lncRNA-DNA hybrids regulate distant genes

Abstract

lncRNAs actively regulate gene expression. They contribute to chromosomal interactions at close or distant genomic regions, which, in turn, regulate transcription [1]. Ariel et al [2] reveal in a recent study a new molecular mechanism of the Arabidopsis lncRNA APOLO. The authors extend previously reported functions of APOLO in cis-regulation of chromosomal looping and transcription of its neighbor gene to a set of distant genes involved in auxin-induced molecular pathways controlling lateral root development. Noteworthy, APOLO recognition of multiple trans-modulated targets occurs through a novel mechanism involving R-loop formation.

Figure 1. The cis‐ and trans‐regulatory mechanisms of the lncRNA APOLO

In basal conditions, chromosomal looping and hypermethylation of the APOLO promoter silence its transcription. During lateral root (LR) development, auxin induces ARF7 binding to the PID‐APOLO intergenic region, promoting APOLO transcription. By forming R‐loops, APOLO modulates chromatin loops in cis and in trans, thereby enhancing transcription of target genes. Since APOLO targets are auxin‐responsive genes, their expression contributes to LR development. APOLO‐dependent PRC1 binding and deposition of repressive histone marks restore chromatin loops and transcription silencing of APOLO targets.