Long non-protein coding RNAs (lncRNAs) are emerging as important regulators of gene expression. In a series of studies, Ariel and co-workers revealed the molecular mechanisms of AUXIN REGULATED PROMOTER LOOP RNA (APOLO) lncRNA actions (Ariel et al., 2014Ariel F. Jegu T. Latrasse D. Romero-Barrios N. Christ A. Benhamed M. Crespi M. Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop.Mol. Cell. 2014; 55: 383-396Abstract Full Text Full Text PDF PubMed Scopus (221) Google Scholar, Ariel et al., 2020Ariel F. Lucero L. Christ A. Mammarella M.F. Jegu T. Veluchamy A. Mariappan K. Latrasse D. Blein T. Liu C. et al.R-loop mediated trans action of the APOLO long noncoding RNA.Mol. Cell. 2020; 77: 1055-1065.e4Abstract Full Text Full Text PDF PubMed Scopus (76) Google Scholar; Moison et al., 2021Moison M. Pacheco J.M. Lucero L. Fonouni-Farde C. Rodríguez-Melo J. Mansilla N. Christ A. Bazin J. Benhamed M. Ibañez F. et al.The lncRNA APOLO interacts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold.Mol. Plant. 2021; https://doi.org/10.1016/j.molp.2021.03.008Abstract Full Text Full Text PDF PubMed Scopus (11) Google Scholar). APOLO integrates endogenous and exogenous signals and, in combination with an intricate network of epigenetic and transcriptional factors, controls multiple aspects of root development. Notably, APOLO acts as both positive and negative regulator to orchestrate gene expression in cis and in trans. A large portion of eukaryotic transcriptome consists of non-protein coding RNAs (ncRNAs). Initially, these transcripts were considered merely transcriptional noise due to their poor conservation, short half-lives, and lack of protein-coding capacity. Recently, an extending number of lncRNAs have been described and characterized molecularly: ncRNAs partner with different types of molecules and act on epigenetic, transcriptional, or translational level to modulate their targets' activities (Statello et al., 2021Statello L. Guo C.J. Chen L.L. Gene regulation by long non-coding RNAs and its biological functions.Nat. Rev. Mol. Cell Biol. 2021; 22: 96-118Crossref PubMed Scopus (741) Google Scholar). APOLO is an auxin-responsive lncRNA encoded by the Arabidopsis genome. Proximal to APOLO locus is located another auxin-responsive gene, PINOID (PID), a gene required for root development. APOLO and PID are co-regulated. Under standard conditions both are epigenetically repressed (Figure 1A): the silenced state is conferred by an intricate interaction of PRC2-mediated H3K27 trimethylation, the PRC1 component LHP1 protein binding, DNA methylation, and a chromosomal gene loop encompassing the 5′ portion of PID and APOLO locus (Ariel et al., 2014Ariel F. Jegu T. Latrasse D. Romero-Barrios N. Christ A. Benhamed M. Crespi M. Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop.Mol. Cell. 2014; 55: 383-396Abstract Full Text Full Text PDF PubMed Scopus (221) Google Scholar). Upon auxin increase (e.g., exogenous treatment) the ROS1, DML2, and DML3 (RDD) demethylases decrease DNA methylation, following which APOLO transcription is initiated (Figure 1B): the de novo produced APOLO lncRNA physically binds and tethers away PRC1 component LIKE HETEROCHROMATIN PROTEIN 1 (LHP1); subsequently, H3K27 trimethylation is also lost and the chromatin loop relaxed at APOLO–PID. Parallel to this, auxin induces production of other transcription factors (TFs), including Auxin Responsive Factor 7 (ARF7). ARF7 binds to APOLO promoter in the absence of repressive chromatin features and further activates divergent Polymerase II (PolII)-mediated transcription of APOLO and PID (Ariel et al., 2020Ariel F. Lucero L. Christ A. Mammarella M.F. Jegu T. Veluchamy A. Mariappan K. Latrasse D. Blein T. Liu C. et al.R-loop mediated trans action of the APOLO long noncoding RNA.Mol. Cell. 2020; 77: 1055-1065.e4Abstract Full Text Full Text PDF PubMed Scopus (76) Google Scholar). In summary, APOLO regulates positively its own and adjacent PID gene transcription in cis upon auxin signaling. Later, as a consequence of strong APOLO transcriptional activity, PolV-mediated transcription is gradually activated at the locus. PolV is a plant-specific central component of the transcriptional gene silencing (TGS) pathway (Zheng et al., 2009Zheng B. Wang Z. Li S. Yu B. Liu J.Y. Chen X. Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis.Genes Dev. 2009; 23: 2850-2860Crossref PubMed Scopus (204) Google Scholar; Haag and Pikaard, 2011Haag J.R. Pikaard C.S. Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing.Nat. Rev. Mol. Cell Biol. 2011; 12: 483-492Crossref PubMed Scopus (294) Google Scholar). Together with RdDM, PRC2 triggers gradual H3K27me3 deposition. LHP1 is recruited by APOLO and recognizes the silencing histone mark (Figure 1A). The chromatin loop is undetectable in TGS mutants (nrpd2a, rdr2, dcl2/3/4, ago4), and APOLO and PID transcripts are induced, suggesting that silencing of these loci requires active TGS. The chromatin loop is also partially impaired in PRC2 mutants. Surprisingly, APOLO-RNAi lines did not restore efficiently the chromatin loop following its transient opening by auxin treatment, suggesting that APOLO lncRNA is required for the repression process as well. During this process, APOLO tethers LHP1 to boost its binding to chromatin. APOLO therefore acts as a negative regulator of its own transcription. What is the purpose of such a complex self-regulation of the APOLO locus? By using a combination of multiple genome-wide and gene-specific technologies including RNA sequencing, chromatin isolation by RNA purification sequencing (Chu et al., 2011Chu C. Qu K. Zhong F.L. Artandi S.E. Chang H.Y. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions.Mol. Cell. 2011; 44: 667-678Abstract Full Text Full Text PDF PubMed Scopus (887) Google Scholar), chromosome conformation capture (Lieberman-Aiden et al., 2009Lieberman-Aiden E. van Berkum N.L. Williams L. Imakaev M. Ragoczy T. Telling A. Amit I. Lajoie B.R. Sabo P.J. Dorschner M.O. et al.Comprehensive mapping of long-range interactions reveals folding principles of the human genome.Science. 2009; 326: 289-293Crossref PubMed Scopus (4589) Google Scholar), DNA:RNA immunoprecipitation (Xu et al., 2017Xu W. Xu H. Li K. Fan Y. Liu Y. Yang X. The R-loop is a common chromatin feature of the Arabidopsis genome.Nat. Plants. 2017; 3: 704-714Crossref PubMed Scopus (88) Google Scholar), and RNA isolation by DNA purification (Ariel et al., 2020Ariel F. Lucero L. Christ A. Mammarella M.F. Jegu T. Veluchamy A. Mariappan K. Latrasse D. Blein T. Liu C. et al.R-loop mediated trans action of the APOLO long noncoding RNA.Mol. Cell. 2020; 77: 1055-1065.e4Abstract Full Text Full Text PDF PubMed Scopus (76) Google Scholar), it was shown that APOLO recognizes multiple independent (not spatially associated) auxin-responsive loci in trans to orchestrate root development in response to auxin (Ariel et al., 2020Ariel F. Lucero L. Christ A. Mammarella M.F. Jegu T. Veluchamy A. Mariappan K. Latrasse D. Blein T. Liu C. et al.R-loop mediated trans action of the APOLO long noncoding RNA.Mol. Cell. 2020; 77: 1055-1065.e4Abstract Full Text Full Text PDF PubMed Scopus (76) Google Scholar). APOLO intercalates into the genomic DNA to form an R-loop structure (RNA::DNA hybrid [Xu et al., 2017Xu W. Xu H. Li K. Fan Y. Liu Y. Yang X. The R-loop is a common chromatin feature of the Arabidopsis genome.Nat. Plants. 2017; 3: 704-714Crossref PubMed Scopus (88) Google Scholar]) and decoys away LHP1 to modulate chromatin 3D conformation and activate these genes. Trans activity of APOLO further rules out the possibility that the transcription act per se, and not the product itself, would have the regulatory role. In a recent study in Molecular Plant, the roles and regulation of APOLO have been further extended (Moison et al., 2021Moison M. Pacheco J.M. Lucero L. Fonouni-Farde C. Rodríguez-Melo J. Mansilla N. Christ A. Bazin J. Benhamed M. Ibañez F. et al.The lncRNA APOLO interacts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold.Mol. Plant. 2021; https://doi.org/10.1016/j.molp.2021.03.008Abstract Full Text Full Text PDF PubMed Scopus (11) Google Scholar). It was shown that APOLO is also cold-induced. APOLO lncRNA interacts with WRKY42 TF to help its binding to RHD6 promoter and enhances its activation (Figure 1C and 1D). RHD6 is a master regulator of root hair development, a typical APOLO target displaying H3K27me3 deposition, LHP1 binding, and APOLO-recognition motif, which is able to form R loops and a chromatin loop. RHD6 promoter contains WRKY-binding W-box motifs. Remarkably, WRKY42 binding to RHD6 promoter was impaired in both APOLO-RNAi and 35S overexpressor lines; RHD6 chromatin loop formation was also impaired in both lines. These observations suggest that, similar to the PID–APOLO cis locus, APOLO is required for both positive and negative trans regulation of RHD6 through TF binding and chromosomal structure remodeling in response to temperature changes. In short, a larger picture of APOLO action mechanisms is emerging, which hints APOLO as an integrator of multiple signals and coordinator of gene networks. Upon induction, APOLO activates itself and in parallel unleashes expression of hundreds of genes in trans. APOLO's main role is perhaps to enhance the sensitivity and robustness of epigenetic/transcriptional switching at multiple target loci. The coordinated expression of many genes provides the required stoichiometry of the relevant factors to support multiple facets of root development. Although the mechanistic understanding of APOLO is profound, there are still some exciting questions to be addressed. For example, what are the features that define APOLO target genes and what mechanism makes targeting efficient? Which factors are required for the invasion of genomic DNA to establish and/or stabilize R-loop structures at cis and trans loci? How are APOLO R loops resolved and APOLO half-life regulated? Is chromatin looping directly or indirectly interfering with TF binding, and what is the precise mechanism of this? How much do the TFs participate in regulation of chromatin looping? Is the APOLO-type mechanism present in other plant species? Answering these and related questions will be essential to deepen our understanding of not only APOLO but also the diverse regulatory pathways and mechanisms of lncRNA actions in general. The Hungarian National Research, Development and Innovation Office NKFIH K-129283 and János Bolyai Research Scholarship supported T.C. No conflict of interest declared.