Genome-wide mapping of binding sites of the MADS domain protein FRUITFULL in Arabidopis thaliana
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE108455 | GEO | 2018/02/13
REPOSITORIES: GEO
Similar Datasets
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.
2022-10-04 | GSE199643 | GEO
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
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
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.
2023-03-30 | PXD037091 | Pride
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
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.
2014-06-23 | GSE49289 | GEO
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
Project description:Genome-wide mapping of binding sites of the MADS domain protein FRUITFULL in Arabidopis thaliana
| PRJNA427320 | ENA
Project description:The floral transition in Arabidopsis is tightly controlled by complex genetic regulatory networks in response to endogenous and environmental flowering signals. SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and SHORT VEGETATIVE PHASE (SVP), two key MADS-domain transcription factors, perceive these signals and function as antagonistic flowering regulators. To understand how they mediate the floral transition, we mapped in vivo binding sites of SOC1 and SVP using chromatin immunoprecipitation followed by hybridization to whole-genome tiling arrays (ChIP-chip). Genes encoding proteins with transcription regulator activity and transcription factor activity were the most enriched groups of genes bound by SOC1 and SVP, indicating their central roles in flowering regulatory networks. In combination with gene expression microarray studies, we further identified the genes whose expression was directly regulated by SOC1 or SVP. Among the common direct targets identified, APETALA2 (AP2)-like genes that repress FT and SOC1 expression were downregulated by SOC1, but upregulated by SVP, revealing a complex feedback regulation among key genes determining the integration of flowering signals. SOC1 regulatory regions were also accessed by SOC1 itself and SVP, suggesting that self-activation and repression by SVP contribute to the regulation of SOC1 expression. In addition, ChIP-chip analysis demonstrated that miR156e and miR172a, which are involved in the regulation of AP2-like genes, were direct targets of SOC1 and SVP, respectively. Taken together, these findings reveal that feedback regulatory loops mediated by SOC1 and SVP are essential components of the gene regulatory networks underpinning the integration of flowering signals during the floral transition. soc1-101D and 35S:SVP ChIPed with SOC1 or SVP polyclonal antibody respectively vs. soc1-2 or svp-41 in Arabidopsis 9-day-old whole seedlings
2012-02-01 | E-GEOD-33297 | biostudies-arrayexpress
Project description:The floral transition in Arabidopsis is tightly controlled by complex genetic regulatory networks in response to endogenous and environmental flowering signals. SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and SHORT VEGETATIVE PHASE (SVP), two key MADS-domain transcription factors, perceive these signals and function as antagonistic flowering regulators. To understand how they mediate the floral transition, we mapped in vivo binding sites of SOC1 and SVP using chromatin immunoprecipitation followed by hybridization to whole-genome tiling arrays (ChIP-chip). Genes encoding proteins with transcription regulator activity and transcription factor activity were the most enriched groups of genes bound by SOC1 and SVP, indicating their central roles in flowering regulatory networks. In combination with gene expression microarray studies, we further identified the genes whose expression was directly regulated by SOC1 or SVP. Among the common direct targets identified, APETALA2 (AP2)-like genes that repress FT and SOC1 expression were downregulated by SOC1, but upregulated by SVP, revealing a complex feedback regulation among key genes determining the integration of flowering signals. SOC1 regulatory regions were also accessed by SOC1 itself and SVP, suggesting that self-activation and repression by SVP contribute to the regulation of SOC1 expression. In addition, ChIP-chip analysis demonstrated that miR156e and miR172a, which are involved in the regulation of AP2-like genes, were direct targets of SOC1 and SVP, respectively. Taken together, these findings reveal that feedback regulatory loops mediated by SOC1 and SVP are essential components of the gene regulatory networks underpinning the integration of flowering signals during the floral transition.
2012-02-01 | GSE33297 | GEO