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

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

PROVIDER: PRJNA820961 | ENA |

REPOSITORIES: ENA

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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

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

2022-10-04 | GSE199643 | GEO

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

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

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

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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

Global identification of targets of the Arabidopsis MADS-domain protein AGAMOUS-Like 15

Project description:Global identification of targets of the Arabidopsis MADS-domain protein AGAMOUS-Like 15

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The ZZ domain of p300 mediates specificity of the adjacent HAT domain for histone H3

Project description:The ZZ domain of p300 mediates specificity of the adjacent HAT domain for histone H3

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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.

2017-11-03 | GSE79553 | 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

Genome-Wide Binding Sites of the MADS-domain protein AGAMOUS-Like 15 (AGL15) in Arabidopsis

Project description:The MADS domain transcriptional regulator AGAMOUS-Like 15 promotes somatic embryogenesis by binding DNA and controlling downstream gene expression. Chromatin immunoprecipitation (ChIP) has been used to identify DNA fragments with which AGL15 is associated in vivo and a low-throughput approach to identify these fragments and determine regulatory consequences has revealed a role for AGL15 in GA catabolism that is relevant to embryogenesis. However, to understand more globally the gene networks in which AGL15 is involved, higher throughput methods to identify direct and indirect targets are needed. Here we report mapping of AGL15 in vivo binding sites using a ChIP-chip approach with Affymetrix tiling arrays for Arabidopsis and find that ~2000 sites represented in three biological replicates of the experiment are annotated to nearby genes.

2009-09-18 | GSE17717 | GEO

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