Single-cell transcriptome analysis dissects lncRNA-associated gene networks in Arabidopsis

The plant genome produces an extremely large collection of long noncoding RNAs (lncRNAs) that are generally expressed in a context-specific manner and have pivotal roles in regulation of diverse biological processes. Here we mapped the transcriptional heterogeneity of lncRNAs and their associated gene regulatory networks at single-cell resolution. We generated a comprehensive cell atlas at the whole-organism level by integrative analysis of 28 published single-cell RNA-sequencing (scRNA-seq) datasets from Arabidopsis juvenile seedlings. We then provided an in-depth analysis of cell type-related lncRNA signatures that shows consistent expression patterns with canonical protein-coding gene markers. We further demonstrated that the cell-type specific expression of lncRNAs largely explains their tissue specificity. In addition, we predicted gene regulatory networks based on motif enrichment and co-expression analysis of lncRNAs and mRNAs, and identified putative transcription factors orchestrating the cell type-specific lncRNA expression. The above analysis results are available at the single cell-based plant lncRNA atlas database (scPLAD; https://biobigdata.nju.edu.cn/scPLAD/). Overall, this work demonstrates the power of integrative single-cell data analysis applied to plant lncRNA biology and provides fundamental insights into lncRNA expression specificity and associated gene regulation.