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Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor

ABSTRACT: Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor

OTHER RELATED OMICS DATASETS IN: GSE63463GSE63462GSE63464

PROVIDER: PRJNA267851 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1657470.fastq.gz	Fastqsanger.gz
	SRR1657471.fastq.gz	Fastqsanger.gz
	SRR1657481.fastq.gz	Fastqsanger.gz
	SRR1657472.fastq.gz	Fastqsanger.gz
	SRR1657473.fastq.gz	Fastqsanger.gz

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Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [RNA-Seq]

Project description:Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [RNA-Seq]

| PRJNA267853 | ENA

Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [ChIP-Seq]

Project description:Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [ChIP-Seq]

| PRJNA267854 | ENA

Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [ChIP-Seq]

Project description:Plant development is controlled by transcription factors (TFs) which form complex gene-regulatory networks. Genome-wide TF DNA-binding studies revealed that these TFs have several thousands of binding sites in the Arabidopsis genome, and may regulate the expression of many genes directly. Given the importance of natural variation in plant developmental programs, there is a need to understand the molecular basis of this variation at the level of developmental gene regulation. However, until now, the evolutionary turnover and dynamics of TF binding sites among plant species has not yet experimentally determined. Here, we performed comparative ChIP-seq studies of the MADS-box TF SEPALLATA3 (SEP3) in inflorescences of two Arabidopsis species: A. thaliana and A. lyrata. Comparative RNA-seq analysis shows that the loss/gain of BSs is often followed by a change in gene expression.

2015-10-11 | GSE63463 | GEO

Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [RNA-Seq]

2015-10-11 | GSE63462 | GEO

The F-box cofactor UFO redirects the LEAFY floral regulator to novel cis-elements

Project description:In angiosperms, flower patterning requires the localized expression of the APETALA3 (AP3) floral homeotic gene involved in petal and stamen development. AP3 is synergistically induced by the master transcription factor LEAFY (LFY) and the F-box protein UNUSUAL FLORAL ORGANS (UFO), but the molecular mechanism underlying this synergy has remained unknown. Here we show that the connection to ubiquitination pathways suggested by the F-box domain of UFO is mostly dispensable and that UFO instead acts by forming a transcriptional complex with LFY on newly discovered regulatory elements. The cryo-electron microscopy structure of the UFO-LFY-DNA complex shows that UFO-DNA contacts allows relocating LFY to novel DNA sites. Finally, we show that this complex has a deep evolutionary origin, largely predating flowering plants. This work unravels an unsuspected role for a member of one of the largest protein families in plants as a modulator of the DNA binding specificity of a master TF.

2023-01-01 | GSE204793 | GEO

Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor

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

2015-10-10 | GSE63464 | GEO

A biophysical DNA binding model for the LEAFY transcription factor reveals the evolutionary fluidity of its binding sites

Project description:Despite great advances in sequencing capacity, generating functional information for non-model organisms remains a challenge. One solution lies in an improved ability to predict genetic circuits based on primary DNA sequence combined with the characterization of regulatory molecules from model species. Here, we focus on the LEAFY (LFY) transcription factor, a conserved master regulator of floral development. Starting with biochemical and structural information, we built a biophysical model describing LFY DNA binding specificity in vitro that accurately predicts in vivo LFY binding sites in the Arabidopsis thaliana genome. Extending the model to other species, we show that it can correctly identify functional homologs of known LFY targets from Arabidopsis thaliana in other angiosperms, even if a functional shift between orthologs and paralogs has occurred. Moreover, this model demonstrates the evolutionary fluidity of the link between LFY and one of its target genes, underlining how this regulatory interaction can be conserved despite changes in position, sequence and affinity of the LFY binding sites. Our study shows that the cis-element fluidity recently illustrated in animals also exists in plants, and that it can be detected without any experimental work in each individual species, using a biophysical transcription factor model. A. thaliana LEAFY ChIP-seq w control, 2 replicates

2011-05-13 | E-GEOD-24568 | biostudies-arrayexpress

A biophysical DNA binding model for the LEAFY transcription factor reveals the evolutionary fluidity of its binding sites

2011-05-13 | GSE24568 | GEO

Spatiotemporal transcriptome atlas of water lily floral organogenesis provide insight into the evolutionary origin of novel traits of angiosperms [RNA-Seq]

Project description:Petals are a key evolutionary innovation of flowers that reshaped plant-pollinator interactions and underlie the dominance of angiosperms in terrestrial ecosystems, yet their evolutionary origin remains debated as the morphological inferences rarely connect directly to the regulatory programs inferred from extant flowering plants. We employed spatial transcriptome sequencing on serial floral buds of the basal angiosperm Nymphaea colorata, producing a spatiotemporal atlas of cell states during primordium initiation and the subsequent formation of tepals (sepals and petals), stamens and carpels. Our analyses identified multiple meristematic cell populations organized hierarchically at the floral base, with one population give rise to both initiating petals (or inner tepals) and stamens whereas a second population forms carpel primordia. Developmental trajectory reconstruction based on thousands of tissue-preferentially expressed genes uncovers a continuous fate transition from stamen primordia via developing stamens to inner tepals undergoing morphogenesis. Quantitative modeling of MADS-box tetramer composition reveals dosage-sensitive shifts that support the hypothesis that petaloid organs evolved from sterile stamens at the outer whorls. Trajectory modules further show stepwise incorporation of vegetative programs, particularly genes for polarity establishment and photosynthetic essential for leaf development into petal organogenesis. These findings support a model in which petal merger occurred through quantitative retuning and redeployment of ancestral regulatory networks that predate the origin of angiosperms, providing clues for understanding the evolutionary innovation and diversification of petaloid organs across flowering plants.

2026-07-10 | GSE338036 | GEO