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 the 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 platform named PERlncDB (Plant Epigenetic Regulation of lncRNAs Database).

The researchers assembled an extensive dataset comprising more than 160,000 high-quality lncRNAs from 19 representative plant species. By integrating 6,715 datasets from ChIP-seq (for histone modifications), BS-seq (for DNA methylation), and RNA-seq, they identified distinct epigenetic patterns associated with lncRNAs.

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

To facilitate data presentation and provide a user-friendly visual query interface for researchers, the team developed PERlncDB. This specialized platform allows users to browse species-specific lncRNAs, access detailed epigenetic annotations, perform cross-species conservation analyses, and visualize complex epigenomic landscapes.

"PERlncDB currently provides the most comprehensive epigenetic characterization with 163,609 lncRNA entries spanning 19 plant species. It serves as a vital bridge, connecting epigenomic data with functional insights and empowering the plant research community to systematically explore lncRNA roles," said LIU Changning of XTBG.

PERlncDB is open access and available at: http://perlncdb.liu-lab.com/

Plant Epigenetic Regulation of lncRNAs Database

First published: 25 November 2025