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Abstract Understanding how transcription factor binding site (TFBS) location influences gene regulation remains a fundamental challenge in plants. Here we integrate conserved TFBS with single-nucleus chromatin accessibility and expression datasets to resolve how TFBS location relates to regulatory function. Although TF binding patterns are conserved and frequently enriched near the TSS, positional enrichment of TFBSs poorly predicts cell type-specific gene expression. Instead, cell type-specific gene expression aligns with conserved TFBSs that are embedded in cell type-restricted chromatin, which show TF family-specific distributions across distal promoter and genic regions. In contrast, TSS-proximal TFBSs are implicated in rapid, tissue-wide transcriptional stress responses, as supported by hormone-induced gene expression analysis. Finally, distal upstream regions contain conserved TF clusters that overlap rare cell type-specific accessible chromatin and are highly enriched for genes controlling embryonic and meristem patterning, including auxin and other hormone pathway components. This positional partitioning of regulatory function indicates that TFBS location encodes distinct regulatory programs for TFs.
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This content will become publicly available on October 1, 2026
A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution
Abstract Cis-regulatory elements (CREs) are essential for regulating gene expression, yet their evolutionary dynamics in plants remain elusive. Here we constructed a single-cell chromatin accessibility atlas forOryza sativafrom 103,911 nuclei representing 126 cell states across nine organs. Comparative genomics betweenO. sativaand 57,552 nuclei from four additional grass species (Zea mays,Sorghum bicolor,Panicum miliaceumandUrochloa fusca) revealed that chromatin accessibility conservation varies with cell-type specificity. Epidermal accessible chromatin regions in the leaf were less conserved compared to other cell types, indicating accelerated regulatory evolution in the L1-derived epidermal layer ofO. sativarelative to other species. Conserved accessible chromatin regions overlapping the repressive histone modification H3K27me3 were identified as potentially silencer-like CREs, as deleting these regions led to up-regulation of gene expression. This study provides a comprehensive epigenomic resource for the rice community, demonstrating the utility of a comparative genomics approach that highlights the dynamics of plant cell-type-specific CRE evolution.
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- Award ID(s):
- 2224729
- PAR ID:
- 10687615
- Author(s) / Creator(s):
- ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more »
- Publisher / Repository:
- Springer Nature
- Date Published:
- Journal Name:
- Nature Plants
- Volume:
- 11
- Issue:
- 10
- ISSN:
- 2055-0278
- Page Range / eLocation ID:
- 2050 to 2071
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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