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Arabidopsis thaliana

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

PROVIDER: PRJNA132641 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR070382.fastq.gz	Fastqsanger.gz
	SRR070383.fastq.gz	Fastqsanger.gz
	SRR070384.fastq.gz	Fastqsanger.gz
	SRR070385.fastq.gz	Fastqsanger.gz

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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

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Project description:A SAM oligomerization domain shapes the genomic binding landscape of the LEAFY transcription factor

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Genome wide binding sites of the Arabidopsis B3 domain protein FUSCA3

Project description:FUSCA3 (FUS3) is a B3 domain transcription factor that is a member of the LEAFY COTYLEDON (LEC) group of genes. The LEC genes encode proteins that also include LEC2, a B3 domain factor related to FUS3, and LEC1, a CCAAT box binding factor. LEC1, LEC2 and FUS3 are essential for plant embryo development. We report ChIP-chip experiments using the Affymetrix tiling array to globally map binding sites for FUS3. Fangfang Wang and Sharyn E. Perry (2013) Plant Physiology preview

2013-01-11 | GSE43291 | GEO

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Project description:Average hydroxymethylation levels on transcription factor binding sites obtained from ENCODE (ChIP-sequencing of GM12878 lymphoblastoid cell line). Data from 6 individuals at different time points.

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Project description:ChIPseq data for 31 CLL samples (12 controls, 19 tumor) of the CancerEpiSys-PRECiSe project; containing histone H3, histone modifications and transcription factor binding sites (CTCF, EBF1).

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