title: Expression data from trichomes and pavement cells

status: Public on Dec 11 2010

city: Golm

first: Berit

last: Ebert

address: Am Mühlenberg 1

department: Willmitzer

institute: Max-Planck Institute of Molecular Plant Physiology

summary: Comparison of cell sap from trichomes and pavement cells.  We performed a detailed transcriptome analysis of cell sap from leaf epidermal cell types using the Affymetrix Ath1 chip.

overall_design: Trichome and pavement cell sap was collected from leaves of 5 week old plants.

first: Daniela

last: Zoeller

first: Carsten

last: Rautengarten

first: Marc

last: Jakoby

first: Arp

last: Schnittger

first: Annette

last: Niehl

first: Joachim

last: Fisahn


title: The association between gene expression and whole genome histone H3K4 mono-, di, and trimethylation

status: Public on Dec 07 2010

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

country: USA

institute: University of Nebraska-Lincoln

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: GENE-counter, a computational and statistical pipeline for assessing RNA-Seq data for genome-wide expression differences

status: Public on Dec 03 2010

city: Corvallis

first: Jeff

last: Chang

state: Oregon

address: 3097 Cordley Hall

institute: Oregon State University

summary:
RNA-Sequencing is a transformative method that captures the quantitative dynamics of a transcriptome with exquisite sensitivity and single-base resolution. There are, however, few computational pipelines for RNA-Seq with statistical tests that evince sufficient robustness and power as demanded by the difficult combination of small sample sizes and high variability in sequence read counts. To this end, we developed GENE-counter, a complete software pipeline for analyzing RNA-Seq data for genome-wide expression differences between replicated treatment groups. One important component of GENE-counter is a statistical test based on the NBP parameterization of the negative binomial distribution for identifying differentially expressed genome features. We used GENE-counter to analyze RNA-Seq data derived from Arabidopsis thaliana infected with a strain of defense-eliciting bacteria. We identified 308 genes that were differentially induced. Using alternative methods, we provided support for the induced expression and biological relevance of a substantial proportion of the genes. These results suggest the NBP parameterization of the negative binomial distribution is well suited for explaining RNA-Seq data and the statistical test makes GENE-counter a powerful pipeline for studying genome-wide expression changes. GENE-counter is freely available at http://changlab.cgrb.oregonstate.edu/.
Our RNA-seq data is uploaded on the NCBI short read archive (SRA) under the SRA025952.

overall_design: 6 samples total.  Two treatments with three biological replicates each. MgCl2 is the mock treatment, and hrcC is the experimental treatment.

first: Jason

middle: S

last: Cumbie

first: Jeffrey

middle: A

last: Kimbrel

first: Yanming

last: Di

first: Daniel

middle: W

last: Schafer

first: Larry

middle: J

last: Wilhelm

first: Samuel

middle: E

last: Fox

first: Christopher

middle: M

last: Sullivan

first: Aron

middle: D

last: Curzon

first: James

middle: C

last: Carrington

first: Todd

last: Mockler

middle: H


title: Expression data from 5-week-old Arabidopsis

status: Public on Dec 20 2010

city: Toledo

first: Scott

last: Leisner

state: OH

address: 2801 West Bancroft Street

department: Biological Sciences

institute: University of Toledo

summary: AGO4 plays an important role in RNA-directed DNA methylation (RdDM). RdDM on specific genomic loci have the potential to silence the nearby protein coding gene. We used wild-type La-er and ago4-1 mutant Arabidopsis to identify AGO4-regulated genes.

overall_design: Five-weeks wild-type and ago4-1 mutant RNA were used for Affymetrix microarrays. Differentially expressed genes were identified to study the role of AGO4 in regulating plant development.

first: Jie

last: He

last: S. Shepard

first: Alexei

last: Fedorov


title: expression data of WT and ced1 under osmotic stress

status: Public on Dec 08 2010

city: Thuwal

first: zhenyu

last: wang

address: PSGC

country: Saudi Arabia

institute: KAUST

summary:
ced1 mutant has reduced expression of NCED3  in response to osmotic stress (polyethylene glycol) treatments compared to the wild type.  Other ABA biosynthesis genes are also greatly reduced in ced1 under osmotic stress.
We used microarrays to detail the global programme of gene expression under osmotic stress treatment and identified distinct classes of up/down-regulated genes in the stress pathway.

overall_design: Arabidopsis seedlings were selected at 16 days with 6hr PEG treatment for RNA extraction and hybridization on Affymetrix microarrays. From Norther data we have known some of well-known stress responsive gene were significantly changed. We sought to obtain whole gene expression to analysis which genes were affected in the osmotic stress pathway.

first: Zhenyu

last: Wang

first: Jiankang

last: Zhu


title: Transcript profiling of Arabidopsis albino msh1 mutants

status: Public on Nov 29 2011

first: Ying-Zhi

last: Xu

address: 1901 Vine St.

department: Center for Plant Science Innovation

institute: University of Nebraska

summary: The soybean msh1 RNAi transgenic line show various growth phenotype. We use microarray analysis to characterize gene expression pattern for two of the phenotypes - variegation and stunted growth.

overall_design: Wild type and Arabidopsis msh1 mutant albino tissues were collected for RNA extration and hybridization on Affymetrix.

first: Sally

last: Mackenzie


title: The association between gene expression and whole genome histone H3K4 mono-, di, and trimethylation: expression data

first: Jean-Jack

last: Riethoven

summary:
These microarrays are part of a study where a comparison was made between the change in transcription and H3K4 mono-, di-, and tri-methylation levels (via ChIP-seq) in the Arabidopsis thaliana genome when plants are subjected to water deficit stress. Water deficit stress causes a large number of genes to change their transcript levels, which provided a large set of genes to examine for corresponding chromatine changes.

Keywords: stress response

overall_design: Arabidopsis thaliana RNA was isolated from control (watered) and treatment (water-deficit) samples for analysis on microarrays with three biological reps.

first: Karin

last: van Dijk

first: Jingyi

last: Yang

first: Peter

last: Laczko

first: Han

last: Chen

first: Yuannan

last: Xia

first: Istvan

last: Ladunga

first: Michael

last: Fromm


title: Transcriptome analysis of CAX1/CAX3 double mutants

status: Public on Oct 20 2010

city: Glen Osmond

first: Ute

last: Baumann

state: SA

address: Hartley Grove

department: Australian Centre for Plant Functional Genomics

country: Australia

institute: University of Adelaide

summary: As part of a larger study on Cell-specific vacuolar calcium compartmentation regulates apoplastic calcium concentration, gas exchange and plant productivity we compared the transcriptome of 40day old CAX1/CAX3 double mutants to Col-0 wildtype plants.

overall_design: comparative: mutant versus wild-type

first: Simon

last: Conn

first: Matthew

last: Gilliham

first: Kendal

last: Hirschi

first: Ning-Hui

last: Cheng


title: Identification of ORS1 target genes using inducible overexpression system

status: Public on Dec 01 2010

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

country: Germany

institute: MPIMP

summary:
The aim was to identify early target genes of the senescence-associated transcription factor: ORS1. For this purpose we used DEX-inducible system and studied the expression profile 5h after treatment using Affymetrix microarray.

Keywords: genetic modification

overall_design: Arabidopsis  46 day-old transgenic plants (Arabidopsis C24 background, inducible overexpression)  were sprayed with 30µM  DEX for 5h. As control mock (0.05% ethanol) treated  ORS1-inducible over-expression plants were used. Whole rosettes were harvested 5h after induction and used for expression profiling using Affymetrix near-full genome ATH1 arrays. Experiment performed in two biological replications.

first: Bernd

last: Mueller-Roeber


title: Expression data from Arabidopsis thaliana PHR1 primary targets genes under phosphate starvation stress

status: Public on Dec 09 2010

city: Campus de Cantoblanco

first: Regla

last: Bustos

state: Madrid

address: Darwin 3

country: Spain

institute: CNB-CSIC

summary: We performed a transcriptomic analysis of Pi starvation responses in Arabidopsis thaliana (Columbia-0) phr1 mutant plants expressing PHR1 in presence of cicloheximide, that inhibit protein translation, thus preventing any effect of PHR1 on the expression of indirect targets. Results show the primary target genes of PHR1 in the responses to Pi starvation.

overall_design: The analysis was performed in phr1 plants and phr1 plants overexpressing a fusion GR:PHR1 (OXGR:PHR1) whose activity is postranslationally controlled by dexamethasone (DEX), that allows studying gene expression upon PHR1 activation and the concomitant inhibition of translation with cycloheximide (CHX), thus preventing any effect of PHR1 on the expression of indirect targets. To perform this study, phr1 and OXGR:PHR1 phr1 plants were grown for seven days in complete Johnson liquid media (+Pi), 2 days in Pi-lacking media (-Pi) and then supplemented with 5 µM DEX and 10 µM CHX for 6 hours before harvesting. Three independent biological samples of total RNA from shoot and root were hybridized separately.

first: Gabriel

last: Castrillo

first: Javier

last: Paz-Ares


title: Expression analysis of the response to wild-type and pye-1 mutants to iron sufficient or iron deficient conditions

status: Public on Oct 12 2010

city: Durham

first: Terri

middle: Anita

last: Long

state: NC

department: Biology

institute: Duke University

summary:
Transcriptional profile of whole roots of wild-type and pye-1 mutants exposed to 24 hours -Fe were generated
Global population increases and climate change underscore the need for better comprehension of how plants acquire and process nutrients such as iron. A systems biology approach was taken to elucidate novel regulatory mechanisms involved in plant responses to iron deficiency (-Fe). Using cell-type specific transcriptional profiling we identified a pericycle-specific iron deficiency response, and a previously uncharacterized transcription factor, POPEYE (PYE), that plays an important role in this response. Functional analysis of PYE suggests that it positively regulates growth and development under iron deficient conditions. ChIP-on-chip analysis and transcriptional profiling reveal that PYE helps maintain iron homeostasis by directly and indirectly regulating the expression of ferric reductases, metal ion transporters, iron storage proteins, and other key iron homeostasis genes. In addition to PYE, we also identified a second protein BRUTUS (BTS), which appears to negatively regulate the response to iron deficiency. BTS is a unique putative E3 ligase protein, with metal ion binding and DNA binding domains. PYE and BTS are tightly co-regulated and physically interact with PYE paralogs, one of which is thought to positively regulate expression of genes involved in iron homeostasis. We propose that iron content is sensed within the pericycle where PYE, perhaps in conjunction with BTS and other regulatory proteins, is then activated to control a regulatory network involved in maintaining proper iron distribution in plants.

Keywords: Expression analysis

overall_design: To determine how loss of PYE expression affects the transcriptional profile of whole roots, pye-1 mutants and wild-type seeds were germinated under standard growth conditions then transferred to standard media (control, MS media) or iron deficient media (-Fe, 0.3mM Ferrozine in MS media containing no ferrous sulfate). After 24 hours of exposure to +Fe or -Fe whole roots were collected and analyzed.

first: Philip

middle: N

last: Benfey


title: wt and opr3 control and systemic wounding

city: Rehovot

first: Robert

last: Fluhr

department: Plant Sciences

country: Israel

institute: Weizmann Institute of Science

summary:
wt plants (ws) and opr3 mutant plants were wounded
Half of the rosette leaves of 6 weeks old plants were wounded by clamping a tweezers across the midvein. RNA was extracted from control and systemic leaves 2 h after wounding, and was subject to affymetrix ATH1 chip.

overall_design: one repeat: wt control, wt systemic wounding, opr3 control, opr3 systemic wounding

first: Yehudit

last: Zohar


title: Expression analysis of pye-1 mutants and root pericycle cells to iron sufficient or iron deficient conditions


title: Comparison of gene expression in wild type and angustifoila3 leaf primorida

status: Public on Sep 28 2010

city: Tokyo

first: Gorou

last: Horiguchi

address: 3-34-1, Nishi-Ikebukuro, Toshima-ku

department: College of Science, Faculty of Life Science

country: Japan

institute: Rikkyo University

summary: Development of a flat structure of leaves depend on active expansion of leaf blades mediated by cell proliferation. The angustifolia3 (an3) mutants of Arabidopsis thaliana are defective in cell proliferation in leaf primorida. AN3 encodes a transcription coactivator and interacts with a putative transcription factor AtGRF5. To investigate how AN3 control cell proliferation, we compared gene expression profiles between an3 and wild type. This analysis provide an insight into AN3-dependent cell proliferation pathway.

overall_design: Comparison between an3-4 and wild type. Two replicates for each sample.

first: Naoko

last: Ishikawa

first: Minoru

last: Kubo

first: Taku

last: Demura

first: Hiroo

last: Fukuda

first: Hirokazu

last: Tsukaya


title: Expression data from esd7-1 mutant vs wt (Ler)

status: Public on Oct 14 2010

city: Madrid

first: Jose Antonio

last: Jarillo

address: Parque Científico y Tecnológico de la U.P.M. Campus de Montegancedo Pozuelo de Alarcón

department: PLANT DEVELOPMENTAL BIOLOGY

institute: Centro de Biotecnología y Genómica de Plantas (UPM-INIA)

summary:
We have characterized a mutation affecting the Arabidopsis EARLY IN SHORT DAYS 7 (ESD7) gene encoding the catalytic subunit of the DNA polymerase epsilon (e), AtPOL2A. esd7-1 mutations causes early flowering independently of photoperiod, shortened inflorescence internodes and altered leaf and root development. esd7-1 was a hypomorphic allele whereas KO alleles displayed an embryo-lethal phenotype. The SAM and the RAM in the esd7-1 seedlings were found to exhibit an altered disposition that might correlate with the abnormal expression pattern of SAM and RAM marker genes. esd7-1 showed higher sensitivity to DNA damaging reagents than wild type plants and altered expression of genes involved in DNA repair mechanisms by homologous recombination. Moreover, esd7 early flowering phenotype requires functional FT and SOC1 proteins and might be also related to the mis-regulation of AG and AG-like gene expression found in esd7. Loci involved in the modulation of the chromatin structural dynamics, such as TFL2 and EBS, which negatively regulate FT expression, were found to interact genetically with ESD7, and the carboxy terminus of ESD7 interacted with TFL2 in vitro. Besides, fasciata2 (fas2) mutations suppressed esd7 early flowering phenotype and INCURVATA 2 (ICU2) was found to be epistatic to ESD7.  Discrete regions of the chromatin of FT and AG loci were enriched in activating epigenetic marks in the esd7-1 mutant. We concluded that ESD7 might be participating in processes involved in chromatin-mediated cellular memory.
We used microarrays to evaluate the genes whose expression was mis-regulated by the esd7-1 mutation

overall_design: Ler and esd7-1 14-d-old seedlings grown under SD photoperiods, were collected 8 h after dawn for RNA extraction and hybridization on Affymetrix microarrays. The experimental design comprised three replicates of each genotype and each replicate corresponded to an RNA extraction of an independent pool of plants.

first: Iván

last: del Olmo

first: Leticia

last: González-López

first: Maria

last: Martín-Trillo

first: José

last: Martínez-Zapater

first: Manuel

last: Piñeiro

first: Jose


title: Different gene expressions in root tips between CLE10 and CLE25 treatment

status: Public on Sep 03 2010

city: Kobe

first: Yuki

last: Kondo

address: 1-1 Rokkodai-cho, Nada-ku

department: Graduate School of Science

institute: Kobe University

summary: Cell–cell communication is critical for tissue and organ development. In plants, secretory CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides function as intercellular signaling molecules in various aspects of tissue development. However, little is known about intracellular signaling pathways functioning in vascular development downstream of the CLE ligands. To elucidate CLE signaling pathway, we performed GeneChip analysis.

overall_design: Arabidopsis roots were treated with chemically synthesized CLE10, or CLE25 at 1000 nM for 12 hours. Comparisons between CLE10 and CLE25 treatment will highlight the genes involved in the cause of different effects.

first: Sayaka

last: Isu

first: Kuninori

last: Iwamoto


title: Expression analysis of root pericycle cell-types after iron deficiency (-Fe) treatment

first: Terri

last: Long

summary:
Pericycle specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) of roots that express a pericycle-specific GFP-reporter. FACS cell populations were isolated from roots grown under standard conditions or roots that had been transferred to -Fe media for 24 hours.
Global population increases and climate change underscore the need for better comprehension of how plants acquire and process nutrients such as iron. A systems biology approach was taken to elucidate novel regulatory mechanisms involved in plant responses to iron deficiency (-Fe). Using cell-type specific transcriptional profiling we identified a pericycle-specific iron deficiency response, and a previously uncharacterized transcription factor, POPEYE (PYE), that plays an important role in this response. Functional analysis of PYE suggests that it positively regulates growth and development under iron deficient conditions. ChIP-on-chip analysis and transcriptional profiling reveal that PYE helps maintain iron homeostasis by directly and indirectly regulating the expression of ferric reductases, metal ion transporters, iron storage proteins, and other key iron homeostasis genes. In addition to PYE, we also identified a second protein BRUTUS (BTS), which appears to negatively regulate the response to iron deficiency. BTS is a unique putative E3 ligase protein, with metal ion binding and DNA binding domains. PYE and BTS are tightly co-regulated and physically interact with PYE paralogs, one of which is thought to positively regulate expression of genes involved in iron homeostasis. We propose that iron content is sensed within the pericycle where PYE, perhaps in conjunction with BTS and other regulatory proteins, is then activated to control a regulatory network involved in maintaining proper iron distribution in plants.

Keywords: Cell-type specific analysis of stress response using FACS

overall_design:
To determine how the pericycle responds to -Fe 6 day old GFP-reporter lines, in which pericycle cells are marked, were germinated under standard growth conditions, then shifted to standard media (control, MS media) or iron deficient media (-Fe, 0.3mM Ferrozine in MS media containing no ferrous sulfate) for 24 hours before protoplasting and sorting.

A file with Q-values that indicate the statistical significance of the difference in expression between + and -Fe for each probeset is linked at the foot of this record.

first: Jean

last: Wang

first: Philip

last: Benfey


title: SET DOMAIN GROUP 2 is the major histone H3 lysine-4 tri-methyltransferase in Arabidopsis thaliana

status: Public on Oct 11 2010

city: Athens

first: Xiaoyu

last: Zhang

state: GA

address: 4520 Miller Plant Sci. bldg, Dept. Plant Biology, UGA

department: Plant Biology

institute: University of Georgia

summary: Post-translational modifications of histones play important roles in modulating chromatin structure and regulating gene expression. We have previously shown that over two thirds of Arabidopsis genes contain histone H3 methylation at lysine-4 (H3K4me), and that tri-methylation of H3K4 (H3K4me3) is preferentially located at actively transcribed genes. In addition, several Arabidopsis mutants with locus-specific loss of H3K4me have been found to display various developmental abnormalities. These findings suggest that H3K4me3 may play important roles in maintaining the normal expression of a large number of genes. However, the major enzyme(s) responsible for H3K4me3 has yet to be identified in plants, making it difficult to address questions regarding the mechanisms and functions of H3K4me3. Here we describe the characterization of SET DOMAIN GROUP 2 (SDG2), a large Arabidopsis protein containing a histone lysine methyltransferase domain. We found that SDG2 homologues are highly conserved in plants, and that the Arabidopsis SDG2 gene is broadly expressed during development. In addition, the loss of SDG2 leads to severe and pleiotropic phenotypes as well as the mis-regulation of a large number of genes. Consistent with our finding that SDG2 is a robust and specific H3K4 methyltransferase in vitro, the loss of SDG2 leads to a drastic decrease in H3K4me3 in vivo. Taken together, these results suggest that SDG2 is the major enzyme responsible for H3K4me3 in Arabidopsis, and that SDG2-dependent H3K4m3 is critical for regulating gene expression and plant development.

overall_design: Transcription profiling of 10-day-old Arabidopsis seedlings of wild type control (3 replicates) and sdg2 mutant (3 replicates).

first: Lin

last: Guo

first: Yanchun

last: Yu

first: Julie

last: Law


title: Cytokinin treatment on roots of seedlings

status: Public on Jul 09 2010

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

summary: According to the well-documented scenario with regard to the cytokinin-mediated phosphorelay signal transduction in Arabidopsis thaliana, certain members of the type-B ARR family are crucially implicated in the regulatory networks that are primarily propagated by the cytokinin-receptors (AHKs) in response to cytokinin. Nevertheless, clarification of the biological impact of these type-B ARR transcription factors is at a very early stage. Here we focused on a pair of highly homologous ARR10 and ARR12 genes by constructing an arr10 and arr12 double-null mutant. The mutant alleles used in this study were arr10-5 and arr12-1. arr10-5 is the SALK_098604 T-DNA insertion line, whose mutation was determined to be located in the fifth exon of the ARR10 coding sequence. arr12-1 is the SALK_054752 T-DNA insertion line, whose mutation was determined to be located in the third exon of the ARR12 coding sequence. The resulting mutant showed remarkable phenotypes with special reference to the cytokinin-action in roots (e.g., inhibition of root elongation, green callus formation from explants). Furthermore, we demonstrated that ARR10 and ARR12 are involved in the AHK-dependent signaling pathway that modulates the differentiation of root-vascular tissues (i.e., protoxylem-specification), suggesting that ARR10 and ARR12 are the prominent players that act redundantly in the AHK-dependent cytokinin signaling in roots. Keeping this in mind, we then collected the root-specific and combinatorial DNA microarray datasets with regard to the cytokinin-responsible genes by employing both the wild-type and arr10 arr12 double-mutant plants. In this study, wild-type and the arr10 arr12 mutant grown vertically on MS agar plates for 2 weeks were treated with 20 microM of the cytokinin trans-zeatin (TZ) or 0.02% DMSO (solvent for trans-zeatin solution) for 1h. These treated plant samples were divided into three portions, from which RNA samples were prepared separately from roots of seedlings with use of RNeasy Plant Mini Kit (Qiagen, Valencia, CA, U.S.A.). The quality of RNAs prepared was analyzed by Bioanalyzer 2100 (Agilent Technologies). These RNA samples were processed as recommended by the Affymetrix instruction (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetrix). These datasets will provide us with bases for understanding the early response to cytokinin on roots of seedlings in Arabidopsis thaliana.

overall_design: 12 samples were used in this experiment.

first: Hitoshi

last: SAKAKIBARA


title: Novel Target Genes Regulated By LEUNIG

institute: Nottingham Arabidopsis Stock Centre (NASC)

summary:
Regulation of homeotic gene expression is critical for proper developmental patterns in plants. The Arabidopsis thaliana floral homeotic gene AGAMOUS is regulated by LEUNIG (LUG). Mutations in LUG result in homeotic transformations of floral organ identity. LUG mutants also exhibit other defects that are independent of AG, including abnormal carpel and ovule development, reduced female and male fertility, and narrower leaves and floral organs, suggesting that LUG has a wider role in development. LUG is structurally similar to the transcription co-repressors Tup1 (S. cerevisiae) and Groucho (Drosophila), suggesting developmental pathways regulated by LUG may be controlled by a conserved eukaryotic repression mechanism.

We aim to determine novel target genes regulated by LUG using transcriptome analysis. A mutant lug-3 line has been obtained from Dr. Zhongchi Liu. This line was used in the initial studies of LUG in the Meyerowitz lab. Lug-3 is a strong allele in the Lansberg erecta background, caused by a nonsense mutation that results in early termination of the protein and is likely null. The Lug-3 mutant exhibits narrow floral organs with staminoid petals and carpelloid sepals, abnormal carpel and ovule development, reduced plant height, increased lateral branching and narrow and smaller leaves.

We proposed to use the lug-3 line in elucidating the role of LUG as a potential general regulator of transcription in Arabidopsis. mRNA populations will be isolated from wild type (Ler) and lug-3 plants that have produced inflorescence. This stage of development has been selected for several reasons. Firstly, mRNA populations from the widest range of tissue types from a single plant can be collected. Secondly, as AGAMOUS, which is involved in the regulation of floral development, is present in the Affymetrix gene chip, it will provided an excellent internal control to monitor between chips.

Results will demonstrate whether LUG is likely to have a more global role in regulating transcription, and will identify pathways under the regulation of this co-repressor-like protein.

first: Deyarina

last: Gonzalez


title: Study of the effect of C2 on the transcriptome and the response to MeJA

status: Public on Sep 10 2010

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

summary:
affy_meja_arabidopsis - We want to determine if the presence of C2 modifies the cell transcriptome and its response to methyl jasmonate. Comparison of control lines and transgenic lines expressing C2 in basal conditions and after treatment with 50uM MeJA for 10 hours. C2 lines are expressing geminivirus C2 under a 35S promoter. PR1-LUC have a luciferase transgene under the control of the promoter of PR1; since the plants are not induced, these are the control plants (resistant to kanamycin, but not expressing anything else)

Keywords: gene knock in (transgenic),treated vs untreated comparison

overall_design: 12 arrays - ATH1

first: Sandrine

last: Balzergue

first: Eduardo-R

last: Bejarano

first: Rosa

last: Lozano durán

first: Marie-Laure

middle: L

last: Martin-Magniette


title: A methyl transferase links the circadian clock to the regulation of alternative splicing

status: Public on Aug 24 2010

city: Buenos Aires

first: Marcelo

middle: Javier

last: Yanovsky

state: Capital Federal

address: Av. San Martín 4453

department: Applied Biology

country: Argentina

institute: IFEVA

type: Expression profiling by genome tiling array

summary:
Study on differential gene expression and splicing between wildtype and clock mutants. This study is part of a comparative analysis of the role of Protein Methyltransferase 5 in the regulation of transcriptional and post-transcriptional processes simultaneously in Arabidopsis and Drosophila.
Circadian rhythms allow organisms to time biological processes to the most appropriate phases of the day/night cycle1. Post-transcriptional regulation is emerging as an important component of circadian networks2-6, but the molecular mechanisms linking the circadian clock to the control of RNA processing are largely unknown. Here we show that Protein Arginine Methyl Transferase 5 (PRMT5), which transfers methyl groups to arginine residues present in histones7 and Sm spliceosomal proteins8,9, links the circadian clock to the control of alternative splicing in plants. Mutations in prmt5impair multiple circadian rhythms in Arabidopsis thaliana and this phenotype is caused, at least in part, by a strong alteration in alternative splicing of the core-clock gene PSEUDO RESPONSE REGULATOR 9 (PRR9). Furthermore, genome wide studies show that PRMT5 contributes to regulate many pre-mRNA splicing events most likely modulating 5´splice site (5´ss) recognition. PRMT5 expression shows daily and circadian oscillations, and this contributes to mediate the circadian regulation of expression and alternative splicing of a subset of genes. Circadian rhythms in locomotor activity are also disrupted in dart5, a mutant affected in the Drosophila melanogaster PRMT5 homolog, and this is associated with alterations in splicing of the core-clock gene period (per) and several clock associated genes. Our results reveal a key role for PRMT5 in the regulation of alternative splicing and indicate that the interplay between the circadian clock and the regulation of alternative splicing by PRMT5 constitutes a common mechanism that helps organisms to synchronize physiological processes with daily changes in environmental conditions.

sample_organism:
Arabidopsis thaliana
Drosophila melanogaster

overall_design:
Each genotype has three replicates, Single channel. Two species, each with wildtype and mutant.
For the gene expression Samples (GSM586328-33): Wild type (WT) plants and prmt5-5 mutant plants were grown under continuous white light for three weeks, at 22 degrees centigrades. Total RNA extracted from aerial tissue was used for microarray analysis.

first: Sabrina

last: Sanchez

first: Ezequiel

last: Petrillo

first: Esteban

last: Beckwith

first: Xu

first: Matias

last: Rugnone

first: C

last: Hernando

first: Juan

last: Cuevas

first: Micaela

last: Godoy Herz

first: Ana

last: Depetris-Chauvin

first: Craig

middle: G

last: Simpson

first: John

last: Brown

first: Pablo

last: Cerdán

first: Justin

middle: O

last: Borevitz

first: Paloma

last: Mas

first: M

middle: F

last: Ceriani

first: Alberto

middle: R

last: Kornblihtt


title: Effect of AAF overexpression on the leaves before bolting

status: Public on Sep 30 2010

city: Taipei

first: Kevin Long-Chi

last: WANG

address: 128 Section 2, Academia Road

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

summary: Analysis of leaves from 3-week old transgenic plants overexpressing AAF, which is a senescence-associated gene. Overexpression of AAF promoted leaf senescence and accumulation of reactive oxygen species (ROS) in transgenic plants. Results provide insight in the role of AAF in ROS homeostasis and the function in leaf senescence.

overall_design: 3-week-old plants of Col-0 (wild type, as control) and AAF-OX (overexpression line) were grown in long day condition (16hr light/8hr dark). Rosette leaves of Col-0 and AAF-OX were used for total RNA extraction and cDNA synthesis. cDNA labeling, array hybridization, and scanning followed standard Affymetrix expression array protocol. Two independent sets of microarray analyses were performed in this study.

first: Guan-Hong

last: Chen

first: Long-Chi

middle: K

last: Wang


title: Microarray analysis of gene expression in the Arabidopsis rlt1-1 rlt2-1 mutant

status: Public on Jul 03 2010

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

country: China

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

summary: The Arabidopsis thaliana Imitation Switch (AtISWI) subfamily of ATP-dependent chromatin remodeling factors play essential roles in plant development. Here we show that the DDT domain transcription factor RINGLET (RLT) form a complex with AtISWI. RLT1 physically interacts with CHR11 in yeast cells. Single mutants rlt1-1 and rlt2-1 show no obvious developmental defects, while the rlt1-1 rlt2-1 double mutant phenocopies the AtISWI mutant chr11-1 chr17-1. In addtion, the RLT-ISWI complex selectively represses SEPALLATA, FRUITFULL and SUPPRESSOR OF OVEREXPRESSION OF CO 1, but not AGAMOUS and PISTILLATA in leaves.

overall_design: Leaves from 15-day-old seedlings of wild-type Col-0 and rlt1-1 rlt2-1 were used for RNA preparation.In the experiment data,3a3b refers to rlt1-1 rlt2-1.

last: Xu

first: Jiawei

last: Zhang


title: Identification of genes regulated by NMD in Arabidopsis

last: Nottingham Arabidopsis Stock Centre (NASC)

summary: The nonsense-mediated mRNA decay pathway (NMD) is a quality control mechanism that detects and degrades mRNAs that contain premature translation termination codons (PTCs), thus preventing the production of potentially harmful truncated proteins. NMD has been studied in a number of organisms including humans, yeast, Drosophila, C. elegans and recently Arabidopsis. Recently the NMD process has been shown to have a wider significance in regulating the levels of mRNA expression for a wide range of genes in yeast and Drosophila. Several genes have been found to be required for NMD in a variety of organisms, including UPF1 and UPF3. We have identified and characterised a number of alleles of UPF1 and UPF3 in Arabidopsis that are defective in NMD. By doing a transcriptomic analysis of two NMD mutants, upf1-1 and upf3-1, and wild type plants we aim to identify the subset of genes that are co-regulated by UPF1 and UPF3 and, therefore, by NMD in Arabidopsis. RNA will be extracted from 17-day-old mutant and wild type seedlings grown at 22-24 C under constant light.

overall_design: 7 samples were used in this experiment.

first: Luis

last: Arciga-Reyes


title: Differentiating Arabidopsis shoots from leaves by combined YABBY activities

status: Public on Aug 01 2010

first: Idan

middle: D.

last: Efroni

address: Weizmann

institute: Weizmann Institute

summary: In seed plants, leaves are born on radial shoots but unlike shoots they are determinate dorsiventral organs made of flat lamina. YABBY genes are found only in seed plants and in all cases studied, are expressed primarily in lateral organs and in a polar manner. Despite their simple expression, Arabidopsis plants lacking all YABBY gene activities have a wide range of morphological defects in all lateral organs as well as the shoot apical meristem. Here we show that leaves lacking all YABBY activities are initiated as dorsiventral appendages but fail to properly activate lamina programs. In particular, the activation of most CIN-TCPs does not commence, SAM-specific programs are reactivated, and a marginal leaf domain is not established. Altered distribution of auxin signalling and the auxin efflux carrier PIN1, highly reduced venation, initiation of multiple cotyledons, and gradual loss of the SAM accompany these defects. We suggest that YABBY functions were recruited to mould modified shoot systems into flat plant appendages by translating organ polarity into lamina specific programs that include marginal auxin flow and activation a maturation schedule directing determinate growth.

overall_design: Four repeats of wild type 14 DAS plants were used to compare to fil,y3 and fil,y3,y5 mutants of similar age (two repeats of each)

first: Rajani

last: Sarojam

first: Pia

last: Sappl

first: Alexander

last: Goldshmidt

first: Sandra

last: Floyd

first: Yuval

last: Eshed

last: Bowman


title: Micro-array analysis of gene expression in the Arabidopsis chr11-1 chr17-1 mutant

status: Public on Jun 11 2010

summary: Chromatin remodeling factors of the Imitation Switch (ISWI) family play important roles in epigenetic regulations of gene expression in yeast and animals, whereas their function in plants remains elusive. Here we report characterization of the Arabidopsis ISWI genes CHR11 and CHR17. Double mutant chr11 chr17 displayed a dramatically reduced plant size with early flowering. In addition, epidermis of the double mutant leaves showed cell characteristics seen only in floral organs. These phenotypes resemble, at least partially, those of the Polycomb mutants curly leaf (clf) and like heterochromatin protein1 (lhp1). Microarray analysis revealed that a number of targets of the Polycomb pathway were derepressed in chr11 chr17 leaves. Furthermore, triple mutants combining chr11 chr17 with clf-29 or lhp1-6 both greatly enhanced clf-29 and lhp1-6 phenotypes, respectively. All these results strongly suggest that the ISWI family genes in Arabidopsis may function in gene silencing via the Polycomb pathway

overall_design: Leaves from 15-day-old seedlings of wild-type Col-0 and chr11-1 chr17-1 were used for RNA preparation.In the experiment data,A refers to Col-0, and B refers to chr11-1 chr17-1.

first: Guang

last: Li


title: Expression data in response to neonicotinoid insecticides

status: Public on Sep 13 2010

city: Berkeley

first: Mary

last: Wildermuth

state: CA

address: 221 Koshland Hall MC3102

department: Plant and Microbial Biology

institute: University of California Berkeley

summary: Neonicotinoid insecticides control crop pests based on their action as agonists at the insect nicotinic acetylcholine receptor which accepts chloropyridinyl- and chlorothiazolyl- analogs almost equally well.  In some cases, these compounds have also been reported to enhance plant vigor and (a)biotic stress tolerance, independent of their insecticidal function.  However, this mode of action has not been specifically defined.  Using Arabidopsis thaliana, we show that the neonicotinoid compounds, imidacloprid (IMI) and clothianidin (CLO), via their 6-chloropyridinyl-3-carboxylic acid and 2-chlorothiazolyl-5-carboxylic acid metabolites, respectively, induce salicylic acid (SA) – associated plant responses.  SA is a phytohormone best known for its role in plant defense against pathogens and as an inducer of systemic acquired resistance; however, it can also modulate abiotic stress responses.  These neonicotinoids effect a similar global transcriptional response to that of SA including genes involved in (a)biotic stress response.  Furthermore, similar to SA, IMI and CLO induce systemic acquired resistance resulting in reduced growth of a powdery mildew pathogen.  The action of CLO induces the endogenous synthesis of SA via the SA biosynthetic enzyme ICS1, with ICS1 required for CLO-induced accumulation of SA, expression of the SA marker PR1, and fully enhanced resistance to powdery mildew.  In contrast, the action of IMI does not induce endogenous synthesis of SA.  Instead, IMI is further bioactivated to 6-chloro-2-hydroxypyridinyl-3-carboxylic acid, which is shown here to be a potent inducer of PR1 and inhibitor of SA-sensitive enzymes.  Thus, via different mechanisms, these chloropyridinyl- and chlorothiazolyl- neonicotinoids induce SA responses associated with enhanced stress tolerance.

overall_design: response to neonicotinoid insecticides

first: Divya

last: Chandran


title: Expression data from adult Arabidopsis roots under 200uM cadmium (Cd) treatment

status: Public on Jun 04 2010

first: Jian Yong

address: 300 Feng lin road

institute: Institute of Plant Physiology and Ecology, SIBS, CAS

summary: To massively identify genes that are up-regulated by Cd and in particular transporter genes which might transport peptides or oligopeptides.

overall_design: Four week old  hydroponically-grown Col-0 plants were treated with/without 200uM Cd for 6 hours. Total RNA was extracted from roots and subjected to hybridization with Affymetrix ATH1 microarrays.

first: Ji-Ming

last: Gong

first: Julian

middle: I

last: Schroeder


title: Gene expression data from Arabidopsis wild-type and pop2-1 mutant flowers

status: Public on Jun 05 2010

city: Tucson

first: RAVISHANKAR

last: PALANIVELU

state: AZ

address: 1140 E. South Campus Drive P.O. Box 210036

institute: University of Arizona

summary: Although two genes responsive to GABA were characterized previously in plants (Kathiresan et al 1997), a comprehensive study in reproductive and vegetative tissues has not been performed. Consequently, genes that mediate GABA response in plants remain unknown. We therefore used microarrays to survey the genome, identifying genes modulated in response to GABA in reproductive tissues.

overall_design: Flowers were collected as described in the protocols section for RNA extraction and hybridization on Affymetrix ATH1 Genechip microarrays. Gene expression in wild-type and pop2-1 mutant flowers containing high levels of endogenous GABA were compared.

first: Ravishankar

last: Palanivelu

first: Emily

last: Updegraff

first: Daphne

last: Preuss


title: Empty-vector control and transgenic 35S-PaWRKY1 Arabidopsis

status: Public on Jul 07 2010

city: Changhua

first: Shih-Feng

last: Fu

state: Changhua

address: No.1 Jin-De Road

institute: National Changhua University of Education

summary:
Transcriptional profiling of genes regulated by PaWRKY1 transcription factor
A PaWRKY transcription factor from orchid plants is expressed in Arabidopsis, and the PaWRKY-regulated genes are studied

overall_design:
Comparison of empty-vector control and transgenic 35S-PaWRKY1 Arabidopsis
Affymetrix GeneChip assay were performed by the Affymetrix Gene Expression Service Lab (http://ipmb.sinica.edu.tw/affy/), supported by Academia Sinica, Taiwan

first: Tsung-Mu

last: Tsai

first: Ying-Ru

last: Chen

first: Ching-Pei

last: Liu

first: Lin-June

last: Haiso

first: Li-Hsin

last: Syue

first: Hao-Jen

last: Huang


title: Global gene expression analysis of Arabidopsis Col-0 under normal and low oxygen conditions

status: Public on Apr 27 2010

city: Acton

first: Jed

last: Christianson

state: ACT

address: Clunies Ross Road

institute: CSIRO Plant Industry

summary: Global gene expression was compared between root RNA samples from three-week-old Arabidopsis Col-0 plants subjected to 0.1% oxygen (balance nitrogen) or ambient atmospheric conditions.

overall_design: Three-week-old Arabidopsis seedlings (4-6 leaves) of ecotype Col-0 were used. Two biological replicates were used for each treatment, and for each biological replicate, five Arabidopsis seedlings grown on the same petri dish were bulked. RNA was extracted from root tissue excised post-treatment. Treatment consisted of moving plants grown on solid MS media containing 3% sucrose to liquid MS media containing 3% sucrose for 24 hours, after which plates were placed in anaerobic cannisters covered in aluminum foil. Cannisters containing plants in the 0.1% oxygen treatment group were flushed with a 0.1% oxygen gas mixture and then sealed, while cannisters in the control group were left unsealed. Treatment lasted 5 hours before plant tissue was harvested and RNA extracted.

first: Dov

last: Moldovan

first: Iain

middle: W

last: Wilson

first: Danny

middle: J

last: Llewellyn

first: Elizabeth

middle: S

last: Dennis


title: microRNA156 resistant SQUAMOSA-PROMOTER-BINDING PROTEIN-LIKE13 (mSPL13) seedlings

status: Public on Apr 30 2010

city: Corvallis

first: Hiro

last: Nonogaki

state: OR

address: 4017 ALS Bldg, Dept. of Horticulture, Oregon State University

department: Horticulture

institute: Oregon State University

summary:
The expression profiles were determined using Affymetrix ATH1 arrays.
Comparisons among the Col-0, SPL13 and mSPL13 sample groups allow the identification of genes regulated by SPL13.
Keywords: Potential upregulated and downregulated genes

overall_design: Arabidopsis 3 days seedling from three independent biological replicates of Col-0, SPL13 and mSPL13 samples, which contain three independent seed lots each, were analyzed.

first: Ruth

last: Martin

first: Masashi

last: Asahina

first: Po-Pu

first: Jessica

last: Kristof

first: Jennifer

last: Coppersmith

first: Hiroyuki


title: Expression data from Arabidopsis gapcp mutant treated with ABA

status: Public on May 11 2010

city: Burjassot

first: Roc

last: Ros

state: valencia

address: Vicent Andres Estelles

department: Biologia Vegetal

institute: Universitat de Valencia

summary: Glycolytic Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) catalyzes the conversion of glyceraldehyde 3-phospate to 1,3-bisphosphoglycerate by coupling with the reduction of NAD+ to NADH. We generated mutants of the Arabidopsis plastidial GAPDH isoforms (At1g79530, At1g16300; GAPCp1, GAPCp2). gapcp double mutants (gapcp1 gapcp2) display a drastic phenotype of arrested root development and sterility.Complex interactions occurring between ABA and sugar signal transduction pathways have been shown, but the molecular mechanisms connecting both pathways are not well understood. Since we found drastic carbohydrate changes in gapcp1 gapcp2, we studied their response to ABA. by performing a microarray analysis comparing gapcp1 gapcp2 and wild type seedlings after a long term treatment with ABA.

overall_design: 15-day old Arabidopsis seedlings (Col 0)  and gapcp1gapcp2 double mutants were used  for RNA extraction and hybridization on Affymetrix microarrays.


title: Polycomb mutant seedlings

status: Public on Apr 20 2010

last: Nottingham Arabidopsis Stock Centre (NASC)

summary: We have identified a histone methyltransferase gene CURLY LEAF (CLF), which is required to repress a floral homeotic gene AGAMOUS (AG).  CLF acts redundantly with a related gene SWINGER (SWN), so that clf swn double mutants have extreme, near lethal phenotypes in which expression of many target genes is disrupted.  To understand better when and where these genes act, we propose to use a system for generating mosaic plants in which marked sectors of cells are created that gain or lose CLF (or other Pc-G) gene function in SWN+ and swn- mutant backgrounds.  This will allow us to address questions such as whether the Pc-G genes are needed throughout development to silence their targets, whether they are needed once cell division has ceased, whether they can silence their targets once the targets have been activated, and whether genes that are epigenetically silenced by CLF are impervious to activating factors.

overall_design: Aim is to compare gene expression in wild-type and polycomb mutant seedlings. Comparison of bulked seedlings of four genotypes: wild-type (Columbia), clf-28, swn-7, clf-28 swn-7 double mutant. 8 samples were used in this experiment, 2 of each genotype. Tissue grown in tissue culture.

first: Justin

last: Goodrich


title: Expression Profile of ASL9 Overexpressor

summary:
In Arabidopsis thaliana, each member of a large family of AS2/LOB (ASYMMETRIC LEAVES 2 / LATERAL ORGAN BOUNDARIES) genes encodes a highly homologous plant-specific protein. A mutational lesion of the representative AS2 gene results in the development of anomalous asymmetric leaves, implying that these family members might commonly play some roles in plant development.
Here, we found that ectopic and over-expression of ASL9 (ASYMMETRIC LEAVES 2 LIKE 9) in transgenic plants displayed a markedly anomalous architecture during development of adult plants. The expression pattern of ASL9 was quite characteristic in that it was expressed at the restricted bases of lateral organs formed from vegetative, inflorescence, and floral meristems. It was also demonstrated that, among the AS2/LOB family members, ASL9 is uniquely distinct from others in that this one is exclusively, markedly, and specifically regulated by the plant hormone cytokinin in a manner dependent on the His-Asp phosphorelay signal transduction.
To gain further insight into the function of ASL9, we carried out transcriptome analysis of transgenic lines that ectopically overexpress ASL9 (ASL9-ox). Wild-type and ASL9-ox plants were grown on agar plates containing MS salt and 1% sucrose under continuous fluorescent light for 2 weeks. For each strain, these 2-week-old plant samples were divided into three portions, from which RNA samples were prepared separately from aerial parts of seedlings with use of RNeasy Plant Mini Kit (Qiagen, Valencia, CA, U.S.A.). The quality of RNAs prepared was analyzed by Bioanalyzer 2100 (Agilent Technologies). These RNA samples were processed as recommended by the Affymetrix instruction (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetrix). The resultant data set will be of help to discuss and hypothesize that ASL9 might be implicated in the regulation of differentiation of lateral organs with a linkage to the actions of cytokinin that is primarily propagated through the His-Asp phosphorelay signal transduction.

overall_design: 6 samples were used in this experiment.

first: Hitoshi

last: Sakakibara


title: HAP5 Triple Mutant vs. Constans Mutant

summary:
Aims: To compare the transcriptional profiles of an AtHAP5 (AtNF-YC, AtCBF-C) triple mutant vs. a Constans mutant.

Background Information on Mutants: AtHAP5 triple mutant created by cross between the following SALK TDNA inserts: SALK_034838, SALK_058903, SALK_032163; these correspond to At1G54830, At1G08970, At5G63470, respectively. co-SAIL TDNA insertion SAIL_24_H04 corresponds to AT5G15840.

Tissue: Above-ground whole plants grown for 10 days, under 16 hr light 8 hrs dark at constant 22C. Tissue collected 14 hrs after lights on. RT-PCR analysis on test RNA confirmed FT levels reduced in mutants lines compared to wild-type.

overall_design: 9 samples were used in this experiment.

first: Ben

last: Holt


title: Nuclear gene expression in response to chloroplast division inhibition

summary: The aim of this investigation is to analyse the effect on nuclear gene expression of inhibition of chloroplast division. Transgenic Arabidopsis lines (Ler) were generated that contained a chemically inducible promoter (XVE) upstream of AtMinD1. AtMinD1 encodes a product involved in chloroplast division; overexpression of AtMinD1 leads to chloroplast division inhibition.

overall_design:
6 samples were used in this experiment.

Three treatments were performed:

Treatment 1: Empty vector control seedlings (transformed with PER-10 only) were sown onto lehle, sprayed at 13 days old with 2uM 17-B-estradiol (inducer) and harvested 24 hours later.

Treatment 2: Seeds were sown on lehle containing inducer and sprayed every 24 hours with 2uM inducer until harvested at 14 days old.

Treatment 3: Seeds were sown on lehle plates, sprayed at 13 days old with 2uM inducer and harvested 24 hours later.

For all three treatments, seedlings were grown in constant light conditions, and tissue was harvested from 14-day-old seedlings (4 rosette leaves) and snap frozen in liquid nitrogen before RNA preparation.

first: Cassie

last: Aldridge


title: Cesium Toxicity in Arabidopsis

summary: Cesium (Cs+) is a potentially toxic mineral element that is released into the environment and taken up by plants. Although Cs+ is chemically similar to potassium (K+), and much is known about K+ transport mechanisms, it is not clear through which K+ transport mechanisms Cs+ is taken up by plant roots. In this study, the role of AtHAK5 in high affinity K+ and Cs+ uptake was characterized. It is demonstrated that AtHAK5 is localized to the plasma membrane under conditions of K+ deprivation, when it is expressed.

first: Corrina

last: Hampton


title: Gametophytic transcription factors

summary:
Following our initial transcriptomic analyses of the male gametophyte development (Honys and Twell, Genome Biol 5:R85, 2004), we identified several candidate genes for the function of transcriptional regulators of the male gametophyte development.
Two transcription factors with verified function (bZIP and C2H2 ZF) were selected for the identification of their regulons. Mature pollen was isolated as published previously (Honys and Twell Plant Physiol 132:640-652, 2003) from Col-0 wild type plants and T-DNA insertion mutants (SAIL) homozygous for tested genes.

first: David

last: Honys


title: Cellulose synthase mutants

status: Public on Apr 19 2010

summary: We compared the transcriptome of homozygous mutants for AtCesA4 and AtCesA6 (cellulose synthase genes) to their heterozygous counterparts that have a wild type phenotype. All plants were 4-weeks-old and grown under short day conditions.

overall_design: 10 samples were used in this experiment: 3 each homozygous and heterozygous AtCesA4 plants, and 2 each homozygous and heterozygous AtCesA6 plants.

first: Marco

last: Yves


title: Arabidopsis thaliana/Phytophthora parasitica compatible interaction transcriptome

summary: Oomycetes from the genus Phytophthora are fungus-like plant pathogens that are devastating for agriculture and natural ecosystems. Due to particular physiological characteristics, no treatments against diseases caused by oomycetes are presently available. To develop such treatments, it appears essential to dissect the molecular mechanisms that determine the interaction between Phytophthora species and host plants. The present project is focused on the molecular mechanisms that underlie the compatible plant-oomycete interaction and plant disease. The laboratory developed a novel interaction system involving the model plant, Arabidopsis thaliana, and Phytophthora parasitica, a soil-borne pathogen infecting a wide host range, thus representing the majority of Phytophthora species. A characteristic feature of the compatible Arabidopsis/P. parasitica interaction is an extended biotrophic phase, before infection becomes necrotrophic. Because the initial biotrophic phase is extremely short on natural (e.g. solanaceous) hosts, the Arabidopsis system provides the opportunity to analyze, for both interaction partners, the molecular events that determine the initiation of infection and the switch to necrotrophy. The present project aims at analyzing the compatible interaction between A. thaliana roots and P. parasitica. The Affymetrix A. thaliana full genome chip will be used to characterize modulations of the transcriptome occurring over a period of 24h from the onset of plant root infection to the beginning of necrotrophy. Parallel to this study, a custom-designed P. parasitica biochip will enable analyzing of P. parasitica gene expression during the same stages.

overall_design: 10 samples were used in this experiment.

first: Agnes

last: Attard


title: Ectopic expression of MYB46 identifies transcriptional regulatory genes in secondary wall biosynthesis in Arabidopsis

status: Public on May 18 2010

city: Yongin

first: Jae-Heung

last: Ko

state: Gyeonggi

address: 1 Seocheon-dong, Giheung-gu

department: Plant & Environmental Resources

country: South Korea

institute: Kyung Hee University

summary: MYB46 functions as a transcriptional switch that turns on the genes necessary for secondary wall biosynthesis. Elucidating the transcriptional regulatory network immediately downstream of MYB46 is crucial to our understanding of the molecular and biochemical processes involved in the biosynthesis and deposition of secondary walls in plants. The transcription factors identified here may include direct activators of secondary wall biosynthesis genes. The current study discovered novel hierarchical relationships among the transcription factors involved in the transcriptional regulation of secondary wall biosynthesis and generated several testable hypotheses.

overall_design: To gain insights into the MYB46-mediated transcriptional regulation, we first established an inducible secondary wall thickening system in Arabidopsis by expressing MYB46 under the control of dexamethasone inducible promoter. Then, we used ATH1 GeneChip microarray to obtain a series of time-course transcriptome profiles with regard to the induction of secondary wall development.

first: Kyung-Hwan

last: Han


title: Gibberellin (GA) Treatment of Arabidopsis Root Tips

summary:
The plant hormone gibberellin (GA) represents an important regulator of growth and development. Early transcriptional events controlled by GA are not well characterised. Previous microarray studies have identified genes responsive to GA treatment in the whole seedling. The whole seedling represents many tissues where subtle effects of GA treatment in specific tissues may be masked. When treated with GA, an effect on the growth rate of roots was observed. More specifically, the shorter root of a GA-deficient plant can be rescued to wild-type length by the application of GA.
This experiment was designed to identify GA-regulated genes in the root tips of Arabidopsis. The use of a GA-deficient mutant provides a greater potential to identify genes responding to GA treatment. Root tips are ideally suited for the quick uptake of the hormone treatment. There will be two biological replicates which will each consist of a control treatment at 0 minutes and 2 hours, as well as the experimental GA-treated 2 hour time point. This system provides an opportunity to compare gene expression between treated and non-treated root tips and allow the identification of early GA-responsive genes.

first: Jayne

last: Griffiths


title: Response of Arabidopsis thaliana to phenanthrene

status: Public on Apr 15 2010

city: Boston

first: Adán

last: Colón-Carmona

state: MA

address: 100 Morrissey Blvd

institute: University of Massachusetts Boston

summary:
Background:

Polycyclic aromatic hydrocarbons (PAHs) are toxic, widely-distributed, environmentally persistent, and carcinogenic byproducts of carbon-based fuel combustion. Previously, plant studies have shown that PAHs induce oxidative stress, reduce growth, and cause leaf deformation as well as tissue necrosis. To understand the transcriptional changes that occur during these processes, we performed microarray experiments on Arabidopsis thaliana L. under phenanthrene treatment, and compared the results to published Arabidopsis microarray data representing a variety of stress and hormone treatments. In addition, to probe hormonal aspects of PAH stress, we assayed transgenic ethylene-inducible reporter plants as well as ethylene pathway mutants under phenanthrene treatment.

Results:

Microarray results revealed numerous perturbations in signaling and metabolic pathways that regulate reactive oxygen species (ROS) and responses related to pathogen defense. A number of glutathione S-transferases that may tag xenobiotics for transport to the vacuole were upregulated. Comparative microarray analyses indicated that the phenanthrene response was closely related to other ROS conditions, including pathogen defense conditions. The ethylene-inducible transgenic reporters were activated by phenanthrene. Mutant experiments showed that PAH inhibits growth through an ethylene-independent pathway, as PAH-treated ethylene-insensitive etr1-4 mutants exhibited a greater growth reduction than WT. Further, phenanthrene-treated, constitutive ethylene signaling mutants had longer roots than the untreated control plants, indicating that the PAH inhibits parts of the ethylene signaling pathway.

Conclusions:

This study identified major physiological systems that participate in the PAH-induced stress response in Arabidopsis. At the transcriptional level, the results identify specific gene targets that will be valuable in finding lead compounds and engineering increased tolerance. Collectively, the results open a number of new avenues for researching and improving plant resilience and PAH phytoremediation.

overall_design: Arabidopsis thaliana (ecotype Columbia) plants were long-day grown with +/- 0.25 mM phenanthrene in sterile plates at 23C for 21d before harvest.  At least 20 plants were pooled prior to each mRNA extraction.

last: Weisman

first: Merianne

last: Alkio


title: Octopus transcriptome (affy_phloem_ath1)

status: Public on Apr 05 2010

first: sandrine

last: balzergue

summary: affy_phloem_ath1 - affy_phloem_ath1 - Transcriptome map of a mutant (versus WT and overexpressor) impaired in phloem differentiation and vascular patterning-Transcriptome map of a mutant (versus WT and overexpressor) impaired in phloem differentiation and vascular patterning.

overall_design: 6 arrays - ATH1

first: Sandrine

last: Balzergue

first: Jean-christophe

last: Palauqui

first: Marie-Laure

last: Martin-Magniette


title: Persistent heat stress in Arabidopsis

status: Public on Mar 01 2010

city: Vienna

first: Ortrun

last: Mittelsten Scheid

address: Dr. Bohrgasse 3

country: Austria

institute: Gregor Mendel Institute

summary: Analysis of transcriptional changes upon persistent heat stress with emphasis on epigenetically regulated genes

overall_design: 3 week old seedling grown in vitro were exposed to 37oC for 30 h (LHS). After heat stress, plants were analyzed immediately (R0) or allowed to recover at ambient temperature for 2 days (R2).

first: Ales

last: Pecinka

middle: M

last: Scheid


title: Cell signalling by microRNA165/6 directs gene dose dependent root cell fate

city: Ithaca

first: Ji-Young

last: Lee

state: NY

address: Tower Rd.

institute: Boyce Thompson Institute

summary: A key question in developmental biology is how cells exchange positional information for proper patterning during organ development. In plant roots the radial tissue organization is highly conserved with a central vascular cylinder in which two water conducting cell types, protoxylem and metaxylem, are patterned centripetally. We show that this patterning occurs through crosstalk between the vascular cylinder and the surrounding endodermis mediated by cell-to-cell movement of a transcription factor in one direction and microRNAs in the other. SHORT ROOT, produced in the vascular cylinder, moves into the endodermis to activate SCARECROW. Together these transcription factors activate MIR165a and 166b. Endodermally produced miR165/6 then acts to degrade its target mRNAs encoding class III homeodomain-leucine zipper transcription factors in the endodermis and stele periphery. The resulting differential distribution of target mRNA in the vascular cylinder determines xylem cell types in a dosage dependent manner.

overall_design: To investigate the global regulation of SHR and SCR in the root, direct and indirect target genes of SHR and SCR were cross-compared with selected cell type specific expression profiles in the Arabidopsis root published in Birnbaum et al. (2003), Nawy et al. (2005), Lee et al. (2006), and Brady et al. (2007) [pubmed IDs: 14671301, 15937229, 16581911, 17975066].  Furthermore, the mature endodermis specific transcript profiles were generated using a GFP marker line, E30, and used together with published profiles in this comparison.

first: Philip

last: Benfey


title: Arabidopsis thaliana/Hyaloperonospora arabidopsidis compatible interaction transcriptome

status: Public on Mar 26 2010

city: SOPHIA ANTIPOLIS

first: Attard

last: Agnes

address: 400 route des chappes

summary: We used Arabidopsis full-genome microarrays to characterize plant transcript accumulations at different stages of infection with the biotrophic oomycete downy mildew pathogen, Hyaloperonospora arabidopsidis : initiation  (< 1 dpi) and maintenance of infection (> 4 dpi).

overall_design: In two independent experiments, cotyledons from the ecotype Wassilewskija (WS) were inoculated with water, or with Hyaloperonospora arabidopsidis to establish a compatible interaction. Affymetrix  ATH1 microarrays were used to profile Arabidopsis transcript accumulations at the initiation (mixed samples at 8 and 24 hours post inoculation, hpi; early stage) and maintenance (mixed samples at 4 and 6 days post inoculation; late stage) of the compatible interaction.

first: H

last: Keller

first: V

last: Allasia

first: A


title: Global gene expression analysis of transgenic, mannitol-producing, and salt-tolerant Arabidopsis thaliana indicates widespread changes in abiotic and biotic stress-related genes

city: Wuhan

first: Zhulong

last: Chan

state: Hubei

address: Wuchang District, Moshan

institute: Wuhan Botanic Garden, Chinese Academy of Sciences

summary: Mannitol is a putative osmoprotectant contributing to salt tolerance in several species. Arabidopsis plants transformed with the mannose-6-phosphate reductase (M6PR) gene from celery were dramatically more salt tolerant (at 100 mM NaCl) as exhibited by reduced salt injury, less inhibition of vegetative growth, and increased seed production relative to the wild type (WT). When treated with 200 mM NaCl, transformants produced no seeds, but did bolt, and exhibited less chlorosis/necrosis and greater survival and dry weights than the WT. Without salt there were no M6PR effects on growth or phenotype, but expression levels of 2272 genes were altered. Many fewer differences (1039) were observed between M6PR and WT plants in the presence of salt, suggesting that M6PR pre-conditioned the plants to stress. Previous work suggested that mannitol is an osmoprotectant, but mannitol levels are invariably quite low, perhaps inadequate for osmoprotectant effects. In this study, transcriptome analysis reveals that the M6PR transgene activated the downstream abscisic acid (ABA) pathway by up-regulation of ABA receptor genes (PYL4, PYL5, and PYL6) and down-regulation of protein phosphatase 2C genes (ABI1 and ABI2). In the M6PR transgenic lines there were also increases in transcripts related to redox and cell wall-strengthening pathways. These data indicate that mannitol-enhanced stress tolerance is due at least in part to increased expression of a variety of stress-inducible genes.

overall_design: Both M6PR transgenic and Col WT plants were grown in the growth chamber in the absence and presence of salt stress. Plants from 20 days after sowing (6 days after salt treatment) were used for RNA extraction and hybridization on Affymetrix microarrays. There were two biological replicates for each genotype and salt treatment combination.

first: Rebecca

last: Grumet

first: Wayne

last: Loescher


title: Transcriptional profiles between mp mutant seedlings and transgenics carrying the dexamethasone-inducible GR-bdl protein

status: Public on Apr 01 2010

city: Wageningen

first: Dolf

last: Weijers

address: Dreijenlaan 3

department: Laboratory of Biochemistry

country: Netherlands

institute: Wageningen University

summary:
In order to identify targets of the transcription factor AUXIN RESPONSE FACTOR5 / MONOPTEROS (ARF5/MP), we compared transcriptomes of mp-B4149 mutant seedlings (9 day-old) and seedlings carrying the dexamethasone-inducible version of the MP inhibitor protein BODENLOS (GR-bdl). Without dexamethasone (DEX) treatment, this line is identical to the wild-type, while DEX treatment leads to strong inhibition of ARF-dependent transcription. To remove all endogenous MP-inhibiting Aux/IAA proteins, we treated mp or GR-bdl seedlings during 1 hour with auxin (50 micromolar Indole-3-Acetic Acid), either with or without a pretreatment with 10 micromolar DEX for 1 hour. Genes that are activated by MP are expected to br downregulated in mp seedlings and in the GR-bdl line afer DEX treatment. We used biological duplicates for each of the three treatments.

Keywords: Transcriptional profiling of transcription factor targets

overall_design: Mp mutant and GR-bdl seeds were germinated on solid 1/2MS media, and transferred to liquid medium after 9 days of horizontal growth. Duplicate cultures were generated for mp mutants, and quadruplicates for the GR-bdl line. 10 micromolar DEX was added to both mp cultures and to two of the GR-bdl cultures, and seedlings were gently shaken during 1 hour. Then, 50 micromolar IAA was added to all 6 cultures and seedlings were incubated with gentle shaking for another hour. Total RNA was isolated from the seedlings using a QIAgen RNeasy kit, and reverse transcription, in-vitro transcription, cRNA labling and fragemntation was done according to established methods (Schmid et al., Nature Genetics [2005] 37, 501-506). Labeled cRNA was hybridized to Arabidopsis ATH1 arrays.

first: Alexandra

last: Schlereth

first: Gerd

last: Juergens


title: RSL4

status: Public on Jan 09 2010

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

summary: Aims to look at the targets of the bHLH transcription factor in Arabidopsis roots.

overall_design: 6 total samples (3 sample types, 2 replicates each) were used in this experiment.

first: Elizabeth

last: Bell


title: Recruitment of GSH into the nucleus during cell proliferation

status: Public on Feb 22 2010

city: Murcia

first: Pedro

last: Diaz-Vivancos

address: Campus Universitario de Espinardo, 25

department: Plant Breeding

institute: CEBAS-CSIC

summary:
The essential thiol antioxidant, glutathione (GSH) is recruited into the nucleus of mammalian cells early in cell proliferation, suggesting a key role of the nuclear thiol pool in cell cycle regulation. However, the functions of nuclear GSH (GSHn) and its integration with the cytoplasmic GSH (GSHc) pools in whole cell redox homeostasis and signaling are unknown. Here we show that GSH is recruited into the nucleus early in cell proliferation in Arabidopsis thaliana, confirming the requirement for localization of GSH in the nucleus as a universal feature of cell cycle regulation.
GSH accumulation in the nucleus was triggered by treatments that synchronize cells at G1/S as identified by flow cytometry and marker transcripts. Significant decreases in transcripts associated with oxidative signaling and stress tolerance occurred when GSH was localized in the nucleus. Increases in GSH1 and GSH2 transcripts accompanied the large increase in total cellular GSH observed during cell proliferation, but only GSH2 was differentially expressed in cells with high GSHn relative to those with an even intracellular distribution of GSH. Of the 7 Bcl-2 associated (BAG) genes in A. thaliana, only the nuclear-localized BAG 6 was differentially expressed in cells with high GSHn compared to GSHc. We conclude that GSHn is associated with decreased oxidative signaling and stress responses and that whole cell redox homeostasis is restored as the cell cycle progresses by enhanced GSH synthesis and accumulation in the cytoplasm.

overall_design: Arabidopsis cells were harvested at points during cell proliferation where GSH was localized either in the nucleus (GSHn) or where GSH was distributed throughout the cytoplasm (GSHc) for RNA extraction and hybridization on Affymetrix microarrays. We selected three stages where the GSH was into the nucleus and three stages where the GSH was distributed throughout the cells.

first: Christine

last: Foyer


title: WT and php mutants

city: East Lansing

first: Sookyung

last: Oh

state: MI

institute: Michigan State University

summary:
Transcriptional profiling for wild-type and php mutants
Expression of >22,600 genes was analyzed in aerial tissues from 14 day old soil grown wild type and php mutant plants using Affymetrix ATH1 GeneChip, and two independent biological replicates. Data from CEL files were adjusted for background and normalized using the Bioconductor GCRMA package (http://www.bioconductor.org).

overall_design:
Affymetrix ATH array with seedling samples from wild-type and php mutants
Aerial tissues from 14-day-old soil grown wild-type and php mutant plants were  collected. Total RNAs were isolated and used for cDNA synthesis/biotin labeling following Affymetrix protocol. Affymetrix ATH1 GeneChip and two biologically independent replicates were used. Data from CEL files were adjusted for background and normalized using Bioconductor GCRMA package (transformed to Log2).

first: Sunchung

last: Park

first: Steve

last: van Nocker


title: Seed development

institute: Nottingham Arabidopsis Stock Centre (NASC)

summary: Reciprocal crosses of a diploid Arabidopsis with different ploidies results in different endosperm development patterns and phenotype. Typically if the ploidy is higher on the maternal side, there are fewer endosperm cells which cellularize early, and conversely, if the paternal ploidy is higher, there is more number of endosperm cells which cellularize late. Crosses involving diploid and tetraploid Arabidopsis (C24) are viable, whereas crosses involving the diploid and hexaploid, even though exhibit the above mentioned directional trend in endosperm development, abort (Scott et al 1998). The 'maternalised' and 'paternalised' development of endosperm is also observed in crosses involving some Arabidopsis mutants. Mutants in the fis class of genes, e.g. fis1-medea, when crossed with a diploid Arabidopsis (pollen parent) show endosperm development-seed development similar to a diploid (seed parent) crossed with hexaploid pollen parent. Reciprocal crosses of homozygous met1 and diploid Arabidopsis also exhibit reciprocal trends in endosperm development, where a homozygous met1 mutant (seed parent) crossed with diploid is similar in phenotype to a diploid (seed parent) - tetraploid cross. Endosperm development in the reciprocal cross has phenotypic similarity to the tetraploid (seed parent)-diploid cross (Adams et al 2000). We are interested in understanding gene profiles and trends in expression underlying the endosperm development in the interploidy crosses as well as the fis and met1 mutant.

overall_design: 11 samples were used in this experiment.

first: Sushma

last: Tiwari


title: Analysis of polyploidy-associated transcriptional gene silencing (paTGS) mutants

status: Public on Feb 01 2010

first: Ortrun

last: Mittelsten Scheid

summary:
A case of transcriptional gene silencing, originally observed in tetraploid Arabidopsis plants, created an epiallele resistant to many mutations or inhibitor treatments that activate other suppressed genes. This raised the question about the molecular basis of this extreme stability.
A combination of forward and reverse genetics, transcriptome profiling and drug application provides evidence for a double safeguard system that is only alleviated upon the simultaneous removal of both DNA methylation and histone methylation by loss of DDM1 or HOG1 acitivity.

overall_design: Three biological replicates per line are provided. C2S1 = Wt line; hog1-7=774; ddm1-12=1135

first: Tuncay

last: Baubec

last: Scheid


title: Arabidopsis transcriptome changes caused by ectopic production of a turtle riboflavin-binding protein

status: Public on Jan 01 2010

city: Nanjing

first: Hansong

last: Dong

address: Weigang NO.1

department: Plant Pathology

institute: Nanjing Agricultural University

summary:
Leaf contents of free riboflavin were modulated by ectopic expression of the turtle gene encoding riboflavin-binding protein (RfBP). Compared to Arabidopsis thaliana (L.) ecotype Col-0 (wild type), REAT (modified type) that constitutive express RfBP had 71%-77% less flavins of free form.

We used microarray to investigate the influence on plants due to the reduced free flavin. One modified line (REAT11) and wild type (WT) were tested by microarray, and the experiments data revealed that abundance of transcripts for 950 genes in REAT was altered compared to the wild type.

overall_design: Four samples were analyzed. Two WT and two REAT11 biological replicates were analyzed (one array each).

first: Shujian

last: Zhang

first: Sheng

last: Deng


title: Indolic metabolites are required for antifungal defense of the Arabidopsis mlo2 mutant

status: Public on Jan 04 2010

city: Cologne

first: Emiel

last: Ver Loren van Themaat

address: Carl von linneweg

institute: Max Planck Institute

summary: Arabidopsis thaliana genes MLO2 (Mildew resistance locus-O 2), MLO6 and MLO12 exhibit unequal genetic redundancy with respect to the modulation of defense responses against powdery mildew fungi and the control of developmental phenotypes such as premature leaf decay. We show that early chlorosis and necrosis of rosette leaves in mlo2 mlo6 mlo12 mutants reflects an authentic but untimely leaf senescence program. Comparative transcriptional profiling revealed that transcripts of several genes encoding tryptophan/indole biosynthetic enzymes hyper-accumulate during vegetative development in the mlo2 mlo6 mlo12 mutant. Elevated expression levels of these genes correlate with altered steady-state levels of several indolic metabolites, including the phytoalexin camalexin and indolic glucosinolates, during development in the mlo2 single and the mlo2 mlo6 mlo12 triple mutant. Results of genetic epistasis analysis suggest a decisive role for indolic metabolites in mlo2-conditioned antifungal defense against both biotrophic powdery mildews and a camalexin-sensitive strain of the necrotrophic fungus, Botrytis cinerea. The wound- and pathogen-responsive callose synthase Powdery mildew resistance 4/Glucan-synthase-like 5 (PMR4/GSL5) was found to be responsible for the spontaneous callose deposits in mlo2 mutant plants but dispensable for mlo2-conditioned penetration resistance. Our data strengthen the notion that powdery mildew resistance of mlo2 genotypes is based on the same defense execution machinery as innate antifungal immune responses that restrict invasion of non-adapted fungal pathogens.

overall_design: Mature rosette leaves from WT and mlo2 mlo6 mlo12 triple mutant plants were harvested at 5, 6 and 7 weeks after sowing. 6 arrays.

first: Chiara

last: Consonni

first: Pawel

last: Bednarek

first: Matt

last: Humphry

first: Fedra

last: Francocci

first: Simone

last: Ferrari

first: Anne

last: Hanzen

first: Ralph

last: Panstruga


title: DEK1 calpain overexpression

status: Public on Dec 10 2009

last: Nottingham Arabidopsis Stock Centre (NASC)

summary:
Aim: To understand the role of DEK1 in Arabidopsis development.
Background: DEK1 has an essential role during embryogenesis and is involved in the maintenance of the epidermis.
Tissues: Comparison of wild-type and ADEK1 calpain-overexpressing line.

overall_design: 9 samples were used in this experiment.

first: Kim

last: Johnson


title: Arabidopsis pvip mutants

status: Public on Dec 11 2009

summary: Transcriptional comparison of Arabidopsis thaliana pvip1;pvip2 RNAi double mutants against Col-0 wildtype. Tissue used: whole rosettes of 4-week-old plants grown under short-day conditions (8h light; 20oC). 3 biological replicates for each. Control = Col-0 and mutant = pvip1;pvip2. PVIP = Potyvirus-VPg-interacting protein (Dunoyer et al. 2004 J. Virol. 78: 2301-2309).

overall_design: 6 samples were used in this experiment.

first: Dominik

last: Schmidt


title: Cold acclimation in the sfr3-1 mutant

status: Public on Dec 04 2009

summary: The sfr3-1 mutation causes freezing-sensitivity in Arabidopsis thaliana. The mutated gene has been identified by positional cloning and is currently being characterised.  The mutant appears normal when grown in the warm (no phenotype has been identified associated with such growth). However, following cold acclimation and subsequent freezing mutant plants are severely damaged whilst wild type plants are not. This suggests that sfr3 is deficient in the cold acclimation process. Micro-array analysis will enable the identification of any transcriptional changes during the cold acclimation process. This information will then be used, together with information obtained by gene characterisation, in order to more fully understand the nature of the sfr3 mutation.

overall_design: 8 samples were used in this experiment.

first: Sarah

last: Garton


title: Determining the downstream genetic targets of the transcription factor AtGLK1

summary:
Aim: To discover the target genes of Golden2-like transcription factors in Arabidopsis.
Background: The Golden2-like (GLK) family of transcription factors is essential for proper chloroplast development in several plant species. In Arabidopsis, there are two largely redundant GLK genes, GLK1 and GLK2. Double mutant plants are pale green and reduced in stature. Their most notable chloroplast-related phenotype is impaired thylakoid membrane appression and reduction in steady-state levels of Photosystem II components. GLK proteins group within the GARP family of myb transcription factors; however, the genes they regulate remain unknown.
Experimental Design: We have employed a two-component dexamethasone-inducible expression system [1]. An overexpressed fusion protein comprising the glucocorticoid receptor (GR), the lac repressor and the Gal4 activation domain resides in the plant cytoplasm. This protein, termed LHGR-N, enters the nucleus once dexamethasone binds to the GR domain. It then activates transcription from the lac operator promoter sequences present on separate transgenes which carry the cDNA to be induced. Since overexpression of either GLK1 or GLK2 is sufficient to complement the mutant phenotype, we reasoned that induction of expression of GLK1 and GLK2 cDNAs in the glk1;glk2 double mutant background should allow determination of their downstream genetic targets. In the first case, we decided to focus on GLK1 only.
Genetic lines: Plants carrying a single copy of the LHGR-N transgene, conferring kanamycin resistance, were crossed with glk1;glk2 double mutant plants. A single homozygous F3 line was selected on the basis of pale green mutant phenotype and kanamycin resistance. This line was transformed with a construct carrying the GLK1 cDNA downstream of six repeats of the lac operator (pOp6) and a single CaMV minimal promoter. This construct confers hygromycin resistance. Transformants were confirmed by PCR and Southern blot, before being selected on the basis of transcript accumulation following induction by dexamethasone. The line with the strongest induction response was chosen for microarray experiments.
Tissues: Approx. 100 10-day-old seedlings were grown on MS plates and transferred to 100 ml liquid MS for two further days prior to induction. Whole seedlings were harvested.
Treatment: Either a) 10 uM dexamethasone dissolved in DMSO (INDUCED samples) or b) 0.1% v/v DMSO (CONTROL samples). Samples were harvested 4 and 24 hours post-treatment. Separate vessels were used for each time point and treatment. Two complete replicates were performed.
Reference1. Craft, J. et al. (2005) Plant J. 41 899-918.

overall_design: 10 samples were used in this experiment.

first: Mark

last: Waters


title: The effect of exogenous strigolactone on gene expression in Arabidopsis seedlings

status: Public on Dec 28 2009

city: Tokyo

first: kiyoshi

last: mashiguchi

address: 1-1-1 Yayoi, Bunkyo-ku

institute: University of Tokyo

summary: Strigolactones (SLs) have recently been found to regulate shoot branching, but the functions of SLs at other stages of development and the regulation of SL-related gene expression are mostly unknown in Arabidopsis. In this study, we performed microarray analysis to understand the molecular mechanisms underlying SL signaling.

overall_design: We performed microarray analysis using strigolactone (SL)-deficient mutants to compare gene expression profiles in response to GR24 to determine whether exogenous applied SL would modulate gene expression. We used cRNAs prepared from max3 seedlings treated with GR24 (1 uM) or DMSO (mock) for 90 min. Two independent analyses were performed, including seedling preparation.

first: Kiyoshi

last: Mashiguchi


title: Genes Involved in Meristemoid Cell Fate

summary:
The objective of this experiment is to identify genes that are regulated by the LRR-receptor-like protein TOO MANY MOUTHS (TMM) to control stomatal precursor (meristemoid) cell fate and behavior.  An interesting aspect of the tmm phenotype is that mutant plants overproduce stomata on leaves, but lack stomata entirely on inflorescence stems and in other locations on the plant.  Despite the failure to produce mature stomata, mutant stems produce presumptive stomatal precursors through asymmetric divisions. This suggests that normal TMM signaling is required to maintain meristemoid cell fate but not to execute formative asymmetric divisions.  Because stem stomata develop in a morphogenetic wave from tip to base, it is possible to harvest tissues that contain meristemoids but not guard mother cells or mature stomata.  This provides an opportunity to compare the gene expression profiles of tissues with meristemoids that maintain their cellular identity and ultimately produce stomata (Col gl1), to tissues in which meristemoids form but rapidly lose their cellular identity due to a failure in TMM signaling (tmm-1).  Because guard mother cells and stomata are not present in the tissue harvested, genes that change in abundance during these developmental stages will be filtered out.  Ultimately we hope to reveal genes that operate downstream of TMM to confer meristemoid cell fate or to provide 'niche factors' suitable for their development into stomata.
For analysis, approximately 90 developing inflorescence stem tips were collected and flower buds and meristems removed prior to flash freezing for each replicate sample.  The region harvested had been previously determined to contain developing meristemoids but not stomata or guard mother cells by microscopic observation.  An identical region was harvested from tmm-1 mutant plants grown at the same time, in the same flat.

overall_design: 4 samples were used in this experiment.

first: Jeanette

last: Nadeau


title: NPA-induced vascular overgrowth in Arabidopsis

status: Public on Dec 05 2009

summary: We used N-(1-naphthyl) phthalamic acid (NPA)-induced vascular overgrowth in Arabidopsis leaves to look for differential up-regulation of genes in NPA-treated tissues that may be involved in vascular differentiation. Arabidopsis thaliana Col-0 plants were grown for approximately 2 weeks on solid ATS medium (1) containing a final concentration of 10 um NPA (dissolved in DMSO) or an equivalent volume of DMSO (control). At this stage plants had approximately 6 rosette leaves. RNA was prepared from entire shoot tissues of control (DMSO) or NPA-treated plants.(1) Lincoln et al., 1990. Plant Cell 2: 1071-1080.

overall_design: 2 samples were used in this experiment.

first: Carol

last: Wenzel


title: Identification of AtATM-dependent X-ray inducible transcript

summary: ATM plays an important role in the response of plants to forms of DNA damage that cause DNA double-strand breaks. Arabidopsis ATM has been shown to be important for the transcriptional induction of several DNA repair genes including AtRAD51 (Garcia et al 2003 Plant Cell 15, 119-132). In our experiment we compare the transcript profiles of wild type and mutant plants exposed to 10Gy X-rays (dose rate ~0.8 Gy/min). Plants will be grown on 0.5*MS + 1%sucrose at 22degC under short (9h) day conditions and treated after 5h light. We will irradiate wild type (Col-0) and atatm-3 mutant (N589805) seedlings at growth stage 1.06 and harvest tissue 1h post irradiation. RNA will be isolated using the SV RNA isolation kit (Promega). Comparison of the transcript profiles will then allow AtATM-dependent X-ray inducible transcripts to be identified.

overall_design: 6 samples (3 wild type, 3 mutant) were used in this experiment.

first: Chris

last: West


title: Interplay between ethylene, ETP1/ETP2 F-box proteins, and degradation of EIN2 triggers ethylene responses in Arabidopsis

status: Public on Dec 01 2009

city: La Jolla

first: Joseph

middle: R.

last: Ecker

address: 10010 N. Torrey Pines Road

department: Genomic Analysis Laboratory

institute: The Salk Institute

summary:
A complex interplay between ethylene, ETP1/ETP2 F-box proteins, and degradation of EIN2 is essential for triggering ethylene responses in plants.

The gaseous plant hormone ethylene can trigger myriad physiological and morphological responses in plants. While many ethylene signaling pathway components have been identified and characterized, little is known about the function of the integral membrane protein EIN2, a central regulator of all ethylene responses. Here, we demonstrate that Arabidopsis thaliana EIN2 is a protein with a short half-life that undergoes rapid proteasome-mediated protein turnover. Moreover, EIN2 protein accumulation is positively regulated by ethylene. We identified two F-box proteins, EIN2 TARGETING PROTEIN and 2 (ETP1 and ETP2), that interact with the EIN2 carboxyl-terminal domain (CEND), which is highly conserved and sufficient to activate most ethylene responses. Overexpression of ETP1 or ETP2 disrupts EIN2 protein accumulation, and these plants manifest a strong ethylene insensitive phenotype. Furthermore, knocking down the levels of both ETP1 and ETP2 mRNAs using an artificial microRNA (amiRNA) leads to accumulation of EIN2 protein, resulting in plants that display constitutive ethylene response phenotypes. Finally, ethylene down-regulates ETP1 and ETP2 proteins, impairing their ability to interact with EIN2. Thus, these studies reveal that a complex interplay between ethylene, the regulation of ETP1/ETP2 F-box proteins, and subsequent targeting and degradation of EIN2 is essential for triggering ethylene responses in plants.

Keywords: ethylene treatment, genetic modification

overall_design: Six samples were analyzed.  There were three treatments with two biological replicates each.  The treatments are as follows:  3 week old Col-0 plants (air control), 3 week old Col-0 plants treated for 4 hours with ethylene gas (10 ppm), and artificial microRNA knockdown mutants, amiR-ETP1/2.

first: Hong

last: Qiao

first: Katherine

last: Chang

first: Junshi

last: Yazaki


title: Root transcript profiles of two Rorippa (Brassicaceae) species and their F1 hybrid after complete submergence

city: Amsterdam

first: Alex

last: Boonman

address: Kruislaan 318

department: IBED

institute: Universiteit van Amsterdam

summary:
Complete submergence represses photosynthesis and aerobic respiration causing rapid mortality in most terrestrial plants, but some species have evolved traits allowing them to survive prolonged flooding. Here, we studied the response to submergence of two species and their F1 hybrid in the genus Rorippa, which is related to the model Arabidopsis. We showed that these species have high tolerance to complete, deep submergence, but R. sylvestris survived longer than R. amphibia and the F1 hybrid. While the former restricted growth upon submergence, the latter two genotypes showed induced stem and petiole elongation and had higher aerenchyma contents, indicative of a low oxygen escape strategy.
Arabidopsis GeneChip microarrays were used for whole-genome transcript profiling of roots of young plants exposed to air or a 24-h submergence treatment, using a probe mask based on hybridisation of genomic DNA of both species to the arrays. The induction by the submergence treatment of genes involved in glycolysis and fermentation and repression of many energy consuming pathways was similar to the response to low oxygen of Arabidopsis and rice. Notably, sucrose synthases, glycolysis and fermentation genes were more strongly induced in the less tolerant R. amphibia than in R. sylvestris, which might indicate faster carbohydrate consumption of the former, while some genes involved in hydrogen peroxide scavenging were strongly and specifically induced in the latter. F1 hybrids showed a generally weaker response to submergence and an additive mode of gene action, which did not change by the submergence treatment.

Keywords: stress response and a comparison of genotypes

sample_organism:
Rorippa amphibia
Rorippa sylvestris
Rorippa anceps

overall_design: We used replicated clones of Rorippa amphibia, Rorippa sylvestris and their F1 hybrid. Plants were grown on sand in pots for three weeks, completely submerged in rain water for 24 h, or kept in air as a control. Three biological controls were collected per genotype, each consisting of a pool of three individuals. Roots were separated from the shoots, quickly rinsed and immediately frozen and used for RNA extraction and hybridization to Arabidopsis Ath1 GeneChips. Genomic DNA of Rorippa amphibia and Rorippa sylvestris was also hybridized to the GeneChips in order to filter out badly performing probes due to sequence divergences from Arabidopsis.

first: Peter

last: van Tienderen


title: Transcriptome analysis during axillary shoot outgrowth

status: Public on Nov 18 2009

summary:
In plant axillary bud dormancy and outgrowth are regulated by phytohoromones, but it is still unknown about its molecular mechanism. We reveal that Arabidopsis axillary buds located at axil of rosette leaves show dormancy and that this is broken by the decapitation of main stem, resulting in the bud outgrowth. To investigate about the molecular mechanisms of dormancy and outgrowth, we carried out gene expression analysis during axillary shoot outgrowth in Arabidopsis wild type Columbia accession. Since axillary buds did not initiate outgrowth (dormancy) at 5 day after bolting of main stem, we used 5-day bolted plants as a control (before decapitation). Then, main stems were decapitated, and axillary shoots were collected at 24 hours after decapitation (named as growing shoot). Total RNA was prepared from either control or growing shoots and used for the microarray analysis. We carried out duplicate microarray analysis using independent plant materials.Ref):Tatematsu et al., Plant Physiol. 138: 757-766 (2005).

Keywords: Expression profilling by array

overall_design: 4 samples were used in this experiment

last: Tatematsu


title: Expression data of ahg2-1, ahg2-1abi1-1, ahg2-1sid2-2, and WT Arabidopsis plants grown under normal growth conditions.

status: Public on Nov 27 2009

city: Kurashiki

first: Takashi

last: Hirayama

state: Okayama

department: Institute of Plant Science and Resources

institute: Okayama University

summary:
Arabidopsis ABA hpersensitive germination2-1 mutant shows an enhanced sensitivity to ABA. This mutant has higher levels of endogenous ABA. This mutant also exhibited SA hypersensitivity and dwarf phenotype. Regarding SA hypersensitivity, ahg2-1 exhibits higher endogenous SA level and an enhanced resistance to pathogenic bacteria. Since AHG2 encodes the Arabidopsis polyA specific ribonuclease that is involved in mRNA degradation, presumably abnormal accumulation of some mRNAs confers the unique phenotype. Transcriptome analyses are expected to offer information on the target of AHG2. In order to eliminate secondary effects of higher levels of ABA and SA, ahg2-1abi1-1 and ahg2-1sid2-2 double mutants were also examined. The transcriptome data revealed that; ahg2-1 confers unique gene expression profiles, ABA and SA affect the expression profiles of this mutant but many genes are independent of those plant hormone responses. Comparing with expression profiles of other mutants indicated that the ahg2-1 might affect mitochondrial function.

Keywords: strain comparison, ABA, SA

overall_design: To investigate the whole genome transcription profiles of an ABA and SA hypersensitive mutant ahg2-1, transcriptome analysis for wild type, ahg2-1, ahg2-1abi1-1, ahg2-1sid2-2 plants were conducted. The plants of those lines were grown on MS-pplante containing 0,2% sucrose for three weeks under normal conditions. Comparing the data among those four lines, the direct targets of the ahg2-1 mutation were analyzed using R. In addition, the deduced data were compared with transcriptome data of various mutants or stimuli deposited in public database.

first: Noriyuki

last: Nishimura