ArticleNature plants2025
Recruitment, rewiring and deep conservation in flowering plant gene regulation.
Article in Nature plants, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Predicting transcriptional regulators in plants in the era of artificial intelligence.Current opinion in plant biology · 2026Review
- Multimodal single cell analysis reveals a link between flowering and leaf initiation.bioRxiv : the preprint server for biology · 2026Article
- Positional grammar of transcription factor binding partitions developmental and stress-response regulation in plants.Nature communications · 2026Article
- ERF transcription factor StPti5 is a regulator of endophyte community maintenance in potato.The New phytologist · 2026Article
- PlantSetDelta: Mining regulatory features to enable interpretable gene set analysis in plants.Plant communications · 2026Article
- System drift in the evolution of plant meristem development.PLoS genetics · 2026Article
- Lineage-specific evolution of regulatory landscapes in a polyploid plant and its diploid progenitors.bioRxiv : the preprint server for biology · 2026Article
- Many roads lead to a plant cistrome: mapping and interpreting transcription factor binding in plants.Genome biology · 2026Review
- Transcription Factor Promiscuity Drives Regulatory Rewiring and Evolvability in Gene Networks in Bacteria.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Widespread turnover of a conserved cis-regulatory code across 589 grass species.Molecular biology and evolution · 2026Article
- Regulatory DNA Sequences Controlling Gene Expression in Leaf Phloem Cells.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Two deeply conserved non-coding sequences control PLETHORA1/2 expression and coordinate embryo and root development.Plant communications · 2025Article
- A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution.Nature plants · 2025Article
- Review
- A binding agreement.Nature plants · 2025Article
- Optimized DNA affinity purification sequencing determines relative binding affinity of transcription factors.Biology methods & protocols · 2025Article
Corrections and comments
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Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription factors (TFs) are proteins that bind DNA to control where and when genes are expressed. In plants, dozens of TF families interact with distinct sets of binding sites (TFBSs) that reflect each TF's role in organismal function and species-specific adaptations. However, defining these roles and understanding broader patterns of regulatory evolution remain challenging, as predicted TFBSs may lack a clear impact on transcription, and experimentally derived TF binding maps to date are modest in scale or restricted to model organisms. Here we present a scalable TFBS assay that we leveraged to create an atlas of nearly 3,000 genome-wide binding site maps for 360 TFs in ten species spanning 150 million years of flowering plant evolution. We found that TF orthologues from distant species retain nearly identical binding preferences, while on the same timescales the gain and loss of TFBSs are widespread. Within lineages, however, conserved TFBSs are over-represented and found in regions harbouring signatures of functional regulatory elements. Moreover, genes with conserved TFBSs showed striking enrichment for cell-type-specific expression in 14 single-nucleus RNA atlases, providing a robust marker of each TF's activity and developmental role. Finally, we compare distant lineages, illustrating how ancient regulatory modules were recruited and rewired to enable adaptations underlying the evolutionary success of grasses.
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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.