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Genome-wide identification of FHY3 binding sites in Arabidopsis floral organ

ABSTRACT: Genome-wide identification of FHY3 binding sites in Arabidopsis floral organ

PROVIDER: PRJNA289111 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2046520_1.fastq.gz	Fastqsanger.gz
	SRR2046520_2.fastq.gz	Fastqsanger.gz
	SRR2046521.fastq.gz	Fastqsanger.gz
	SRR2046522.fastq.gz	Fastqsanger.gz
	SRR2046523.fastq.gz	Fastqsanger.gz

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Genome-wide identification of FHY3 binding sites in Arabidopsis floral organ (ChIP-Seq)

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Genome-wide identification of FHY3 binding sites in Arabidopsis floral organ (RNA-Seq)

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Genome-wide identification of FHY3 binding sites in Arabidopsis floral organ (ChIP-Seq)

Project description:To identify FHY3 associated genes in floral organ. We performed ChIP-seq using 35S:3FLAG-FHY3-3HA fhy3-4 tansgenic plants. A total of 21, 24 and 37 million reads were obtained from two replicates and input library, respectively, which were uniquely mapped to the Arabidopsis genome by Bowtie2 software resulting in 1885 FHY3 binding peaks. 84% of FHY3 binding sites (1580 loci) were subsequently assigned to genic regions and grouped into 2192 genes in flower. Inflorescence of 35S:3FLAG-FHY3-3HA fhy3-4 containing stage 8 and younger flowers were harvested for ChIP-seq analysis with anti-FLAG antibodies. No antibody served as negative control. The chromatin DNA from two distinct biological replicates and an input DNA sample were subjected to ultra-high-throughput Solexa (Illumina) sequencing.

2016-07-28 | E-GEOD-69422 | biostudies-arrayexpress

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Project description:To identify FHY3 regulated genes in floral organ. We performed RNA-seq using Ler, ag-10, fhy3-68, ag-10 fhy3-68. Inflorescence of Ler, ag-10, fhy3-68, ag-10 fhy3-68 containing stage 8 and younger flowers were harvested forRNA-seq analysis two distinct biological replicates were subjected to ultra-high-throughput Solexa (Illumina) sequencing.

2016-07-28 | E-GEOD-69424 | biostudies-arrayexpress

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.

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Arabidopsis thaliana

Project description:Genome-wide identification of FHY3 binding sites in Arabidopsis floral organ (ChIP-Seq)

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Project description:Genome-wide identification of FHY3 binding sites in Arabidopsis floral organ (RNA-Seq)

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Project description:DLX3 is a homeodomain transcription factor involved in amelogenesis. Mutations in DLX3 in human lead to Tricho-Dento-Osseous syndrome featuring enamel hypoplasia and hypomineralization. Here we investigated the distribution of DLX3 DNA binding sites in rat enamel organ using ChIP-seq.

2020-02-11 | GSE85451 | GEO

Genome-wide binding sites for Arabidopsis REPLUMLESS

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Project description:The MADS-domain transcription factor APETALA1 (AP1) is a key regulator of Arabidopsis flower development. To understand the molecular mechanisms underlying AP1 function, we identified its target genes during floral initiation using a combination of gene expression profiling and genome-wide binding studies. Many of its targets encode transcriptional regulators, including known floral repressors. The latter genes are down-regulated by AP1, suggesting that it initiates floral development by abrogating the inhibitory effects of these genes. While AP1 acts predominantly as a transcriptional repressor during the earliest stages of flower development, regulatory genes known to be required for floral organ formation were found to be activated by AP1 at more advanced stages, indicating a dynamic mode of action. Our results further imply that AP1 orchestrates floral initiation by integrating growth, patterning and hormonal pathways. We used the AP1-GR system to conduct chromatin immunoprecipitation experiments with AP1-specific antibodies followed by deep-sequencing (ChIP-Seq) in order to determine AP1 binding sites on a genome-wide scale. Samples were generated from tissue in which the AP1-GR protein was induced for 2h using a single treatment of 1 uM DEX to the shoot apex. As control, we performed ChIP experiments using the same antibody on uninduced tissue. Experiments were done in two biological replicates.

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