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Expression profiling and identification of targets of FRUITFULL in the Arabidopsis pistil/silique

ABSTRACT: Expression profiling and identification of targets of FRUITFULL in the Arabidopsis pistil/silique

PROVIDER: PRJNA316149 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR3288010.fastq.gz	Fastqsanger.gz
	SRR3288011.fastq.gz	Fastqsanger.gz
	SRR3288012.fastq.gz	Fastqsanger.gz
	SRR3288009.fastq.gz	Fastqsanger.gz

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Targets of FRUITFULL in the pistil/silique [ChIP-Seq]

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.

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Expression profile of Arabidopsis pistil/silique upon induction of FRUITFULL

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.

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Arabidopsis thaliana

Project description:Targets of FRUITFULL in the pistil/silique [ChIP-Seq]

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Arabidopsis thaliana

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Arabidopsis unfertilized pistil development and senescence

Project description:Transcription profiling of post-anthesis unfertilized pistil development and senescence in Arabidopsis, in a serie including samples from seven different stages according to pistil age in days post-anthesis (dpa). The time course started at anthesis and ended at 12-14 dpa, several days later of the loss of fruit set capacity. Keywords: Developmental time course

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Expression profiling and identification of targets of FRUITFULL in the Arabidopsis pistil/silique

Project description:This SuperSeries is composed of the SubSeries listed below.

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Identification of RoxS targets

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A plant-specific ISWI subunit is involved in fertility by inhibiting the pistil overgrowth

Project description:we identified the forkhead-associated domain 2 (FHA2) as a plant-specific subunit of an ISWI chromatin-remodeling complex in Arabidopsis. By in vivo and in vitro analyses, we demonstrated that FHA2 directly binds to RLT1 and RLT2, two redundant subunits of the ISWI complex in Arabidopsis. A reduced-fertility phenotype was observed in both the fha2 and rlt1/2 mutant plants and the phenotype was ascribed to overgrowth of the pistil during the floral development. However, the early-flowering phenotype of the rlt1/2 mutant was not shared by the fha2 mutant. Consistently, our RNA-seq analysis indicated that the fha2 mutant affects a subset of rlt1/2-regulated genes but not genes involved in the regulation of flowering time. This study demonstrates that FHA2 functions as a previously uncharacterized subunit of the Arabidopsis ISWI complex to exclusively regulate the pistil growth during the floral development.

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Identification of direct target genes of the tomato FRUITFULL homologs during ripening by promoter ChIP-chip

Project description:Tomato (Solanum lycopersicum) has two MADS-box FRUITFULL homologs, FUL1 and FUL2, both of which are able to interact with the master ripening regulator RIN. Here, we performed chromatin immunoprecipitation coupled with a DNA microarray (ChIP-chip) for the 2-kb upstream putative promoters of whole tomato predicted genes (ITAG2) for a large-scale identification of the direct target genes of FUL1 and FUL2 during ripening. The ChIP-chip with antibodies of FUL1 and FUL2 identified 1,877 and 1,919 of FUL1- and FUL2-binding sites, respectively, each of which was assigned a significantly high peak score (FDR<0.05) in at least two of the three biologically independent analyses. Using the information about genomic position of the FUL1- and FUL2-binding sites, we found 1,943 and 2,051 potential direct targets of FUL1 and FUL2, respectively, that carried one or more binding sites in the putative promoter or in other gene regions, such as exons, introns or a downstream region from the translation termination site (1-kb), where the promoter region of a neighbor gene are overlapped. The majority of the direct target genes are common between FUL1, FUL2 and RIN, suggesting that FUL1 and FUL2 act redundantly in the regulation of fruit ripening, and that these factors regulate the expression of their targets in a form of heteromer complex. Interestingly, the analysis also found direct targets unique to each of FUL1, FUL2 and RIN, implying their exclusive roles during ripening. Three biologically independent samples (chromatin-immunoprecipitated DNA and input DNA) recovered from the ripening tomato fruits.

2014-06-23 | E-GEOD-49125 | biostudies-arrayexpress