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R-Loop Mediated trans Action of the APOLO Long Noncoding RNA
Federico Ariel1, Leandro Lucero2, Aurelie Christ3
1Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Universities Paris-Sud, Evry and Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France; Instituto de Agrobiotecnología del Litoral, CONICET, FBCB, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe, Argentina.
Molecular Cell
|January 19, 2020
Summary
The long noncoding RNA APOLO (AUXIN-REGULATED PROMOTER LOOP) binds distant Arabidopsis DNA sites via R-loops. This interaction alters chromatin structure and regulates gene expression, crucial for plant development.
Area of Science:
- Molecular Biology
- Genetics
- Plant Biology
Background:
- Three-dimensional genome organization is essential for gene regulation in eukaryotes.
- Long noncoding RNAs (lncRNAs) are known to influence chromatin conformation and gene expression.
- The specific mechanisms by which lncRNAs interact with distant genomic loci are not fully understood.
Purpose of the Study:
- To investigate the function of the lncRNA APOLO (AUXIN-REGULATED PROMOTER LOOP) in Arabidopsis thaliana.
- To elucidate the mechanism by which APOLO interacts with genomic targets.
- To understand APOLO's role in transcriptional regulation and plant development.
Main Methods:
- Identifying APOLO target loci in the Arabidopsis genome.
- Investigating DNA-RNA duplex (R-loop) formation at target sites.
- Analyzing the interaction of APOLO with chromatin proteins, specifically LHP1.
- Assessing the impact of APOLO on chromatin 3D conformation and gene expression.
Main Results:
- APOLO recognizes multiple, spatially distant, and independent loci in the Arabidopsis genome.
- APOLO binding to target DNA occurs through sequence complementarity and R-loop formation.
- APOLO binding decoys the Polycomb Repressive Complex 1 component LHP1, altering local 3D chromatin conformation.
- APOLO coordinates the expression of distal, unrelated auxin-responsive genes during lateral root development.
Conclusions:
- R-loop formation and chromatin protein decoy are key mechanisms for lncRNA trans-acting functions on distant loci.
- APOLO utilizes R-loop formation to mediate chromatin changes and regulate distal gene expression in Arabidopsis.
- This study reveals a novel mechanism for lncRNA-mediated genome organization and gene regulation in plants.
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