R-Loop Mediated trans Action of the APOLO Long Noncoding RNA.

Federico Ariel, Leandro Lucero, Aurelie Christ, Maria Florencia Mammarella, Teddy Jegu, Alaguraj Veluchamy, Kiruthiga Mariappan, David Latrasse, Thomas Blein, Chang Liu, Moussa Benhamed, Martin Crespi

Research output: Contribution to journalArticlepeer-review

132 Scopus citations


In eukaryotes, three-dimensional genome organization is critical for transcriptional regulation of gene expression. Long noncoding RNAs (lncRNAs) can modulate chromatin conformation of spatially related genomic locations within the nucleus. Here, we show that the lncRNA APOLO (AUXIN-REGULATED PROMOTER LOOP) recognizes multiple distant independent loci in the Arabidopsis thaliana genome. We found that APOLO targets are not spatially associated in the nucleus and that APOLO recognizes its targets by short sequence complementarity and the formation of DNA-RNA duplexes (R-loops). The invasion of APOLO to the target DNA decoys the plant Polycomb Repressive Complex 1 component LHP1, modulating local chromatin 3D conformation. APOLO lncRNA coordinates the expression of distal unrelated auxin-responsive genes during lateral root development in Arabidopsis. Hence, R-loop formation and chromatin protein decoy mediate trans action of lncRNAs on distant loci. VIDEO ABSTRACT.
Original languageEnglish (US)
Pages (from-to)1055-1065.e4
Number of pages10648946
JournalMolecular cell
Issue number5
StatePublished - Jan 14 2020

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: We want to thank Dr. Tom Beeckman for the seeds of ProARF7:ARF7-GR transformed plants. This work was supported by grants from ANPCyT (PICT 2016-0289 and 2016-0007, Agencia Nacional de Promocio´ n Cientı´fica y Tecnolo´ gica, Argentina); CNRS (Laboratoire International Associe´ NOCOSYM); the Laboratoire d’Excellence (LABEX) Saclay Plant Sciences (SPS; ANR-10-LABX-40); and ANR grants (ANR 15-CE20-0002-01 and ANR 16-CE20-0003-04 SPLISIL), as well as the EPIMMUNITY International project between IPS2, France, and KAUST University, Saudi Arabia.


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