Unearthing the hidden trove of long non-coding RNAs in plants

Long non-coding RNAs, an enigmatic class of genes that do not encode proteins, exhibit greater variability and are subject to more silencing mechanisms than previously known, a new study in Arabidopsis shows. Some lncRNAs even resemble transposons and are controlled by transposon silencing mechanisms. This is the result of a study by researchers from the Nordborg group at the Gregor Mendel Institute of the Austrian Academy of Sciences.

Researchers at the GMI shed light on a dark aspect of plant genomes: the prevalence and regulation of the enigmatic genetic elements called “long non-coding RNAs” (lncRNAs). While lncRNAs do not encode proteins, they can regulate important biological processes in plants and animals. However, the elements’ prevalence, biological roles, and regulation in plants are not well known. Using RNA-seq data spanning hundreds of natural Arabidopsis lines and several developmental stages, researchers from the Nordborg Group at the Gregor Mendel Institute (GMI) provide a population-wide annotation of lncRNAs in Arabidopsis. The research reveals a multitude of lncRNAs in the model plant’s natural variants and uncovers silencing mechanisms reminiscent of those regulating transposons.

Led by GMI postdoctoral fellow Aleksandra Kornienko, the research team made several major findings. Firstly, Kornienko, Nordborg, and colleagues demonstrated that almost 12,000 lncRNA cover 10% of the Arabidopsis genome. Moreover, plant lncRNAs exhibited considerable variability in their expression patterns: only half of the lncRNAs expressed in one Arabidopsis natural variant were expressed in another. However, the GMI scientists also revealed that the majority of lncRNAs appear to be actively silenced. By looking closer, they could show that this variability in expression might arise from the high variability in silencing mechanisms, including repressive chromatin.

Crucially, Kornienko and the team established that many lncRNAs located in-between protein-coding genes (called “intergenic lncRNAs” or “lincRNAs” for short) resembled transposons. These lincRNAs exhibited distinctive epigenetic silencing patterns reminiscent of those seen in transposon regulation. In fact, half of these lincRNAs contained segments of transposable elements (TEs), leading them to attract the TE silencing machinery. However, the researchers emphasize that these TE-like lincRNAs are distinct from intact TEs, making the attraction of the TE silencing machinery to such lincRNAs an intriguing area for further investigation.

This new research not only provides a valuable data resource for plant biologists but also raises fundamental questions about how transcription and silencing are regulated across the genome.