya Sakurai,5 Masakazu Satou,5 Racquel Tamse,4 Maria Vaysberg,1 Erika K. Wallender,1 Cecilia Wong,1 Yuki Yamamura,1 Shiaulou Yuan,1 Kazuo Shinozaki,5,8 Ronald W. Davis,4,9 Athanasios Theologis,1*{dagger} Joseph R. Ecker2,3*{dagger}

Functional analysis of a genome requires accurate gene structure information and a complete gene inventory. A dual experimental strategy was used to verify and correct the initial genome sequence annotation of the reference plant Arabidopsis. Sequencing full-length cDNAs and hybridizations using RNA populations from various tissues to a set of high-density oligonucleotide arrays spanning the entire genome allowed the accurate annotation of thousands of gene structures. We identified 5817 novel transcription units, including a substantial amount of antisense gene transcription, and 40 genes within the genetically defined centromeres. This approach resulted in completion of ~30% of the Arabidopsis ORFeome as a resource for global functional experimentation of the plant proteome.

1 Plant Gene Expression Center, Albany, CA 94710, USA.
2 Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
3 The Arabidopsis thaliana Genome Center, Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
4 Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA.
5 Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Tsukuba 305-0074, Japan.
6 Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, Wako 351-0198, Japan.
7 Laboratory for Genome Exploration Research Group, RIKEN GSC, Yokohama Institute, Kanagawa 230-0045, Japan.
8 Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, Tsukuba 305-0074, Japan.
9 Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.



* These authors contributed equally to this manuscript.

{dagger} To whom correspondence should be addressed. E-mail: theo{at}nature.berkeley.edu (A.T.) or ecker{at}salk.edu (J.R.E.)

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Establishing legitimacy and function in the new transcriptome.
H. van Bakel and T. R. Hughes (2009)
Brief Funct Genomic Proteomic 8, 424-436
   Abstract »    Full Text »    PDF »
Deletion-Based Reverse Genetics in Medicago truncatula.
C. Rogers, J. Wen, R. Chen, and G. Oldroyd (2009)
Plant Physiology 151, 1077-1086
   Abstract »    Full Text »    PDF »
The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.
J. W. Nicol, G. A. Helt, S. G. Blanchard Jr., A. Raja, and A. E. Loraine (2009)
Bioinformatics 25, 2730-2731
   Abstract »    Full Text »    PDF »
Arabidopsis thaliana T-DNA Mutants Implicate GAUT Genes in the Biosynthesis of Pectin and Xylan in Cell Walls and Seed Testa.
K. H. Caffall, S. Pattathil, S. E. Phillips, M. G. Hahn, and D. Mohnen (2009)
Mol Plant
   Abstract »    Full Text »    PDF »
Evolutionary and Expression Signatures of Pseudogenes in Arabidopsis and Rice.
C. Zou, M. D. Lehti-Shiu, F. Thibaud-Nissen, T. Prakash, C. R. Buell, and S.-H. Shiu (2009)
Plant Physiology 151, 3-15
   Abstract »    Full Text »    PDF »
Metabolomic Screening Applied to Rice FOX Arabidopsis Lines Leads to the Identification of a Gene-Changing Nitrogen Metabolism.
D. Albinsky, M. Kusano, M. Higuchi, N. Hayashi, M. Kobayashi, A. Fukushima, M. Mori, T. Ichikawa, K. Matsui, H. Kuroda, et al. (2009)
Mol Plant
   Abstract »    Full Text »    PDF »
Bell-like homeodomain selectively regulates the high-irradiance response of phytochrome A.
R. J. Staneloni, M. J. Rodriguez-Batiller, D. Legisa, M. R. Scarpin, A. Agalou, P. D. Cerdan, A. H. Meijer, P. B. F. Ouwerkerk, and J. J. Casal (2009)
PNAS 106, 13624-13629
   Abstract »    Full Text »    PDF »
Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression.
J. D. Hollister and B. S. Gaut (2009)
Genome Res. 19, 1419-1428
   Abstract »    Full Text »    PDF »
PosMed-plus: An Intelligent Search Engine that Inferentially Integrates Cross-Species Information Resources for Molecular Breeding of Plants.
Y. Makita, N. Kobayashi, Y. Mochizuki, Y. Yoshida, S. Asano, N. Heida, M. Deshpande, R. Bhatia, A. Matsushima, M. Ishii, et al. (2009)
Plant Cell Physiol. 50, 1249-1259
   Abstract »    Full Text »    PDF »
The Transcription Factor ABI4 Is a Regulator of Mitochondrial Retrograde Expression of ALTERNATIVE OXIDASE1a.
E. Giraud, O. Van Aken, L. H.M. Ho, and J. Whelan (2009)
Plant Physiology 150, 1286-1296
   Abstract »    Full Text »    PDF »
Evidence for Base Excision Repair of Oxidative DNA Damage in Chloroplasts of Arabidopsis thaliana.
B. L. Gutman and K. K. Niyogi (2009)
J. Biol. Chem. 284, 17006-17012
   Abstract »    Full Text »    PDF »
Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes.
P. A. Ziolkowski, G. Koczyk, L. Galganski, and J. Sadowski (2009)
Nucleic Acids Res. 37, 3189-3201
   Abstract »    Full Text »    PDF »
Analysis of Multiple Occurrences of Alternative Splicing Events in Arabidopsis thaliana Using Novel Sequenced Full-Length cDNAs.
K. Iida, K. Fukami-Kobayashi, A. Toyoda, Y. Sakaki, M. Kobayashi, M. Seki, and K. Shinozaki (2009)
DNA Res 16, 155-164
   Abstract »    Full Text »    PDF »
Transcriptionally active gene fragments derived from potentially fast-evolving donor genes in the rice genome.
X. Wang, Z. Yu, X. Yang, X.-W. Deng, and L. Li (2009)
Bioinformatics 25, 1215-1218
   Abstract »    Full Text »    PDF »
A Collection of Ds Insertional Mutants Associated With Defects in Male Gametophyte Development and Function in Arabidopsis thaliana.
L. C. Boavida, B. Shuai, H.-J. Yu, G. C. Pagnussat, V. Sundaresan, and S. McCormick (2009)
Genetics 181, 1369-1385
   Abstract »    Full Text »    PDF »
Peroxisome-associated matrix protein degradation in Arabidopsis.
M. J. Lingard, M. Monroe-Augustus, and B. Bartel (2009)
PNAS 106, 4561-4566
   Abstract »    Full Text »    PDF »
Isolation and Characterization of cul1-7, a Recessive Allele of CULLIN1 That Disrupts SCF Function at the C Terminus of CUL1 in Arabidopsis thaliana.
J. Gilkerson, J. Hu, J. Brown, A. Jones, T.-p. Sun, and J. Callis (2009)
Genetics 181, 945-963
   Abstract »    Full Text »    PDF »
Highly Diversified Molecular Evolution of Downstream Transcription Start Sites in Rice and Arabidopsis.
T. Tanaka, K. O. Koyanagi, and T. Itoh (2009)
Plant Physiology 149, 1316-1324
   Abstract »    Full Text »    PDF »
Substrates Related to Chromatin and to RNA-Dependent Processes Are Modified by Arabidopsis SUMO Isoforms That Differ in a Conserved Residue with Influence on Desumoylation.
R. Budhiraja, R. Hermkes, S. Muller, J. Schmidt, T. Colby, K. Panigrahi, G. Coupland, and A. Bachmair (2009)
Plant Physiology 149, 1529-1540
   Abstract »    Full Text »    PDF »
Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis.
Y. Kurihara, A. Matsui, K. Hanada, M. Kawashima, J. Ishida, T. Morosawa, M. Tanaka, E. Kaminuma, Y. Mochizuki, A. Matsushima, et al. (2009)
PNAS 106, 2453-2458
   Abstract »    Full Text »    PDF »
Interplay between ethylene, ETP1/ETP2 F-box proteins, and degradation of EIN2 triggers ethylene responses in Arabidopsis.
H. Qiao, K. N. Chang, J. Yazaki, and J. R. Ecker (2009)
Genes & Dev. 23, 512-521
   Abstract »    Full Text »    PDF »
rasiRNA pathway controls antisense expression of Drosophila telomeric retrotransposons in the nucleus.
S. Shpiz, D. Kwon, Y. Rozovsky, and A. Kalmykova (2009)
Nucleic Acids Res. 37, 268-278
   Abstract »    Full Text »    PDF »
Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa.
X. Zhou, R. Sunkar, H. Jin, J.-K. Zhu, and W. Zhang (2009)
Genome Res. 19, 70-78
   Abstract »    Full Text »    PDF »
Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses.
B. Ben Amor, S. Wirth, F. Merchan, P. Laporte, Y. d'Aubenton-Carafa, J. Hirsch, A. Maizel, A. Mallory, A. Lucas, J. M. Deragon, et al. (2009)
Genome Res. 19, 57-69
   Abstract »    Full Text »    PDF »
Sequencing and Analysis of Approximately 40 000 Soybean cDNA Clones from a Full-Length-Enriched cDNA Library.
T. Umezawa, T. Sakurai, Y. Totoki, A. Toyoda, M. Seki, A. Ishiwata, K. Akiyama, A. Kurotani, T. Yoshida, K. Mochida, et al. (2008)
DNA Res 15, 333-346
   Abstract »    Full Text »    PDF »
Arabidopsis thaliana class II poly(A)-binding proteins are required for efficient multiplication of turnip mosaic virus.
P. J. Dufresne, E. Ubalijoro, M. G. Fortin, and J.-F. Laliberte (2008)
J. Gen. Virol. 89, 2339-2348
   Abstract »    Full Text »    PDF »
Integration of Cytological Features with Molecular and Epigenetic Properties of Rice Chromosome 4.
B.-L. Yin, L. Guo, D.-F. Zhang, W. Terzaghi, X.-F. Wang, T.-T. Liu, H. He, Z.-K. Cheng, and X. W. Deng (2008)
Mol Plant 1, 816-829
   Abstract »    Full Text »    PDF »
Enhanced Tolerance to Oxidative Stress in Transgenic Arabidopsis Plants Expressing Proteins of Unknown Function.
S. Luhua, S. Ciftci-Yilmaz, J. Harper, J. Cushman, and R. Mittler (2008)
Plant Physiology 148, 280-292
   Abstract »    Full Text »    PDF »
Functional Characterization of the Arabidopsis AtSUC2 Sucrose/H+ Symporter by Tissue-Specific Complementation Reveals an Essential Role in Phloem Loading But Not in Long-Distance Transport.
A. C. Srivastava, S. Ganesan, I. O. Ismail, and B. G. Ayre (2008)
Plant Physiology 148, 200-211
   Abstract »    Full Text »    PDF »
Genome Structure of the Legume, Lotus japonicus.
S. Sato, Y. Nakamura, T. Kaneko, E. Asamizu, T. Kato, M. Nakao, S. Sasamoto, A. Watanabe, A. Ono, K. Kawashima, et al. (2008)
DNA Res 15, 227-239
   Abstract »    Full Text »    PDF »
Arabidopsis Transcriptome Analysis under Drought, Cold, High-Salinity and ABA Treatment Conditions using a Tiling Array.
A. Matsui, J. Ishida, T. Morosawa, Y. Mochizuki, E. Kaminuma, T. A. Endo, M. Okamoto, E. Nambara, M. Nakajima, M. Kawashima, et al. (2008)
Plant Cell Physiol. 49, 1135-1149
   Abstract »    Full Text »    PDF »
Identification of Regulatory Pathways Controlling Gene Expression of Stress-Responsive Mitochondrial Proteins in Arabidopsis.
L. H.M. Ho, E. Giraud, V. Uggalla, R. Lister, R. Clifton, A. Glen, D. Thirkettle-Watts, O. Van Aken, and J. Whelan (2008)
Plant Physiology 147, 1858-1873
   Abstract »    Full Text »    PDF »
A Second GDP-L-galactose Phosphorylase in Arabidopsis en Route to Vitamin C: COVALENT INTERMEDIATE AND SUBSTRATE REQUIREMENTS FOR THE CONSERVED REACTION.
C. L. Linster, L. N. Adler, K. Webb, K. C. Christensen, C. Brenner, and S. G. Clarke (2008)
J. Biol. Chem. 283, 18483-18492
   Abstract »    Full Text »    PDF »
Comparative expression analysis uncovers novel features of endogenous antisense transcription.
Y. Okada, C. Tashiro, K. Numata, K. Watanabe, H. Nakaoka, N. Yamamoto, K. Okubo, R. Ikeda, R. Saito, A. Kanai, et al. (2008)
Hum. Mol. Genet. 17, 1631-1640
   Abstract »    Full Text »    PDF »
Knocking Out Cytosolic Cysteine Synthesis Compromises the Antioxidant Capacity of the Cytosol to Maintain Discrete Concentrations of Hydrogen Peroxide in Arabidopsis.
M. C. Lopez-Martin, M. Becana, L. C. Romero, and C. Gotor (2008)
Plant Physiology 147, 562-572
   Abstract »    Full Text »    PDF »
Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics.
K. Baerenfaller, J. Grossmann, M. A. Grobei, R. Hull, M. Hirsch-Hoffmann, S. Yalovsky, P. Zimmermann, U. Grossniklaus, W. Gruissem, and S. Baginsky (2008)
Science 320, 938-941
   Abstract »    Full Text »    PDF »
Alternative Splicing at NAGNAG Acceptor Sites Shares Common Properties in Land Plants and Mammals.
K. Iida, M. Shionyu, and Y. Suso (2008)
Mol. Biol. Evol. 25, 709-718
   Abstract »    Full Text »    PDF »
The Arabidopsis Information Resource (TAIR): gene structure and function annotation.
D. Swarbreck, C. Wilks, P. Lamesch, T. Z. Berardini, M. Garcia-Hernandez, H. Foerster, D. Li, T. Meyer, R. Muller, L. Ploetz, et al. (2008)
Nucleic Acids Res. 36, D1009-D1014
   Abstract »    Full Text »    PDF »
Transcript Profiling by 3'-Untranslated Region Sequencing Resolves Expression of Gene Families.
A. L. Eveland, D. R. McCarty, and K. E. Koch (2008)
Plant Physiology 146, 32-44
   Abstract »    Full Text »    PDF »
Transcriptomics resources for functional genomics.
J. Kawai, P. Carninci, and Y. Hayashizaki (2007)
Brief Funct Genomic Proteomic
   Abstract »    Full Text »    PDF »
Cell-Fate Switch of Synergid to Egg Cell in Arabidopsis eostre Mutant Embryo Sacs Arises from Misexpression of the BEL1-Like Homeodomain Gene BLH1.
G. C. Pagnussat, H.-J. Yu, and V. Sundaresan (2007)
PLANT CELL 19, 3578-3592
   Abstract »    Full Text »    PDF »
Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D.
F. Perocchi, Z. Xu, S. Clauder-Munster, and L. M. Steinmetz (2007)
Nucleic Acids Res. 35, e128
   Abstract »    Full Text »    PDF »
Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray.
H. He, J. Wang, T. Liu, X. S. Liu, T. Li, Y. Wang, Z. Qian, H. Zheng, X. Zhu, T. Wu, et al. (2007)
Genome Res. 17, 1471-1477
   Abstract »    Full Text »    PDF »
Differential Expression of Genes Important for Adaptation in Capsella bursa-pastoris (Brassicaceae).
T. Slotte, K. Holm, L. M. McIntyre, U. Lagercrantz, and M. Lascoux (2007)
Plant Physiology 145, 160-173
   Abstract »    Full Text »    PDF »
The phosphatase laforin crosses evolutionary boundaries and links carbohydrate metabolism to neuronal disease.
M. S. Gentry, R. H. Dowen III, C. A. Worby, S. Mattoo, J. R. Ecker, and J. E. Dixon (2007)
J. Cell Biol. 178, 477-488
   Abstract »    Full Text »    PDF »
Distinct Expression Patterns of Natural Antisense Transcripts in Arabidopsis.
S. R. Henz, J. S. Cumbie, K. D. Kasschau, J. U. Lohmann, J. C. Carrington, D. Weigel, and M. Schmid (2007)
Plant Physiology 144, 1247-1255
   Abstract »    Full Text »    PDF »
Arabidopsis VTC2 Encodes a GDP-L-Galactose Phosphorylase, the Last Unknown Enzyme in the Smirnoff-Wheeler Pathway to Ascorbic Acid in Plants.
C. L. Linster, T. A. Gomez, K. C. Christensen, L. N. Adler, B. D. Young, C. Brenner, and S. G. Clarke (2007)
J. Biol. Chem. 282, 18879-18885
   Abstract »    Full Text »    PDF »
The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci.
J. S. Rozowsky, D. Newburger, F. Sayward, J. Wu, G. Jordan, J. O. Korbel, U. Nagalakshmi, J. Yang, D. Zheng, R. Guigo, et al. (2007)
Genome Res. 17, 732-745
   Abstract »    Full Text »    PDF »
Mutation of E1-CONJUGATING ENZYME-RELATED1 Decreases RELATED TO UBIQUITIN Conjugation and Alters Auxin Response and Development.
A. W. Woodward, S. E. Ratzel, E. E. Woodward, Y. Shamoo, and B. Bartel (2007)
Plant Physiology 144, 976-987
   Abstract »    Full Text »    PDF »
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs.
J. Ponjavic, C. P. Ponting, and G. Lunter (2007)
Genome Res. 17, 556-565
   Abstract »    Full Text »    PDF »
A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection.
K. Hanada, X. Zhang, J. O. Borevitz, W.-H. Li, and S.-H. Shiu (2007)
Genome Res. 17, 632-640
   Abstract »    Full Text »    PDF »
Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays.
S. C. Popescu, G. V. Popescu, S. Bachan, Z. Zhang, M. Seay, M. Gerstein, M. Snyder, and S. P. Dinesh-Kumar (2007)
PNAS 104, 4730-4735
   Abstract »    Full Text »    PDF »
PIC1, an Ancient Permease in Arabidopsis Chloroplasts, Mediates Iron Transport.
D. Duy, G. Wanner, A. R. Meda, N. von Wiren, J. Soll, and K. Philippar (2007)
PLANT CELL 19, 986-1006
   Abstract »    Full Text »    PDF »
Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of Development.
J. Lee, K. He, V. Stolc, H. Lee, P. Figueroa, Y. Gao, W. Tongprasit, H. Zhao, I. Lee, and X. W. Deng (2007)
PLANT CELL 19, 731-749
   Abstract »    Full Text »    PDF »
Arabidopsis intragenomic conserved noncoding sequence.
B. C. Thomas, L. Rapaka, E. Lyons, B. Pedersen, and M. Freeling (2007)
PNAS 104, 3348-3353
   Abstract »    Full Text »    PDF »
Small RNA-mediated chromatin silencing directed to the 3' region of the Arabidopsis gene encoding the developmental regulator, FLC.
S. Swiezewski, P. Crevillen, F. Liu, J. R. Ecker, A. Jerzmanowski, and C. Dean (2007)
PNAS 104, 3633-3638
   Abstract »    Full Text »    PDF »
Profile of Joseph R. Ecker.
B. P. Trivedi (2007)
PNAS 104, 3023-3025
   Full Text »    PDF »
Protein Domain-Domain Interactions and Requirements for the Negative Regulation of Arabidopsis CDC48/p97 by the Plant Ubiquitin Regulatory X (UBX) Domain-containing Protein, PUX1.
S. Park, D. M. Rancour, and S. Y. Bednarek (2007)
J. Biol. Chem. 282, 5217-5224
   Abstract »    Full Text »    PDF »
GEK1, a gene product of Arabidopsis thaliana involved in ethanol tolerance, is a D-aminoacyl-tRNA deacylase.
S. Wydau, M.-L. Ferri-Fioni, S. Blanquet, and P. Plateau (2007)
Nucleic Acids Res. 35, 930-938
   Abstract »    Full Text »    PDF »
A Conserved Carboxylesterase Is a SUPPRESSOR OF AVRBST-ELICITED RESISTANCE in Arabidopsis.
S. Cunnac, A. Wilson, J. Nuwer, A. Kirik, G. Baranage, and M. B. Mudgett (2007)
PLANT CELL 19, 688-705
   Abstract »    Full Text »    PDF »
Transcriptional Profiling of the Arabidopsis Embryo.
M. W.B. Spencer, S. A. Casson, and K. Lindsey (2007)
Plant Physiology 143, 924-940
   Abstract »    Full Text »    PDF »
High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing.
K. Juneau, C. Palm, M. Miranda, and R. W. Davis (2007)
PNAS 104, 1522-1527
   Abstract »    Full Text »    PDF »
The proteomics of plant cell membranes.
S. Komatsu, H. Konishi, and M. Hashimoto (2007)
J. Exp. Bot. 58, 103-112
   Abstract »    Full Text »    PDF »
The blossoming of RNA biology: Novel insights from plant systems.
J. Bove, C. L.H. Hord, and M. A. Mullen (2006)
RNA 12, 2035-2046
   Full Text »    PDF »
RNA editing in Drosophila melanogaster: New targets and functional consequences.
M. Stapleton, J. W. Carlson, and S. E. Celniker (2006)
RNA 12, 1922-1932
   Abstract »    Full Text »    PDF »
Testing for Effects of Recombination Rate on Nucleotide Diversity in Natural Populations of Arabidopsis lyrata.
S. I. Wright, J. P. Foxe, L. DeRose-Wilson, A. Kawabe, M. Looseley, B. S. Gaut, and D. Charlesworth (2006)
Genetics 174, 1421-1430
   Abstract »    Full Text »    PDF »
CER4 Encodes an Alcohol-Forming Fatty Acyl-Coenzyme A Reductase Involved in Cuticular Wax Production in Arabidopsis.
O. Rowland, H. Zheng, S. R. Hepworth, P. Lam, R. Jetter, and L. Kunst (2006)
Plant Physiology 142, 866-877
   Abstract »    Full Text »    PDF »
The Arabidopsis Unannotated Secreted Peptide Database, a Resource for Plant Peptidomics.
K. A. Lease and J. C. Walker (2006)
Plant Physiology 142, 831-838
   Abstract »    Full Text »    PDF »
Signatures of adaptive evolution within human non-coding sequence.
C. P. Ponting and G. Lunter (2006)
Hum. Mol. Genet. 15, R170-R175
   Abstract »    Full Text »    PDF »
Morphological and molecular phylogenetic context of the angiosperms: contrasting the 'top-down' and 'bottom-up' approaches used to infer the likely characteristics of the first flowers.
R. M. Bateman, J. Hilton, and P. J. Rudall (2006)
J. Exp. Bot. 57, 3471-3503
   Abstract »    Full Text »    PDF »
Ribosomal DNA in the Grasshopper Podisma pedestris: Escape From Concerted Evolution.
I. Keller, I. C. Chintauan-Marquier, P. Veltsos, and R. A. Nichols (2006)
Genetics 174, 863-874
   Abstract »    Full Text »    PDF »
Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3.
G. Wu and R. S. Poethig (2006)
Development 133, 3539-3547
   Abstract »    Full Text »    PDF »
Inaugural Article: ETHYLENE-INSENSITIVE5 encodes a 5'->3' exoribonuclease required for regulation of the EIN3-targeting F-box proteins EBF1/2.
G. Olmedo, H. Guo, B. D. Gregory, S. D. Nourizadeh, L. Aguilar-Henonin, H. Li, F. An, P. Guzman, and J. R. Ecker (2006)
PNAS 103, 13286-13293
   Abstract »    Full Text »    PDF »
Unraveling the dynamic transcriptome..
S. M. Brady, T. A. Long, and P. N. Benfey (2006)
PLANT CELL 18, 2101-2111
   Full Text »    PDF »
Transcript mapping with high-density oligonucleotide tiling arrays.
W. Huber, J. Toedling, and L. M. Steinmetz (2006)
Bioinformatics 22, 1963-1970
   Abstract »    Full Text »    PDF »
A Versatile and Reliable Two-Component System for Tissue-Specific Gene Induction in Arabidopsis.
L. Brand, M. Horler, E. Nuesch, S. Vassalli, P. Barrell, W. Yang, R. A. Jefferson, U. Grossniklaus, and M. D. Curtis (2006)
Plant Physiology 141, 1194-1204
   Abstract »    Full Text »    PDF »
Cytosolic Triacylglycerol Biosynthetic Pathway in Oilseeds. Molecular Cloning and Expression of Peanut Cytosolic Diacylglycerol Acyltransferase.
S. Saha, B. Enugutti, S. Rajakumari, and R. Rajasekharan (2006)
Plant Physiology 141, 1533-1543
   Abstract »    Full Text »    PDF »
Identification of Genes with Potential Roles in Apple Fruit Development and Biochemistry through Large-Scale Statistical Analysis of Expressed Sequence Tags.
S. Park, N. Sugimoto, M. D. Larson, R. Beaudry, and S. van Nocker (2006)
Plant Physiology 141, 811-824
   Abstract »    Full Text »    PDF »
STABILIZED1, a Stress-Upregulated Nuclear Protein, Is Required for Pre-mRNA Splicing, mRNA Turnover, and Stress Tolerance in Arabidopsis.
B.-h. Lee, A. Kapoor, J. Zhu, and J.-K. Zhu (2006)
PLANT CELL 18, 1736-1749
   Abstract »    Full Text »    PDF »
MicroRNA-Targeted and Small Interfering RNA-Mediated mRNA Degradation Is Regulated by Argonaute, Dicer, and RNA-Dependent RNA Polymerase in Arabidopsis.
M. Ronemus, M. W. Vaughn, and R. A. Martienssen (2006)
PLANT CELL 18, 1559-1574
   Abstract »    Full Text »    PDF »
The Arabidopsis thaliana MND1 homologue plays a key role in meiotic homologous pairing, synapsis and recombination.
C. Kerzendorfer, J. Vignard, A. Pedrosa-Harand, T. Siwiec, S. Akimcheva, S. Jolivet, R. Sablowski, S. Armstrong, D. Schweizer, R. Mercier, et al. (2006)
J. Cell Sci. 119, 2486-2496
   Abstract »    Full Text »    PDF »
Transposon-Mediated Expansion and Diversification of a Family of ULP-like Genes.
D. R. Hoen, K. C. Park, N. Elrouby, Z. Yu, N. Mohabir, R. K. Cowan, and T. E. Bureau (2006)
Mol. Biol. Evol. 23, 1254-1268
   Abstract »    Full Text »    PDF »
Highly Specific Gene Silencing by Artificial MicroRNAs in Arabidopsis.
R. Schwab, S. Ossowski, M. Riester, N. Warthmann, and D. Weigel (2006)
PLANT CELL 18, 1121-1133
   Abstract »    Full Text »    PDF »
A high-resolution map of transcription in the yeast genome.
L. David, W. Huber, M. Granovskaia, J. Toedling, C. J. Palm, L. Bofkin, T. Jones, R. W. Davis, and L. M. Steinmetz (2006)
PNAS 103, 5320-5325
   Abstract »    Full Text »    PDF »
Relaxed transcription in Arabidopsis mitochondria is counterbalanced by RNA stability control mediated by polyadenylation and polynucleotide phosphorylase..
S. Holec, H. Lange, K. Kuhn, M. Alioua, T. Borner, and D. Gagliardi (2006)
Mol. Cell. Biol. 26, 2869-2876
   Abstract »    Full Text »    PDF »
Arabidopsis thaliana proteomics: from proteome to genome.
S. Baginsky and W. Gruissem (2006)
J. Exp. Bot. 57, 1485-1491
   Abstract »    Full Text »    PDF »
Role of the SPIRAL1 Gene Family in Anisotropic Growth of Arabidopsis thaliana.
K. Nakajima, T. Kawamura, and T. Hashimoto (2006)
Plant Cell Physiol. 47, 513-522
   Abstract »    Full Text »    PDF »
Characterization of 43 Non-Protein-Coding mRNA Genes in Arabidopsis, Including the MIR162a-Derived Transcripts.
J. Hirsch, V. Lefort, M. Vankersschaver, A. Boualem, A. Lucas, C. Thermes, Y. d'Aubenton-Carafa, and M. Crespi (2006)
Plant Physiology 140, 1192-1204
   Abstract »    Full Text »    PDF »


To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)