ArticleNature communications2022
Limited conservation in cross-species comparison of GLK transcription factor binding suggested wide-spread cistrome divergence.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed, 63 citations in OpenAlex.
- Arabidopsis GOLDEN2-LIKE transcription factors interact with ABA-INSENSITIVE 4 to modulate cotyledon greening in light-exposed etiolated seedlings.Journal of experimental botany · 2026Article
- Reactivation of a loss-of-function SlGLK2 allele by frame-restoring genome editing in tomato.Plant cell reports · 2026Article
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- Single-Cell CRISPR: An Efficient Strategy for Decoding Plant Cis-Regulatory Complexity.Plant biotechnology journal · 2026Review
- An OsGLK1/2-DGP1/2/3 feedback module regulates rice photosynthesis and yield.Science advances · 2026Article
- tRUBY: A convenient in planta tool for the detection of protein-DNA and protein-protein interactions.Molecules and cells · 2026Article
- Copper-sensitive OsSPL9 TF regulates expression of indica rice domestication-associated miRNAs and phenotypes.Communications biology · 2026Article
- Cis-regulatory editing of SD1 promoter enhances TCP19-mediated repression to optimize plant height in Kam sweet rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- How tomato leaves stay green: the role of SlGRAS17 and its partners.Plant physiology · 2026Article
- Regulation of chloroplast biogenesis and differentiation.Journal of experimental botany · 2026Review
- Biogenic retrograde signaling via GUN1 ensures thermotolerant chloroplast biogenesis during seedling establishment in Arabidopsis thaliana.Journal of integrative plant biology · 2026Article
- Many roads lead to a plant cistrome: mapping and interpreting transcription factor binding in plants.Genome biology · 2026Review
- Widespread turnover of a conserved cis-regulatory code across 589 grass species.Molecular biology and evolution · 2026Article
- Genome-scale transcriptome augmentation during Arabidopsis thaliana photomorphogenesis.Nature communications · 2025Article
- Organ-level gene-regulatory networks inferred from transcriptomic data reveal context-specific regulation and highlight novel regulators of ripening and ABA-mediated responses in tomato.Plant communications · 2025Article
- The chloroplast-targeted long noncoding RNA CHLORELLA mediates chloroplast functional transition across leaf ageing via anterograde signalling.Nature plants · 2025Article
- Altered chromatin accessibility in light and hormone responses of rice seedlings.Plant physiology · 2025Article
- Genomic and Cis-Regulatory Basis of a Plastic CAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Retrograde signals control dynamic changes to the chromatin state at photosynthesis-associated loci.Nature communications · 2025Article
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Authors and funding
14 authors at 6 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Non-coding cis-regulatory variants in animal genomes are an important driving force in the evolution of transcription regulation and phenotype diversity. However, cistrome dynamics in plants remain largely underexplored. Here, we compare the binding of GOLDEN2-LIKE (GLK) transcription factors in tomato, tobacco, Arabidopsis, maize and rice. Although the function of GLKs is conserved, most of their binding sites are species-specific. Conserved binding sites are often found near photosynthetic genes dependent on GLK for expression, but sites near non-differentially expressed genes in the glk mutant are nevertheless under purifying selection. The binding sites' regulatory potential can be predicted by machine learning model using quantitative genome features and TF co-binding information. Our study show that genome cis-variation caused wide-spread TF binding divergence, and most of the TF binding sites are genetically redundant. This poses a major challenge for interpreting the effect of individual sites and highlights the importance of quantitatively measuring TF occupancy.
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