ArticleGenome biology2022
The Arabidopsis APOLO and human UPAT sequence-unrelated long noncoding RNAs can modulate DNA and histone methylation machineries in plants.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 51 citations in OpenAlex.
- Structure-driven function of plant lncRNAs: conserved RNA architectures in transcriptional and post-transcriptional regulation.RNA biology · 2026Review
- DNA methylation either antagonizes or promotes Polycomb recruitment at transposable elements in Arabidopsis.Nature communications · 2026Article
- RNA regulation in plants.Science China. Life sciences · 2026Review
- RNA modifications and epigenetic regulation in plants.aBIOTECH · 2026Review
- Domestication-Selected Promoter Insertion in WRKY17 Increases Cadmium Sensitivity in Apple.Plant biotechnology journal · 2026Article
- In vivo RNA structure influences the translation and stability of plant long non-coding RNAs.Plant communications · 2026Article
- Integrative multi-omics analysis widens annotation and functional insights into long non-coding RNAs of Arabidopsis thaliana.Biology direct · 2026Article
- Long Non-Coding RNAs in the Cold-Stress Response of Horticultural Plants: Molecular Mechanisms and Potential Applications.International journal of molecular sciences · 2025Review
- Regulatory Landscapes of Non-Coding RNAs During Drought Stress in Plants.International journal of molecular sciences · 2025Review
- Review
- Noncoding RNAs as tools for advancing translational biology in plants.The Plant cell · 2025Review
- R-loops and small RNA regulatory interactions: mechanisms and clinical perspectives.Frontiers in cell and developmental biology · 2025Review
- Transcriptome Profiling Reveals Key Regulatory Networks for Age-Dependent Vernalization in Welsh Onion (International journal of molecular sciences · 2024Article
- LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) partially inhibits the transcriptional activation of FT by MYB73 and regulates flowering in Arabidopsis.The Plant journal : for cell and molecular biology · 2024Article
- LHP1 and INO80 cooperate with ethylene signaling for warm ambient temperature response by activating specific bivalent genes.Cell reports · 2024Article
- Epigenetics and plant hormone dynamics: a functional and methodological perspective.Journal of experimental botany · 2024Review
- Article
- GhVIM28, a negative regulator identified from VIM family genes, positively responds to salt stress in cotton.BMC plant biology · 2024Article
- Epiallelic variation of non-coding RNA genes and their phenotypic consequences.Nature communications · 2024Article
- Long noncoding RNA-mediated epigenetic regulation of auxin-related genes controls shade avoidance syndrome in Arabidopsis.The EMBO journal · 2023Article
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Authors and funding
14 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRNA-DNA hybrid (R-loop)-associated long noncoding RNAs (lncRNAs), including the Arabidopsis lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO), are emerging as important regulators of three-dimensional chromatin conformation and gene transcriptional activity.
resultsHere, we show that in addition to the PRC1-component LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), APOLO interacts with the methylcytosine-binding protein VARIANT IN METHYLATION 1 (VIM1), a conserved homolog of the mammalian DNA methylation regulator UBIQUITIN-LIKE CONTAINING PHD AND RING FINGER DOMAINS 1 (UHRF1). The APOLO-VIM1-LHP1 complex directly regulates the transcription of the auxin biosynthesis gene YUCCA2 by dynamically determining DNA methylation and H3K27me3 deposition over its promoter during the plant thermomorphogenic response. Strikingly, we demonstrate that the lncRNA UHRF1 Protein Associated Transcript (UPAT), a direct interactor of UHRF1 in humans, can be recognized by VIM1 and LHP1 in plant cells, despite the lack of sequence homology between UPAT and APOLO. In addition, we show that increased levels of APOLO or UPAT hamper VIM1 and LHP1 binding to YUCCA2 promoter and globally alter the Arabidopsis transcriptome in a similar manner.
conclusionsCollectively, our results uncover a new mechanism in which a plant lncRNA coordinates Polycomb action and DNA methylation through the interaction with VIM1, and indicates that evolutionary unrelated lncRNAs with potentially conserved structures may exert similar functions by interacting with homolog partners.
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