Global identification of targets of the Arabidopsis MADS-domain protein AGAMOUS-Like 15
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ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-17610GSE17742
PROVIDER: PRJNA118373 | ENA |
REPOSITORIES: ENA
Similar Datasets
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: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:This SuperSeries is composed of the SubSeries listed below.
2009-09-18 | GSE17742 | GEO
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. Keywords: ChIP-chip
2009-04-21 | GSE14635 | GEO
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.
2009-04-21 | GSE14600 | GEO
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 genes encode transcription factors (TF) that act as master regulators of plant reproduction and flower development. The SEPALLATA (SEP) MADS subfamily is not only absolutely required for the development of floral organs, but also plays roles in inflorescence architecture and determinacy of the floral meristem. The SEPs act as organizers of MADS complexes and are able to form both heterodimers and heterotetramers in vitro. To date, the MADS TF complexes characterized in angiosperm floral organ development contain at least one SEP TF. Whether DNA-binding by SEP-containing dimeric MADS complexes are sufficient for launching floral organ identity programs, however, is not clear as only defects in floral meristem determinacy were observed in tetramerization impaired SEP mutants. Here we used a combination of genome-wide binding studies, high resolution structural studies of the SEP3-AGAMOUS tetramerisation domain, structure-based mutagenesis and complementation experiments in sep1 sep2 sep3 and sep1 sep2 sep3 ag-4 plants transformed with versions of SEP3 encoding tetramerization mutants. We demonstrate that while SEP3 heterodimers are able to bind DNA both in vitro and in vivo and recognize the majority of SEP3 wild type binding sites genome-wide, tetramerisation is not only required for floral meristem determinacy, but also absolutely required for floral organ identity in the second, third and fourth whorls.
2024-04-30 | GSE227012 | 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: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: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. Comparison of transcriptomes of non-transgenic tissue to 35S:GmAGL15 tissue at the time of explant preparation (0 days) and 3 and 7 days after induction of somatic embryogenesis by placement on medium containing 2,4-D.
2014-01-30 | E-GEOD-54523 | biostudies-arrayexpress