The soil emergence-related transcription factor PIF3 regulates root penetration by interacting with the receptor kinase FER
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ABSTRACT:
PROVIDER: PRJNA934914 | ENA |
REPOSITORIES: ENA
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Project description:The cotyledons of etiolated seedlings from terrestrial flowering plants must emerge from the soil surface, while roots must penetrate the soil to ensure plant survival. We show here that the soil emergence related transcription factor PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) regulates root penetration via transducing external signals perceived by the receptor kinase FERONIA (FER) in Arabidopsis thaliana. The loss of FER function in the fer-4 mutant resulted in a severe defect in root penetration into hard soil or medium. Single-cell RNA-seq profiling of roots revealed a distinct cell clustering pattern, especially for root cap cells, and revealed PIF3 as a putative FER-regulated transcription factor. Biochemical, imaging, and genetic experiments confirmed that PIF3 is required for root soil penetration. Moreover, FER interacted with and stabilized PIF3, which then modulated the expression of mechanosensitive ion channels and the sloughing of outer cells in the root cap. We propose a novel mechanism of soil penetration by plant roots.
2023-12-31 | GSE225299 | GEO
Project description:Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF1, 3, 4 and 5) are critically necessary to maintaining this developmental state, and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using combined ChIP-seq and RNA-seq analyses, we have identified genes that are direct targets of PIF3 transcriptional regulation, and we provide evidence that the quartet collectively regulate these genes by shared, direct binding to the target promoters in promoting skotomorphogenesis. Four biological replicates data of PIF3-binding sites were collected by comparing the parallel ChIP samples from transgenic seedlings overexpressing Myc-epitope-tagged PIF3 (35S:PIF3-5xMyc, P3M) in pif3-3 null mutant background and the wild-type (WT) control.
2013-02-01 | E-GEOD-39215 | biostudies-arrayexpress
Project description:EGFR antagonism using monoclonal antibodies remains the only approved and targeted first line treatment option for non-resectable head and neck squamous cell carcinoma (HNSCC), yielding a modest 13% response rate. While it is clear that alternative growth factor receptor (GFR) signals govern refractory behavior towards EGFR antagonism, it remains unknown which upstream mechanisms control subcellular GFR activation. Here, we show that FER, a non-receptor tyrosine kinase, controls invasive tumor growth through dynamic GFR activation and recycling. Using patient derived organoid (PDO) models HNSCC we demonstrate that FER is essential for invasive growth in collagen extracellular matrix (ECM) networks. We show that inactivation of FER impairs growth factor dependent phosphorylation of EGFR-Y1068 and MET-Y1234/5. Additionally, FER controls ligand dependent endocytic recycling, and endocytic velocity, implying multifactorial functional regulation of proximal receptors during HNSCC invasion. Loss of function experiments using either genetic intervention or a FER PROteolysis-TArgeting Chimera (PROTAC) strategy in PDO-based xenograft mouse models, demonstrate that FER is essential for invasive growth and metastasis of HNSCC. Finally, we demonstrate direct clinical relevance by showing that FER expression levels correlate with poor survival in HNSCC patients. In sum, we conclude that FER is a master regulator of HNSCC invasive growth and metastasis, and nominate FER as a prominent candidate for targeted clinical intervention in HNSCC patients.
2024-03-31 | GSE255878 | GEO
Project description:Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF1, 3, 4 and 5) are critically necessary to maintaining this developmental state, and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using combined ChIP-seq and RNA-seq analyses, we have identified genes that are direct targets of PIF3 transcriptional regulation, and we provide evidence that the quartet collectively regulate these genes by shared, direct binding to the target promoters in promoting skotomorphogenesis. Transcriptomic profiles of the wild-type (WT), pif3 monogenic mutant, pif1pif4pif5 (pif145) triple mutant, and pif1pif3pif4pif5 (pifq) quadruple mutant were collected from biological triplicates using 3'-end-captured directional RNA-seq analysis.
2013-02-01 | E-GEOD-39214 | biostudies-arrayexpress
Project description:To identify changes in gene expression in daf-16 mutants, we compared expression in fer-15 young adults to expression in fer-15(b26); daf-16(m26) young adults grown at 25?C. At Stanford University, four samples of fer-15 and five samples of fer-15; daf-16 animals were prepared. At the University of Colorado, seven samples of fer-15 and six samples of fer-15; daf-16 was prepared. Set of arrays that are part of repeated experiments Place of growth: At Stanford vs Colorado Genotype: mutant strains vs wt (N2) mixed stage; some expts are reverse dye (wt in channel 2) Biological Replicate Computed
2008-07-29 | E-GEOD-12167 | biostudies-arrayexpress
Project description:To identify changes in gene expression in daf-16 mutants, we compared expression in fer-15 young adults to expression in fer-15(b26); daf-16(m26) young adults grown at 25?C. At Stanford University, four samples of fer-15 and five samples of fer-15; daf-16 animals were prepared. At the University of Colorado, seven samples of fer-15 and six samples of fer-15; daf-16 was prepared. Set of arrays that are part of repeated experiments Place of growth: At Stanford vs Colorado Genotype: mutant strains vs wt (N2) mixed stage; some expts are reverse dye (wt in channel 2)
2008-07-29 | GSE12167 | GEO
Project description:To identify the genes regulated by PIF3 under higher temperatures in the endosperm and embryo, we performed an RNA-seq analysis. We compared the transcriptome of WT and pif3 endosperm from seeds imbibed for 24h and 48h at 30˚C, which is a time when WT and pif3 seeds have not yet germinated We also compared the transcriptome of WT and pif3 embryos, after removing their endosperm 4h upon seed imbibition, cultured for 24h and 48h at 30˚C, which are times when WT and pif3 hypocotyl length was comparable
2023-06-23 | GSE224926 | GEO
Project description:To identify changes in gene expression in age-1 mutants, we compared expression in fer-15(b26) animals to expression in fer-15(b26); age-1(hx542) mutants. We prepared RNA from young adult fer-15(b26) mutants grown at 25?C (five samples prepared at Stanford University and six samples prepared at the University of Colorado) and young adult fer-15(b26); age-1(hx542) mutants (four samples at Stanford University and six samples at the University of Colorado). Set of arrays that are part of repeated experiments Place of growth: Stanford vs Colorado Genotype: mutant strains vs wt (N2) mixed stage; some expts are reverse dye Biological Replicate Computed
2008-07-29 | E-GEOD-12166 | biostudies-arrayexpress
Project description:To identify changes in gene expression in age-1 mutants, we compared expression in fer-15(b26) animals to expression in fer-15(b26); age-1(hx542) mutants. We prepared RNA from young adult fer-15(b26) mutants grown at 25?C (five samples prepared at Stanford University and six samples prepared at the University of Colorado) and young adult fer-15(b26); age-1(hx542) mutants (four samples at Stanford University and six samples at the University of Colorado). Set of arrays that are part of repeated experiments Place of growth: Stanford vs Colorado Genotype: mutant strains vs wt (N2) mixed stage; some expts are reverse dye
2008-07-29 | GSE12166 | GEO
Project description:Catharanthus roseus Receptor-Like Kinase 1-like (CrRLK1L) family proteins are considered as potential cell wall sensors in plants. CrRLK1L subfamily proteins harbor two extracellular malectin-like domains that may bind to cell wall polymers, and an intracellular kinase domain that transmits signals via the phosphorylation of intracellular substrates. In Arabidopsis, there are 17 CrRLK1L family members, among which FER is the most widely studied. A growing body of evidence support that FER not only regulates plant growth and development, such as root hair development, pavement cell morphogenesis, flowering, and fertilization, but also controls plant responses to biotic and abiotic stresses. To decipher molecular mechanisms underlying the FER-mediated regulation of plant growth and development, we performed an immunoprecipitation-mass spectrometry (IP-MS) assay using FER-GFP transgenic plants to search for FER-interacting proteins.
2024-08-30 | PXD047595 | Pride