Long non-coding RNAs (lncRNAs) are RNA transcripts longer than 200 nucleotides that do not code for proteins. Once considered mere transcriptional noise, lncRNAs are now known to play vital roles in plant growth, development, and responses to environmental stress. However, few studies have used epigenomic data to investigate functions of lncRNAs in plants.

In a study published in The Plant Journal, researchers from Xishuangbanna Tropical Botanical Garden (XTBG) of the Chinese Academy of Sciences constructed comprehensive epigenetic regulatory landscapes for lncRNAs across diverse plant species, and developed a novel, specialized, open-access platform named Plant Epigenetic Regulation of lncRNAs Database (PERlncDB).

Researchers collected a comprehensive dataset of more than 160,000 high-quality lncRNAs from 19 representative plant species. They identified distinct epigenetic patterns associated with lncRNAs by integrating 6,715 datasets from ChIP-seq for histone modifications, BS-seq for DNA methylation, and RNA-seq.

Researchers found that DNA methylation levels were significantly higher in lncRNA regions than in protein-coding genes (PCGs) with the highest levels found in lncRNAs associated with transposable elements. And they found that activating histone modifications at lncRNA loci showed clear tissue specificity and distinct preferences different from those at PCG loci, indicating that lncRNA loci are selectively regulated by specific epigenetic factors.

To facilitate data presentation and to provide a user-friendly visual query interface, researchers developed a specialized platform PERlncDB. This platform currently provides the most comprehensive epigenetic characterization with 163,609 lncRNA entries spanning 19 plant species. It allows users to browse species-specific lncRNAs, access detailed epigenetic annotations, perform cross-species conservation analyses, and visualize complex epigenomic landscapes.

"PERlncDB serves as a bridge connecting epigenomic data with functional insights, which empowers the plant research community to systematically explore lncRNA functions," said LIU Changning from XTBG.