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Sequential DNA affinity purification sequencing (seq-DAP-seq) data of SEP3-AGAPI

ABSTRACT: sequential DNA affinity purification sequencing (seq-DAP-seq) data of SEP3-AGAPI

PROVIDER: PRJNA699584 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13633402_1.fastq.gz	Fastqsanger.gz
	SRR13633402_2.fastq.gz	Fastqsanger.gz
	SRR13633403_1.fastq.gz	Fastqsanger.gz
	SRR13633403_2.fastq.gz	Fastqsanger.gz
	SRR13633404_1.fastq.gz	Fastqsanger.gz

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sequential DNA affinity purification sequencing (seq-DAP-seq) data of SEP3-AGAPI

Project description:In this study, we applied sequential DNA affinity purification sequencing (seq-DAP-seq) to identiy genome-wide binding of a heterocomplex formed by two transcription factors of the MADS familly SEP3 and AG(AP1-I) (AG with its I domain switched with that of AP1). We compared the genome wide binding of SEP3-AG(AP1-I) to that of our previously published SEP3-AG data

2021-07-08 | GSE166205 | GEO

Genome-wide binding of SEPALLATA3 (SEP3) and AGAMOUS (AG) complexes determined by sequential DNA-affinity purification sequencing

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

sequential DNA affinity purification sequencing (seq-DAP-seq) data of MADS SEP3-AG tetramerization mutants.

Project description:sequential DNA affinity purification sequencing (seq-DAP-seq) data of MADS SEP3-AG tetramerization mutants.

| PRJNA942911 | ENA

sequential DNA affinity purification sequencing (seq-DAP-seq) data of MADS SEP3-AG tetramerization mutants.

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

Genome-wide binding of FRUITFULL complexes (FUL-SOC1, FUL-AG-SEP3, FUL, FUL-AG, FUL-SEP3) determined by DNA-affinity purification sequencing (DAP-seq)

Project description:With this experiment, our objective is to identify the binding sites of MADS-domain protein complexes and determine if they exhibit binding to different targets or with differing affinities, which could be a mechanism to acquire target gene specificity. Specifically, we aim to investigate this phenomenon for the tetramers FUL-SOC1 and FUL-AG-SEP3, as they are enriched in different tissues, thus likely regulating distinct functions. FUL-SOC1 is enriched in the inflorescence meristem, whereas the FUL-AG-SEP3 complex is enriched in the siliques. Using the DAP-seq protocol, we established their genome-wide binding profiles and included other FUL complexes (FUL, FUL-AG, and FUL-SEP3) as controls.

2024-10-14 | GSE263113 | GEO

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Project description:In this study, we use DNA affinity purification sequencing to identiy genome-wide binding of LFY transcription factor, a master regulator of flower development in Arabidopsis. We generated two sets of data, one using genomic DNA from plant tissue, thus retain DNA methylation, as probe for DNA affinity purification (DAP-seq dataset), and the other using PCR amplified genomic DNA (without DNA methylation; AmpDAP-seq dataset).

2021-03-25 | GSE160013 | GEO

Genome-wide binding of SEPALLATA3 (SEP3) and AGAMOUS (AG) complexes determined by sequential DNA-affinity purification sequencing

Project description:Genome-wide binding of SEPALLATA3 (SEP3) and AGAMOUS (AG) complexes determined by sequential DNA-affinity purification sequencing

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The DNA affinity purification DAP-Seq assay [ChIP-seq]

Project description:As 5-15% of higher eukaryotes genes are transcription factors (TFs), the lack of transcription factor binding site (TFBS) information for most factors in most organisms limits the study of gene regulation. Here we describe a next-generation sequencing method, DNA affinity purification (DAP-Seq), an in vitro gDNA/TF interaction assay that produces whole-genome TFBS annotation for any factor from any organism. Like ChIP-Seq, DAP-Seq resolves TFBS as discrete peaks at genomic locations which allows for accurate motif prediction direct assignment of functionally relevant target genes, and shows better overlap with ChIP-Seq peaks than indirect motif assignment approaches. We applied DAP-Seq to a set of 50 transcription factors in eight Arabidopsis thaliana and one Zea Mays families to gain novel biological insight into TFBS architectures, functions, evolution and methylation-sensitivity. Overall, DAP-Seq offers a low-cost high-throughput approach to identify TFBS in native sequence context for any organism complete with all DNA chemical modifications.

2016-05-25 | GSE60142 | GEO

Genome-wide binding of FRUITFULL complexes (FUL-SOC1, FUL-AG-SEP3, FUL, FUL-AG, FUL-SEP3) determined by DNA-affinity purification sequencing (DAP-seq)

Project description:Genome-wide binding of FRUITFULL complexes (FUL-SOC1, FUL-AG-SEP3, FUL, FUL-AG, FUL-SEP3) determined by DNA-affinity purification sequencing (DAP-seq)

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DNA affinity purification sequencing (DAP-seq) data of LEAFY (LFY)

Project description:DNA affinity purification sequencing (DAP-seq) data of LEAFY (LFY)

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