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.

中文翻译：

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R-Loop介导的APOLO长非编码RNA的反式作用。

在真核生物中，三维基因组组织对于基因表达的转录调控至关重要。长的非编码RNA（lncRNA）可以调节核内空间相关基因组位置的染色质构象。在这里，我们显示了lncRNA APOLO（AUXIN调控的启动子环）识别拟南芥基因组中的多个遥远的独立基因座。我们发现，APOLO靶在核中在空间上不相关，并且APOLO通过短序列互补性和DNA-RNA双链体（R环）的形成识别其靶。APOLO对目标DNA的入侵诱骗了植物Polycomb Repressive Complex 1组分LHP1，从而调节了局部染色质3D构象。APOLO lncRNA协调拟南芥侧根发育过程中远端无关的生长素应答基因的表达。因此，R环的形成和染色质蛋白诱饵介导lncRNA对遥远基因座的反式作用。视频摘要。