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

ABSTRACT: 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.

ORGANISM(S): synthetic construct

PROVIDER: GSE199643 | GEO | 2022/10/04

REPOSITORIES: GEO

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

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.

2022-10-03 | GSE194055 | GEO

Genome-wide mapping of binding sites of the MADS domain protein FRUITFULL in Arabidopis thaliana

Project description:FUL has a dual role in regulating floral transition and fruit development. We used ChIP-seq to map and compare the FUL binding events in the two different tissues.

2018-02-13 | GSE108455 | GEO

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.

2014-06-23 | E-GEOD-49289 | biostudies-arrayexpress

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

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

| PRJNA798963 | ENA

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

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

| PRJNA820961 | ENA

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

2014-06-23 | GSE49289 | GEO

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

Project description: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.

2017-11-03 | GSE79554 | GEO

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.

2017-11-03 | GSE79553 | GEO

A Functional Allele of CsFUL1 Regulates Fruit Length through Repressing CsSUP and Inhibiting Auxin Transport in Cucumber

Project description:Cucumber (Cucumis sativus L.) is an important vegetable crop bearing fleshy pepo fruits that harvested immature. The fruit length is one of the most important agricultural traits that directly determine the fruit yield and affects fruit quality, but the regulatory mechanism of fruit length variation remains elusive. Here we found a FRUITFULL-like MADS-box gene CsFUL1 functions as a key repressor for fruit length regulation in cucumber. The expression of CsFUL1 is highly enriched in male flowers and fruits, and negatively correlated with fruit length in different cucumber lines. Notably, a key SNP in CsFUL1 was selected during cucumber domestication for long fruit. Ectopic expression of CsFUL1 was unable to rescue the indehiscent fruit phenotype of ful-1 in Arabidopsis. Overexpression of CsFUL1 resulted in increased floral organs and reduced fruit length, whereas knockdown of CsFUL1 led to elongated fruit in cucumber. Transcriptome and biochemical analyses showed that CsFUL1 regulates fruit length through two pathways: one by inhibiting the PIN-FORWED (PIN1/7)-mediated auxin transport and thus downregulates auxin related genes in the fruit, and the other by forming a tetramer with other MADS-box genes to repress the CsSUP-mediated cell division and cell expansion. In addition, we found that CsFUL1 promotes locule number variation through the classical CsWUS-CsCLV pathway. Our findings uncover the regulatory commonality and specificity during development of different fruit types, and provide an important candidate gene to customize fruit length during cucumber breeding.

2020-03-28 | GSE103592 | GEO

Differences in DNA-binding specificity of floral homeotic protein complexes predict organ-specific target genes

Project description:Floral organ identities in plants are specified by the combinatorial action of homeotic master regulatory transcription factors (TFs). How these factors achieve their regulatory specificities is however still largely unclear. Genome-wide in vivo DNA binding data show that homeotic MADS-domain proteins recognize partly distinct genomic regions, suggesting that DNA binding specificity contributes to functional differences of homeotic protein complexes. We used in vitro systematic evolution of ligands by exponential enrichment followed by high throughput DNA sequencing (SELEX-seq) on several floral MADS-domain protein homo- and heterodimers to measure their DNA-binding specificities. We show that specification of reproductive organs is associated with distinct binding preferences of a complex formed by SEPALLATA3 (SEP3) and AGAMOUS (AG). Binding specificity is further modulated by different binding site (BS) spacing preferences. Combination of SELEX-seq and genome-wide DNA binding data allows to differentiate between targets in specification of reproductive versus perianth organs in the flower. We validate the importance of DNA-binding specificity for organ-specific gene regulation by modulating promoter activity through targeted mutagenesis. Our study shows that intrafamily protein interactions affect DNA-binding specificity of floral MADS-domain proteins. DNA-binding specificity of individual dimers, as well as DNA-binding preferences of higher-order complexes differ between floral homeotic protein complexes. Differential DNA-binding of MADS-domain protein complexes plays a role in the specificity of target gene regulation.

2017-10-16 | GSE95730 | GEO

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