Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA407477 | ENA |
REPOSITORIES: ENA
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Project description:How plants determine the final size of growing cells is an important, yet unanswered question. Root hairs provide an excellent model system to study this question since their final cell size is remarkably constant under given environmental conditions. In this study we demonstrate that a trihelix transcription factor GT-2-LIKE1 (GTL1) and its homolog DF1 repress root hair growth in Arabidopsis. Our transcriptional data, combined with genome-wide chromatin binding data, show that GTL1 and DF1 directly bind the RSL4 promoter and regulate its expression to repress root hair growth. Our data further show that GTL1 and RSL4 regulate each other as well as a set of common downstream genes, many of which have previously been implicated in root hair growth. This study therefore uncovers a core regulatory module that fine-tunes the extent of root hair growth by orchestrated actions of opposing transcription factors.
2018-02-15 | GSE103917 | GEO
Project description:RNAseq analysis of NGATHA loss and gain of function alleles
| PRJNA242915 | ENA
Project description:We performed a chromatin immunoprecipitation-based microarray experiment (ChIP chip) in order to identify GTL1 and DF1 direct target genes
2018-02-15 | GSE104010 | GEO
Project description:To understand how GTL1 regulates cell growth, we first identified its potential direct targets by the chromatin immunoprecipitation followed by the hybridization on an Affymetrix Arabidopsis Tiling 1.0R array (ChIP-chip). To enrich the genomic region bound by GTL1 in vivo, we harvested whole aerial parts of 12-day-old gtl1-1 plants complemented with the pGTL:GTL1:GFP constructs and immunoprecipitated the chromatin fragments associated with GTL1-GFP proteins using antibodies against GFP. After applying a cut-off P-values of 0.001of MAT (Model-based analysis of tiling array), we identified a total number of 3,900 putative immediate target genes that showed consistent binding by GTL1.
2013-08-01 | GSE40519 | GEO
Project description:To understand how GTL1 regulates cell growth, we first identified its potential direct targets by the chromatin immunoprecipitation followed by the hybridization on an Affymetrix Arabidopsis Tiling 1.0R array (ChIP-chip). To enrich the genomic region bound by GTL1 in vivo, we harvested whole aerial parts of 12-day-old gtl1-1 plants complemented with the pGTL:GTL1:GFP constructs and immunoprecipitated the chromatin fragments associated with GTL1-GFP proteins using antibodies against GFP. After applying a cut-off P-values of 0.001of MAT (Model-based analysis of tiling array), we identified a total number of 3,900 putative immediate target genes that showed consistent binding by GTL1. Two IP chips compared to two Input chips.
2013-08-01 | E-GEOD-40519 | biostudies-arrayexpress
Project description:Cyanide is stoichiometrically produced as a co-product of the ethylene biosynthesis pathway, and it is detoxified by the b-cyanoalanine synthase enzyme. The molecular and phenotypical analysis of T-DNA insertional mutants of the mitochondrial b-cyanoalanine synthase CYS-C1 suggests that discrete accumulation of cyanide is not toxic for the plant and does not alter mitochondrial respiration rates, but does act as a strong inhibitor of root hair development. The cys-c1 null allele is defective in root hair formation and accumulates cyanide in root tissues. The root hair defect is phenocopied in wild type plants by the exogenous addition of cyanide to the growth medium and is reversed by the addition of hydroxocobalamin. Hydroxocobalamin not only recovers the root phenotype of the mutant, but also the formation of ROS at the initial step of the root hair tip. Transcriptional profile analysis of the cys-c1 mutant reveals that cyanide accumulation acts as a repressor signal for several genes encoding enzymes involved in cell wall rebuilding and the formation of the root hair tip, as well as genes involved in ethylene signaling and metabolism. Our results demonstrate that mitochondrial b-cyanoalanine synthase activity is essential to maintain a low level of cyanide for proper root hair development.
2010-10-01 | GSE19242 | GEO
Project description:Phosphate (Pi) deficiency alters root hair length and frequency as a means of increasing the absorptive surface area of roots. Three partly redundant single R3 MYB proteins, CAPRICE (CPC), ENHANCER OF TRY AND CPC1 (ETC1) and TRIPTYCHON (TRY), positively regulate the root hair cell fate by participating in a lateral inhibition mechanism. To identify putative targets and processes that are controlled by these three transcription factors (TFs), we conducted transcriptional profiling of roots from Arabidopsis thaliana wild-type plants, and cpc, etc1 and try mutants grown under Pi-replete and Pi-deficient conditions using RNA-seq.
2015-06-20 | E-MTAB-4396 | biostudies-arrayexpress
Project description:Cyanide is stoichiometrically produced as a co-product of the ethylene biosynthesis pathway, and it is detoxified by the b-cyanoalanine synthase enzyme. The molecular and phenotypical analysis of T-DNA insertional mutants of the mitochondrial b-cyanoalanine synthase CYS-C1 suggests that discrete accumulation of cyanide is not toxic for the plant and does not alter mitochondrial respiration rates, but does act as a strong inhibitor of root hair development. The cys-c1 null allele is defective in root hair formation and accumulates cyanide in root tissues. The root hair defect is phenocopied in wild type plants by the exogenous addition of cyanide to the growth medium and is reversed by the addition of hydroxocobalamin. Hydroxocobalamin not only recovers the root phenotype of the mutant, but also the formation of ROS at the initial step of the root hair tip. Transcriptional profile analysis of the cys-c1 mutant reveals that cyanide accumulation acts as a repressor signal for several genes encoding enzymes involved in cell wall rebuilding and the formation of the root hair tip, as well as genes involved in ethylene signaling and metabolism. Our results demonstrate that mitochondrial b-cyanoalanine synthase activity is essential to maintain a low level of cyanide for proper root hair development. Using Affymetrix ATH1 GeneChips, we performed a comparative transcriptomic analysis of roots of the cys-c1 and wild type plants. Total RNA was extracted from roots of 14-days-old plants grown under identical conditions on MS medium (three biological replicates for each genotype), and these samples were used to prepare complementary RNA and and analyzed using the Affymetrix-Arabidopsis ATH1GeneChip array.
2010-10-01 | E-GEOD-19242 | biostudies-arrayexpress
Project description:Physiological mechanisms involved in root hair development in response to magnesium (Mg) availability are unclear. This study investigated the influence of Mg availability on root hair development in arabidopsis grown in different Mg concentrations ranging from 0.5 μM to 10 mM. After 7-d treatment, root hair development was enhanced in roots exposed to low Mg but was inhibited severely in roots grown in high Mg. Low Mg (0.5 µM) enhanced many genes like LRX1, COW1, EXP7 and ROP2 that control root hair development. Low Mg supply also increased concentrations of total Ca2+ and ROS in roots, but application of either BAPTA or DPI to low Mg treatment blocked the enhanced development of root hairs. The opposite was true when the plants under high Mg (3 mM) were supplied with Ca2+ or PMS. Besides, in roots under low Mg and high Mg, the most significant biological function enrichment were in the ‘oxidation reduction’, ‘cell wall organization’, ‘ion response’. This study demonstrated that Ca2+ and ROS played critically in controlling the Mg-induced development of root hairs. Meanwhile, transcriptome analysis associated with Mg supply contributed to a better understanding of molecular events responsible for sensing Mg status. Roots were sampled from five-week-cultivated Arabidopsis after 7 d treatment of low Mg (supplied with 0.5 μM Mg2+) and high Mg (supplied with 10 mM Mg2+).
2012-12-14 | E-GEOD-42899 | biostudies-arrayexpress
Project description:Gain-of-function mutants of SOC1 vs soc1-2
| PRJNA92935 | ENA