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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

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

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

Direct regulons of the master virulence regulator AtxA of Bacillus anthracis

Project description:Direct regulons of the master virulence regulator AtxA of Bacillus anthracis

| PRJNA705366 | ENA

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

Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor.

Project description:Flower development is controlled by the action of key regulatory transcription factors of the MADS-domain family. The function of these factors appears to be highly conserved among species based on mutant phenotypes. However, the conservation of their downstream processes is much less well understood, mostly because the evolutionary turnover and variation of their DNA-binding sites (BSs) among plant species have not yet been experimentally determined. Here, we performed comparative ChIP (chromatin immunoprecipitation)-seq experiments of the MADS-domain transcription factor SEPALLATA3 (SEP3) in two closely related Arabidopsis species: Arabidopsis thaliana and A. lyrata which have very similar floral organ morphology. We found that BS conservation is associated with DNA sequence conservation, the presence of the CArG-box BS motif and on the relative position of the BS to its potential target gene. Differences in genome size and structure can explain that SEP3 BSs in A. lyrata can be located more distantly to their potential target genes than their counterparts in A. thaliana. In A. lyrata, we identified transposition as a mechanism to generate novel SEP3 binding locations in the genome. Comparative gene expression analysis shows that the loss/gain of BSs is associated with a change in gene expression. In summary, this study investigates the evolutionary dynamics of DNA BSs of a floral key-regulatory transcription factor and explores factors affecting this phenomenon.

| S-EPMC4693976 | biostudies-literature

Evolutionary trends in the floral transcriptome: insights from one of the basalmost angiosperms, the water lily Nuphar advena (Nymphaeceae)

Project description:Current understanding of floral developmental genetics comes primarily from the core-eudicot model Arabidopsis thaliana. Here we explore the floral transcriptome of the basal angiosperm, Nuphar advena (water lily), for insights into the ancestral developmental program of flowers. Several thousand Nuphar genes with significantly up-regulated floral expression are identified, including homologs of the well-known ABCE floral regulators. However, strong similarities in the expression profiles of different organ categories contradict the organ-specific spatial expression domains predicted by the ABCE model. The broadly overlapping transcriptional programs observed among floral organs in Nuphar are shared with the magnoliid Persea americana (avocado), supporting the inference that this is the ancestral condition in angiosperms. Consequently, the predominantly organ-specific transcriptional programs that characterize Arabidopsis flowers (and perhaps other eudicots) are derived. The transcriptional landscapes in Arabidopsis correlate with a shift toward morphologically distinct floral organs, including differentiated sepals and petals, and a perianth distinct from stamens and carpels. In contrast to most eudicots, perianth organs are weakly differentiated in Nuphar and Persea, with staminodial intermediates between stamens and perianth in Nuphar, and between stamens and carpels in Persea. Our findings suggest that genetic regulation of more spatially discrete transcriptional programs underlies the evolution of floral morphology.

2011-07-20 | GSE23082 | GEO

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