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. 2025 Jul 3;198(3):kiaf263.
doi: 10.1093/plphys/kiaf263.

Conserved language of plant gene regulation

Neeta Lohani  1   2
Affiliations

Conserved language of plant gene regulation

Neeta Lohani. Plant Physiol. .
No abstract available

PubMed Disclaimer

Conflict of interest statement

Conflict of interest statement. None declared.

Figures

Figure.
Figure.
TFBM conservation analysis reveals 450-million-year evolutionary constraint in plant gene regulation. A) Phylogenetic relationships of major plant groups with available TFBM data and Chlorophytes (in grey) as an outgroup. Time scale indicates approximate divergence times, with the bryophyte-angiosperm split occurring ∼450 million years ago. B) Example of multiple TFs binding to the promoter of CRF5 (AT2G46310). Each colored bar represents a different TF binding site, with stronger binding shown in purple and weaker binding in orange. Green bars show accessible DNA regions. The overlapping binding events demonstrate competition between TFs for the same regulatory sequences. C) TFBM analysis pipeline. 764 TFs with experimentally validated motifs were subjected to TF family assignment and phylogenetic analysis, resulting in classification into 3 evolutionary categories: conserved (21 families with identical motifs across all members), semi-conserved (5 families with 2 to 4 motifs per family), and diverse (5 families with high motif diversity). Predictions were validated through amplified DNA affinity purification sequencing experiments using orthologous TFs in M. polymorpha. D) Experimental validation of motif conservation across 450 million years of evolution. Sequence logos show predicted motifs from Arabidopsis thaliana (left) compared to experimentally determined motifs from Marchantia polymorpha (right) for 7 TF families. High similarity between bryophyte and angiosperm motifs demonstrates remarkable evolutionary conservation of DNA-binding specificities across major plant lineages.
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