ABA-responsive transcription factors converge on evolutionarily layered MIR loci potentially integrating developmental and stress adaptation programs
Abstract
Abscisic acid (ABA) is a central regulator of plant drought adaptation, orchestrating extensive transcriptional reprogramming through multiple stress-responsive transcription factors (TFs). Although ABA-associated TF networks regulating protein-coding genes have been extensively studied, how these TFs are associated with microRNA (miRNA) regulation during stress adaptation remains poorly understood. Here, we re-analyzed publicly available ChIP-seq datasets for 21 ABA-responsive TFs in Arabidopsis thaliana to systematically examine TF occupancy at miRNA loci. We identified ten MIR loci co-occupied by at least 18 ABA-associated TFs, including members of the bZIP, NAC, MYB, HD-ZIP, NF-Y, AP2/ERF, and zinc-finger TF families. ChIP-seq peak analysis revealed substantial TF occupancy at several MIR loci, including MIR156D, MIR166A, MIR408, MIR168A, MIR824, MIR163, MIR779, and MIR170, whereas MIR399C displayed distal peak localization and was excluded from subsequent analyses. Quantitative RT-PCR analyses further showed that most pri-miRNAs were transcriptionally repressed by ABA and PEG-induced osmotic stress, while pri-miR824 was strongly induced under both treatments. Together, our findings reveal associations between ABA-responsive TF occupancy and MIR loci and provide expression-based evidence for their responsiveness to ABA and osmotic stress. In light of the distinct evolutionary histories previously reported for these MIR families, we propose that ABA-responsive MIR loci constitute an evolutionarily layered regulatory landscape that may link ABA-responsive transcriptional networks with developmental and stress-related processes in plants.
Related
- An evolutionarily conserved interferon-responsive oligodendroglial state emerges during white matter aging
- Multi‐Omics Analysis Uncovers the Salicylic Acid and Ethylene‐Responsive Transcription Factor‐Mediated Defence Mechanism of Panax notoginseng to Panax notoginseng Virus Y
- Generative design of functional disordered regions in a developmental transcription factor
- A phosphorylation-gated GAPDH-MAPK6-LBD1 module controls drought-responsive transcription
- Jasmonate-responsive group IX AP2/ERF transcription factors control the biosynthesis of benzylisoquinoline alkaloids
BibTeX
@article{liu2026abaresponsive,
title = {{ABA-responsive transcription factors converge on evolutionarily layered MIR loci potentially integrating developmental and stress adaptation programs}},
author = {Wenli Liu and Xin Zhao and Junjie Liu and Lei Li and Yanzhi Yang},
journal = {Frontiers in Plant Science},
year = {2026},
month = nov,
doi = {10.3389/fpls.2026.1884351},
url = {https://www.frontiersin.org/articles/10.3389/fpls.2026.1884351},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - ABA-responsive transcription factors converge on evolutionarily layered MIR loci potentially integrating developmental and stress adaptation programs
AU - Wenli Liu
AU - Xin Zhao
AU - Junjie Liu
AU - Lei Li
AU - Yanzhi Yang
PY - 2026
DA - 2026/11/02
JO - Frontiers in Plant Science
DO - 10.3389/fpls.2026.1884351
UR - https://www.frontiersin.org/articles/10.3389/fpls.2026.1884351
AB - Abscisic acid (ABA) is a central regulator of plant drought adaptation, orchestrating extensive transcriptional reprogramming through multiple stress-responsive transcription factors (TFs). Although ABA-associated TF networks regulating protein-coding genes have been extensively studied, how these TFs are associated with microRNA (miRNA) regulation during stress adaptation remains poorly understood. Here, we re-analyzed publicly available ChIP-seq datasets for 21 ABA-responsive TFs in Arabidopsis thaliana to systematically examine TF occupancy at miRNA loci. We identified ten MIR loci co-occupied by at least 18 ABA-associated TFs, including members of the bZIP, NAC, MYB, HD-ZIP, NF-Y, AP2/ERF, and zinc-finger TF families. ChIP-seq peak analysis revealed substantial TF occupancy at several MIR loci, including MIR156D, MIR166A, MIR408, MIR168A, MIR824, MIR163, MIR779, and MIR170, whereas MIR399C displayed distal peak localization and was excluded from subsequent analyses. Quantitative RT-PCR analyses further showed that most pri-miRNAs were transcriptionally repressed by ABA and PEG-induced osmotic stress, while pri-miR824 was strongly induced under both treatments. Together, our findings reveal associations between ABA-responsive TF occupancy and MIR loci and provide expression-based evidence for their responsiveness to ABA and osmotic stress. In light of the distinct evolutionary histories previously reported for these MIR families, we propose that ABA-responsive MIR loci constitute an evolutionarily layered regulatory landscape that may link ABA-responsive transcriptional networks with developmental and stress-related processes in plants.
SN - 1664-462X
ER -