ArticleThe Plant cell2011
Prediction of regulatory interactions from genome sequences using a biophysical model for the Arabidopsis LEAFY transcription factor.
Article in The Plant cell, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed, 160 citations in OpenAlex.
- Two LEAFY homologs regulate floral patterning and development without affecting flowering time in kiwifruit.Journal of experimental botany · 2026Article
- Exploring silique number in Brassica napus L.: Genetic and molecular advances for improving yield.Plant biotechnology journal · 2024Review
- Reflections on the ABC model of flower development.The Plant cell · 2024Review
- The Function of Florigen in the Vegetative-to-Reproductive Phase Transition in and around the Shoot Apical Meristem.Plant & cell physiology · 2024Review
- LEAFY homeostasis is regulated via ubiquitin-dependent degradation and sequestration in cytoplasmic condensates.iScience · 2023Article
- Roles and evolution of four LEAFY homologs in floral patterning and leaf development in woodland strawberry.Plant physiology · 2023Article
- The F-box protein UFO controls flower development by redirecting the master transcription factor LEAFY to new cis-elements.Nature plants · 2023Article
- Estimating DNA-Binding Specificities of Transcription Factors Using SELEX-Seq.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Flower Development in Arabidopsis.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Greenscreen: A simple method to remove artifactual signals and enrich for true peaks in genomic datasets including ChIP-seq data.The Plant cell · 2022Article
- Article
- Temporal Dynamic Transcriptome Landscape Reveals Regulatory Network During the Early Differentiation of Female Strobilus Buds inFrontiers in plant science · 2022Article
- Beyond the Genetic Pathways, Flowering Regulation Complexity inInternational journal of molecular sciences · 2021Review
- LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate.Nature communications · 2021Article
- LEAFY, a Pioneer Transcription Factor in Plants: A Mini-Review.Frontiers in plant science · 2021Review
- Spatio-Temporal Dynamics of the Patterning ofFrontiers in plant science · 2021Article
- TERMINAL FLOWER1 Functions as a Mobile Transcriptional Cofactor in the Shoot Apical Meristem.Plant physiology · 2020Article
- Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana.Genome biology · 2020Article
- Identification, Characterization and Functional Analysis of C-Class Genes Associated with Double Flower Trait in Carnation (Plants (Basel, Switzerland) · 2020Article
- Proteomic analysis of a clavata-like phenotype mutant in Brassica napus.Genetics and molecular biology · 2020Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite great advances in sequencing technologies, generating functional information for nonmodel organisms remains a challenge. One solution lies in an improved ability to predict genetic circuits based on primary DNA sequence in combination with detailed knowledge of regulatory proteins that have been characterized in 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. Applying the model to other plant species, we could follow the evolution of the regulatory relationship between LFY and the AGAMOUS (AG) subfamily of MADS box genes and show that this link predates the divergence between monocots and eudicots. Remarkably, our model succeeds in detecting the connection between LFY and AG homologs despite extensive variation in binding sites. This demonstrates that the cis-element fluidity recently observed in animals also exists in plants, but the challenges it poses can be overcome with predictions grounded in a biophysical model. Therefore, our work opens new avenues to deduce the structure of regulatory networks from mere inspection of genomic sequences.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.