ArticleGenomics, proteomics & bioinformatics2022
Structural and Functional Analyses of Hub MicroRNAs in An Integrated Gene Regulatory Network of Arabidopsis.
Article in Genomics, proteomics & bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 25 citations in OpenAlex.
- Cascaded regulatory network composed of small RNAs involves in the symbiosis of Panax notoginseng and fungus Acremonium sp. D212.Scientific reports · 2026Article
- Single-molecule views of chromatin accessibility and structure during photomorphogenesis.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Cell-Type Specific miRNA Regulatory Network Responses to ABA Stress Revealed by Time Series Transcriptional Atlases in Arabidopsis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- The microRNA408-plantacyanin module balances plant growth and drought resistance by regulating reactive oxygen species homeostasis in guard cells.The Plant cell · 2024Article
- Differential regulation of miRNAs involved in the susceptible and resistance responses of wheat cultivars to wheat streak mosaic virus and Triticum mosaic virus.BMC genomics · 2024Article
- Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL.Nature communications · 2024Article
- Miniature Inverted-repeat Transposable Elements Drive Rapid MicroRNA Diversification in Angiosperms.Molecular biology and evolution · 2022Article
- PmiREN2.0: from data annotation to functional exploration of plant microRNAs.Nucleic acids research · 2022Article
- Integration of multi-omics technologies for crop improvement: Status and prospects.Frontiers in bioinformatics · 2022Article
- The Construction and Exploration of a Comprehensive MicroRNA Centered Regulatory Network in Foxtail Millet (Frontiers in plant science · 2022Article
- MicroRNA775 regulates intrinsic leaf size and reduces cell wall pectin levels by targeting a galactosyltransferase gene in Arabidopsis.The Plant cell · 2021Article
- Comprehensive Annotation and Functional Exploration of MicroRNAs in Lettuce.Frontiers in plant science · 2021Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MicroRNAs (miRNAs) are trans-acting small regulatory RNAs that work coordinately with transcription factors (TFs) to shape the repertoire of cellular mRNAs available for translation. Despite our growing knowledge of individual plant miRNAs, their global roles in gene regulatory networks remain mostly unassessed. Based on interactions obtained from public databases and curated from the literature, we reconstructed an integrated miRNA network in Arabidopsis that includes 66 core TFs, 318 miRNAs, and 1712 downstream genes. We found that miRNAs occupy distinct niches and enrich miRNA-containing feed-forward loops (FFLs), particularly those with miRNAs as intermediate nodes. Further analyses revealed that miRNA-containing FFLs coordinate TFs located in different hierarchical layers and that intertwined miRNA-containing FFLs are associated with party and date miRNA hubs. Using the date hub MIR858A as an example, we performed detailed molecular and genetic analyses of three interconnected miRNA-containing FFLs. These analyses revealed individual functions of the selected miRNA-containing FFLs and elucidated how the date hub miRNA fulfills multiple regulatory roles. Collectively, our findings highlight the prevalence and importance of miRNA-containing FFLs, and provide new insights into the design principles and control logics of miRNA regulatory networks governing gene expression programs in plants.
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