Battles and hijacks: noncoding transcription in plants

• Long noncoding RNAs (lncRNAs) are emerging as key regulators of plant development.
• lncRNAs can also hijack proteins and miRNAs to fine-tune RNA processing and stability.
• Dual transcription by alternative polymerase complexes with lncRNAs shapes genome topology.
• RNA-directed DNA methylation (RdDM) controls genome activity and involves Pol IV and Pol V lncRNAs and siRNAs.

Noncoding RNAs have emerged as major components of the eukaryotic transcriptome. Genome-wide analyses revealed the existence of thousands of long noncoding RNAs (lncRNAs) in several plant species. Plant lncRNAs are transcribed by the plant-specific RNA polymerases Pol IV and Pol V, leading to transcriptional gene silencing, as well as by Pol II. They are involved in a wide range of regulatory mechanisms impacting on gene expression, including chromatin remodeling, modulation of alternative splicing, fine-tuning of miRNA activity, and the control of mRNA translation or accumulation. Recently, dual noncoding transcription by alternative RNA polymerases was implicated in epigenetic and chromatin conformation dynamics. This review integrates the current knowledge on the regulatory mechanisms acting through plant noncoding transcription.