ArticleThe Plant cell2014
A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana.
Article in The Plant cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers, 1 of them a synthesis that pooled it.
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Who cites it
64 citing papers in PubMed, 1 synthesis or guideline pooled it, 119 citations in OpenAlex.
- ChIP-Hub provides an integrative platform for exploring plant regulome.Nature communications · 2022Pooled it
- Unveiling previously undescribed circadian clock regulators and action mechanisms via TurboID-based profiling of the LWD1 interactome inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Positional grammar of transcription factor binding partitions developmental and stress-response regulation in plants.Nature communications · 2026Article
- Widespread turnover of a conserved cis-regulatory code across 589 grass species.Molecular biology and evolution · 2026Article
- Protocols for Chromatin Immunoprecipitation Sequencing and qPCR to Investigate Pytohormone-Responsive Transcriptional Regulation in Plants.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Chromatin state architecture governs transcription factor accessibility across plant genomes.PLoS genetics · 2026Article
- BADDADAN: Mechanistic modelling of time-series gene module expression.Quantitative plant biology · 2025Article
- Genome-wide profiling of soybean WRINKLED1 transcription factor binding sites provides insight into seed storage lipid biosynthesis.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Comprehensive analysis of computational approaches in plant transcription factors binding regions discovery.Heliyon · 2024Article
- A dynamic regulome of shoot-apical-meristem-related homeobox transcription factors modulates plant architecture in maize.Genome biology · 2024Article
- Pectin methylesterification state and cell wall mechanical properties contribute to neighbor proximity-induced hypocotyl growth in Arabidopsis.Plant direct · 2024Article
- Review
- Methodology for Constructing a Knowledgebase for Plant Gene Regulation Information.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Characterization of Gene Regulatory Networks in Plants Using New Methods and Data Types.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Prediction of Transcription Factor Regulators and Gene Regulatory Networks in Tomato Using Binding Site Information.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Class I TCP transcription factor AtTCP8 modulates key brassinosteroid-responsive genes.Plant physiology · 2022Article
- Structural and Functional Analyses of Hub MicroRNAs in An Integrated Gene Regulatory Network of Arabidopsis.Genomics, proteomics & bioinformatics · 2022Article
- Cis-regulatory sequences in plants: Their importance, discovery, and future challenges.The Plant cell · 2022Review
- Both Binding Strength and Evolutionary Accessibility Affect the Population Frequency of Transcription Factor Binding Sequences in Arabidopsis thaliana.Genome biology and evolution · 2021Article
- Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators.Nature plants · 2021Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding the mechanisms underlying gene regulation is paramount to comprehend the translation from genotype to phenotype. The two are connected by gene expression, and it is generally thought that variation in transcription factor (TF) function is an important determinant of phenotypic evolution. We analyzed publicly available genome-wide chromatin immunoprecipitation experiments for 27 TFs in Arabidopsis thaliana and constructed an experimental network containing 46,619 regulatory interactions and 15,188 target genes. We identified hub targets and highly occupied target (HOT) regions, which are enriched for genes involved in development, stimulus responses, signaling, and gene regulatory processes in the currently profiled network. We provide several lines of evidence that TF binding at plant HOT regions is functional, in contrast to that in animals, and not merely the result of accessible chromatin. HOT regions harbor specific DNA motifs, are enriched for differentially expressed genes, and are often conserved across crucifers and dicots, even though they are not under higher levels of purifying selection than non-HOT regions. Distal bound regions are under purifying selection as well and are enriched for a chromatin state showing regulation by the Polycomb repressive complex. Gene expression complexity is positively correlated with the total number of bound TFs, revealing insights in the regulatory code for genes with different expression breadths. The integration of noncanonical and canonical DNA motif information yields new hypotheses on cobinding and tethering between specific TFs involved in flowering and light regulation.
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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.