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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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A basic helix-loop-helix transcription factors network mediates the brassinosteroid signal [RNA-seq]

ABSTRACT: To understand how atypical bHLH, INCREASED LEAF INCLINATION1 (ILI1)-BINDING bHLH-1 (IBH1) (At2g43060), and close homologue, IBH1-like1 (IBL1) (At4g30410), interact to regulate cell elongation, genome-wide RNA-Seq expression analyses of IBH1 and IBL1 gain-(IBH1OE, IBL1OE) and loss-of-function (ibh1 (SALK 049177), ibl1(SALK 119457)) mutants were conducted. For loss-of-function mutant, homozygous ibh1(SALK 049177) and ibl1(SALK 119457) were compared to wild type (Col). For gain-of-function mutant, homozygous 35Spro:IBH1-GFP and 35Spro:IBL1-GFP were compared to wild type (Col). Total RNAs were extracted from seedling of each genotypes. For each genotype two biological replicates were sequenced.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Kengo Morohashi

PROVIDER: E-GEOD-51119 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Helix-loop-helix/basic helix-loop-helix transcription factor network represses cell elongation in Arabidopsis through an apparent incoherent feed-forward loop.

Zhiponova Miroslava K MK Morohashi Kengo K Vanhoutte Isabelle I Machemer-Noonan Katja K Revalska Miglena M Van Montagu Marc M Grotewold Erich E Russinova Eugenia E

Proceedings of the National Academy of Sciences of the United States of America 20140206 7

Cell elongation is promoted by different environmental and hormonal signals, involving light, temperature, brassinosteroid (BR), and gibberellin, that inhibit the atypical basic helix-loop-helix (bHLH) transcription factor INCREASED LEAF INCLINATION1 BINDING bHLH1 (IBH1). Ectopic accumulation of IBH1 causes a severe dwarf phenotype, but the cell elongation suppression mechanism is still not well understood. Here, we identified a close homolog of IBH1, IBH1-LIKE1 (IBL1), that also antagonized BR ...[more]

PMID: 24505057

Similar Datasets

A basic helix-loop-helix transcription factors network mediates the brassinosteroid signal [RNA-seq]

Project description:To understand how atypical bHLH, INCREASED LEAF INCLINATION1 (ILI1)-BINDING bHLH-1 (IBH1) (At2g43060), and close homologue, IBH1-like1 (IBL1) (At4g30410), interact to regulate cell elongation, genome-wide RNA-Seq expression analyses of IBH1 and IBL1 gain-(IBH1OE, IBL1OE) and loss-of-function (ibh1 (SALK 049177), ibl1(SALK 119457)) mutants were conducted.

2014-03-05 | GSE51119 | GEO

A basic helix-loop-helix transcription factors network mediates the brassinosteroid signal [ChIP-seq]

Project description:To investigate the genome-wide occupancies of INCREASED LEAF INCLINATION1 (ILI1)-BINDING bHLH-1 (IBH1) (At2g43060), IBH1 ChIP analysis followed by direct sequencing (ChIP-Seq) on the p35S::IBH1-GFP (IBH1OE) line and a control line p35S::GFP (GFP OE) were conducted. Antibodies against GFP in the GFP-tagged IBH1 were utilized for immunoprecipitation of the endogenous protein-DNA complex, and the obtained DNA was subjected to next generation sequencing. Observation of genome-wide occupancies of atypical bHLH, INCREASED LEAF INCLINATION1 (ILI1)-BINDING bHLH-1 (IBH1) (At2g43060)

2014-03-05 | E-GEOD-51120 | biostudies-arrayexpress

A triple-HLH/bHLH Cascade Controls Cell Elongation Downstream of Multiple Hormonal and Environmental Signaling Pathways

Project description:The environmental and endogenous signals, light, temperature, brassinosteroid (BR), and gibberellin (GA), regulate cell elongation largely by controlling the expression of the PRE family helix-Loop-helix (HLH) factors, which promote cell elongation by interacting antagonistically with another HLH factor, IBH1. But the molecular mechanism by which PREs and IBH1 regulate gene expression has remained unknown. Here we show that IBH1 interacts with and inhibits a DNA-binding bHLH protein HBI1. Overexpression of HBI1 increased hypocotyl and petiole elongation, whereas dominant inactivation of HBI1 and its homologs caused a dwarf phenotype, indicating that HBI1 is a positive regulator of cell elongation. In vitro and in vivo experiments showed that HBI1 directly bound to the promoters and activated two EXPANSIN genes encoding cell wall-loosening enzymes; HBI1's DNA-binding and transcriptional activities were inhibited by IBH1, but the inhibitory effects of IBH1 were abolished by PRE1. The results indicate that PREs activate the DNA-binding bHLH factor HBI1 by sequestering its inhibitor IBH1. Altering each of the three factors affected plant sensitivities to BR, GA, temperature, and light. Our study demonstrates that PREs, IBH1 and HBI1 form a chain of antagonistic switches that controls cell elongation downstream of multiple external and endogenous signals. Compare the transcriptome of IBH1 and PRE1

2015-01-01 | E-GEOD-41766 | biostudies-arrayexpress

A basic helix-loop-helix transcription factors network mediates the brassinosteroid signal [ChIP-seq]

2014-03-05 | GSE51120 | GEO

HBI1 integrates hormonal and environmental signals to regulate the trade-off between growth and immunity (RNA-seq)

Project description:The trade-off between growth and immunity is crucial for survival in plants. An antagonistic interaction has been observed between the growth-promoting hormone brassinosteroid and pathogen associated molecular pattern (PAMP) signals, which induce immunity but inhibit growth, however the underlying molecular mechanism has remained unclear. The PRE-IBH1-HBI1 triple helix-loop-helix/basic helix-loop-helix (HLH/bHLH) cascade has been shown to mediate growth responses to several hormonal and environmental signals, but its downstream targets and role in immunity remain unknown. Here, we performed genome-wide analyses of HBI1 target genes in Arabidopsis. The results show that HBI1 regulates a set of genes that largely overlaps with targets of PIFs, but displays both similar and unique transcriptional activities compared to PIFs, supporting a role in fine-tuning the network through cooperation and antagonism with other DNA-binding factors of the network. Furthermore, HBI1 also negatively regulates a subset of defense response genes. Two PAMPs, flagellin and elongation factor, repressed HBI1 expression, whereas overexpression of HBI1 reduced the PAMP-induced growth inhibition, defense gene expression, reactive oxygen species (ROS) production, and flg22-induced resistance to Pseudomonas syringae pathovar tomato DC3000. These data indicate that HBI1 is a node for crosstalk between hormone and immune pathways. This study demonstrates that the PRE-IBH1-HBI1 module integrates hormone and pathogen signals, and thus plays a central role in the balance between growth and immunity in plants. Compare the transcriptome of HBI1-Ox and wild type.

2014-05-30 | E-GEOD-53078 | biostudies-arrayexpress

HBI1 integrates hormonal and environmental signals to regulate the trade-off between growth and immunity (ChIP-seq)

2014-05-30 | E-GEOD-53099 | biostudies-arrayexpress

35S:AtIBH1-SRDX Arabidopsis vs. wild type

Project description:In plants, basic helix-loop-helix (bHLH) transcription factors play important roles in the control of cell elongation. Two bHLH proteins, PACLOBTRAZOL RESISTANCE1 (PRE1) and Arabidopsis ILI1 binding bHLH1 (IBH1), antagonistically regulate cell elongation in response to brassinosteroid and gibberellin signaling, but the detailed molecular mechanisms by which these factors regulate cell elongation remain unclear. Here, we identify the bHLH transcriptional activators for cell elongation (ACEs) and demonstrate that PRE1, IBH1, and the ACEs constitute a triantagonistic bHLH system that competitively regulates cell elongation. In this system, the ACE bHLH transcription factors directly activate the expression of enzyme genes for cell elongation by interacting with their promoter regions. IBH1 negatively regulates cell elongation by interacting with the ACEs and thus interfering with their DNA binding. PRE1 interacts with IBH1 and counteracts the ability of IBH1 to affect ACEs. Therefore, PRE1 restores the transcriptional activity of ACEs, resulting in induction of cell elongation. The balance of triantagonistic bHLH proteins, ACEs, IBH1, and PRE1, might be important for determination of the size of plant cells. The expression of IBH1 and PRE1 is regulated by brassinosteroid, gibberellins, and developmental phase dependent factors, indicating that two phytohormones and phase-dependent signals are integrated by this triantagonistic bHLH system.

2012-11-19 | GSE35098 | GEO

Transcriptome profiling of Arabidopsis using strand-specific RNA-seq

Project description:We applied single-end strand-specific RNA-seq experiments to compare the abundance of natural antisense transcripts in Arabidopsis. Examination of 3 wild type (WT) organs, including leaves, inflorescences and siliques.

2013-12-23 | E-GEOD-49950 | biostudies-arrayexpress

ChIP-Seq analysis of Phytochrome Interacting Factor 5 DNA binding in low R/FR condition

Project description:Phytochrome Interacting Factor 5 plays an important role in adaptive responses of plants to shaded environment collectively called shade avoidance syndrome. PIF 5 belongs to the bHLH transcription factor family and regulated gene expression in a low R/FR dependent fashion. In this experiment we investigate PIF5-DNA-binding genome wide to generate a candidate list of genes, which are directly regulated by PIF5. ChIP-Seq sample of whole seedlings treated with low R/FR light

2012-05-02 | E-GEOD-35059 | biostudies-arrayexpress

Acute effects of light on alternative splicing in light-grown plants

Project description:We report the results of a genome-wide analysis of AS in Arabidopsis thaliana plants exposed to a 2h light pulse given in the middle of the night, a treatment that simulates the effects of early dawn or late dusk signals. This light affects the plant transcriptome at multiple regulatory layers, and that light regulation of mRNA levels of splicing regulatory factors is likely to mediate light effects on AS contributing to adjust plant physiological processes to the prevailing light environment. Arabidopsis seedlings of the Columbia ecotype were grown under 12 hr light/12 hr dark cycles for 9 days. On the 10th day, half of the plants were exposed to a two-hour pulse of white light given in the middle of the night (ZT18), while the other half were kept in darkness as controls. Both groups of plants were harvested at ZT 20 and light effects on mRNA levels and AS were analyzed through RNA-seq.

2016-08-09 | E-GEOD-68560 | biostudies-arrayexpress

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