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Targets of FRUITFULL in the pistil/silique [ChIP-Seq]

ABSTRACT: To learn more about the role of FRUITFULL (FUL), in pistil/silique development, we performed a ChIP-seq experiment to identify direct targets of FUL in the pistil/silique.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE79554 | GEO | 2017/11/03

SECONDARY ACCESSION(S): PRJNA316152

REPOSITORIES: GEO

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Expression profile of Arabidopsis pistil/silique upon induction of FRUITFULL

Project description:To determine the genes that are regulated by FRUITFULL (FUL) in the pistil/silique, we identied differentially expressed genes after induction of FRUITFULL in ful-1 FUL-GR lines using the AGRONOMICS1 tiling array. The inflorescences of flowering plants were dipped in 10 uM DEX solution or in Mock Solution, and the flowers/siliques from stages 12-16 were harvested after 8 hours. RNA was extracted and DNase treated, and subsequent steps and hybridization to the AGRONOMICS Tiling array were performed by the Functional Genomics Center Zurich.

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Expression profiling and identification of targets of FRUITFULL in the Arabidopsis pistil/silique

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Protein interaction partners of FRUITFULL in inflorescence meristems and pistils by IP-MS.

Project description:To study the possibility that the tissue-specific gene targets and regulation by FUL are due to a different composition in the FUL transcription factor (TF) protein complex/es in both tissues, we determined the protein-protein interactions of FUL in planta. Inflorescence meristems (IMs) of 35S:AP1-GR ap1 cal pFUL:FUL-GFP plants were collected to identify meristem-specific protein complexes of FUL, and stage 12 - 16 pistils of pFUL:FUL-GFP ful-1 plants were collected for the pistil-specific FUL protein complexes. Protein complexes were isolated by immunoprecipitation (IP) using anti-GFP antibodies and protein identification was performed using LC-MS/MS, followed by label-free protein quantification.

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Project description:How transcription factors of a single family confer different functional specificities in vivo, is an important question in molecular biology. Even more intriguingly, a single transcription factor can regulate context- or tissue-specific target genes to achieve distinct functions. Here we show, using a variety of genome-wide techniques, that gene regulation and DNA binding site selection by the MADS domain protein FRUITFULL (FUL) is tissue-specific. FUL has a dual role in regulating floral transition and fruit development.

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Dual specificity and target gene selection by the MADS domain protein FRUITFULL

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Expression profiling and identification of targets of FRUITFULL in the Arabidopsis pistil/silique

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-11-03 | GSE79555 | GEO

Arabidopsis thaliana

Project description:Targets of FRUITFULL in the pistil/silique [ChIP-Seq]

| PRJNA316152 | ENA

Arabidopsis thaliana

Project description:Expression profile of Arabidopsis pistil/silique upon induction of FRUITFULL

| PRJNA316153 | ENA

Transcriptome profiling of tomato fruits of a FRUITFULL-suppressed line and rin mutant by next generation RNA sequencing

Project description:The tomato MADS-box FRUITFULL (FUL) homologs, FUL1 and FUL2, interact with the main ripening regulator RIPENING INHIBITOR (RIN). To clarify their role in fruit ripening, we generated FUL1/FUL2-suppressed transgenic lines by RNAi. We found that five transgenic lines bearing fruits that did not ripen normally: lycopene accumulation and increase of ethylene production were severely inhibited. We then performed next generation RNA sequencing (RNA-Seq) analysis of the fruits of a FUL1/FUL2-suppressed line (TF18) with those of the wild type (Ailsa Craig cultivar; AC) and rin mutant. The comparison of RNA-Seq data among them indicated that FUL1/FUL2-suppression significantly affected the expression of a larger portion of ripening-induced and -repressed genes than the rin mutation did. Moreover, the effect of FUL1/FUL2-suppression was observed not only in the fruits harvested at the wild type ripening age [45 days after pollination (DAP)] but also in those at the pre-ripening age (35 DAP). This suggests that the FUL homologs play an essential role in the regulation of fruit development and ripening, the role which covers a wider range of biological processes than RIN does. Differentially expressed genes (DEGs) between the wild type and TF18 fruits included known ripening-related genes such as ACS2 and ACS4 involved in ethylene production and PSY1 in carotenoid biosynthesis, consistent with the phenotype of TF18 fruits described above. The DEGs also included many direct RIN target genes, which supports the hypothesis that the FUL homologs regulate fruit ripening in a form of MADS-box complex with RIN. mRNA profiles of wild type (Ailsa Craig cultivar), rin mutant and FUL1/FUL2-suppressed tomato fruits harvested at 35DAP and 45 DAP were generated by next generation sequencing, in triplicate, using Illumina Hiseq2000.

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Genome-wide binding of FRUITFULL complexes (FUL-SOC1, FUL-AG-SEP3, FUL, FUL-AG, FUL-SEP3) determined by DNA-affinity purification sequencing (DAP-seq)

Project description:With this experiment, our objective is to identify the binding sites of MADS-domain protein complexes and determine if they exhibit binding to different targets or with differing affinities, which could be a mechanism to acquire target gene specificity. Specifically, we aim to investigate this phenomenon for the tetramers FUL-SOC1 and FUL-AG-SEP3, as they are enriched in different tissues, thus likely regulating distinct functions. FUL-SOC1 is enriched in the inflorescence meristem, whereas the FUL-AG-SEP3 complex is enriched in the siliques. Using the DAP-seq protocol, we established their genome-wide binding profiles and included other FUL complexes (FUL, FUL-AG, and FUL-SEP3) as controls.

2024-10-14 | GSE263113 | GEO

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