Arabidopsis thaliana
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-17610GSE17742
PROVIDER: PRJNA123281 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Global identification of targets of the Arabidopsis MADS-domain protein AGAMOUS-Like 15
| PRJNA118373 | ENA
Project description:Genome wide binding sites of the Arabidopsis B3 domain protein FUSCA3
| PRJNA185307 | ENA
Project description:The molecular mechanisms by which floral homeotic genes act as major developmental switches to specify the identity of floral organs, are still largely unknown. Floral homeotic genes encode transcription factors of the MADS-box family, which are supposed to assemble in a combinatorial fashion into organ-specific multimeric protein complexes. Major mediators of protein interactions are MADS-domain proteins of the SEPALLATA subfamily, which play a crucial role in the development of all types of floral organs. In order to characterize the roles of the SEPALLATA3 transcription factor complexes at the molecular level, we analyzed genome-wide the direct targets of SEPALLATA3. We used chromatin immunoprecipitation followed by ultrahigh-throughput sequencing or hybridization to whole-genome tiling arrays to obtain genome-wide DNA-binding patterns of SEPALLATA3. The results demonstrate that SEPALLATA3 binds to thousands of sites in the genome. Most potential target sites that were strongly bound in wild-type inflorescences, are also bound in the floral homeotic agamous mutant, which displays only the perianth organs, sepals and petals. Characterization of the target genes shows that SEPALLATA3 integrates and modulates different growth-related and hormonal pathways in a combinatorial fashion with other MADS-box proteins and possibly with non-MADS transcription factors. In particular, the results suggest multiple links between SEPALLATA3 and auxin signaling pathways. Our gene expression analyses link the genomic binding site data with the phenotype of plants expressing a dominant repressor version of SEPALLATA3, suggesting that it modulates auxin response to facilitate floral organ outgrowth and morphogenesis. Furthermore, the binding of the SEPALLATA3 protein to cis-regulatory elements of other MADS-box genes and expression analyses reveal that this protein is a key component in the regulatory transcriptional network underlying the formation of floral organs. ChIP experiments were performed on Arabidopsis wildtype and agamous mutant inflorescences using an antibody raised against a C-terminal peptide of SEP3. As control, ChIP experiments were performed on the sep3 mutant.
2009-04-20 | E-GEOD-14600 | biostudies-arrayexpress
Project description:A soybean ortholog of the Arabidopsis MADS-domain transcription factor (called GmAGL15) enhanced somatic embryogenesis from immature cotyledon explants of soybean when expressed via the 35S promoter compared to non transgenic tissue (cultivar Jack). To better understand how this occurs an expression microarray experiment was performed. publication: Q. Zheng and S.E. Perry. (2014). Alterations in the transcriptome of soybean in response to enhance somatic embryogenesis promoted by orthologs of AGAMOUS-Like 15 and AGAMOUS-Like 18. Plant Physiology, in press.
2014-01-30 | GSE54523 | GEO
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
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
Project description:In this study, we compare the DNA binding specifify and affinity of SEPALLATA3 and AGAMOUS complexes The MADS transcription factors, SEPALLATA3 (SEP3) and AGAMOUS (AG), are required for floral organ identity and determinacy of the floral meristem in Arabidopsis. Dimerization is obligatory for their DNA binding, however SEP3 and SEP3-AG also form tetrameric complexes. The goal of this study is to understand how homo and hetero-dimerization and tetramerization of MADS TFs affect genome-wide DNA-binding patterns. Using a modified sequential DNA affinity purification sequencing protocol (seq-DAP-seq), we selectively purified SEP3 homomeric and SEP3-AG heteromeric complexes, including the dimeric SEP3 tet-AG complex and the tetrameric SEP3-AG complex, and determined their genome-wide binding.
2020-09-07 | GSE150528 | GEO
Project description:Genome-wide mapping of binding sites of the MADS domain protein FRUITFULL in Arabidopis thaliana
| PRJNA427320 | ENA
Project description:Genome-Wide binding sites of two MADS-domain transcription factors SOC1 and SVP in Arabidopsis during the floral transition
| PRJNA149273 | ENA
Project description:Transcript accumulation was measured using the Affymetrix Arabidopsis ATH1 Genome Array [ATH1-121501] to document changes in response to the MADS-domain transcription factor AGAMOUS-Like 15 during somatic embryogenesis. A somatic embryo system was used where mature seed is allowed to complete germination in liquid MS media containing 2,4-D and seedlings produce somatic embryos from the shoot apical meristem (SAM) region. The frequency with which these embryos are produced directly correlates with AGL15 accumulation.
2009-09-18 | GSE17610 | GEO