Introduction
Intronic RNAs have been overlooked for a long time: They are functional, but treated as “junk.” In this work, we designed a new sequencing strategy to investigate intronic RNAs. By using intron-capture RNA-seq, we systematically analyzed the intronic RNAs in Arabidopsis by zooming into the intronic regions an order of magnitude deeper than in previous work. Our key findings include: (1) Intron-capture RNA-seq is a much more efficient approach to analyze intronic RNAs than total RNA-seq and mRNA-seq. (2) We identified three types of intronic RNAs, and found that the GC pattern differs significantly between the introns with and without intronic RNAs. (3) We detected many hidden elements in introns, including circular RNAs, splice junctions, and transcripts that have previously been overlooked. (4) The expression of these intronic RNAs varies during the time course of pathogen infection, which indicates that an unknown mechanism may exist for these RNAs. (5) We also demonstrated that intronic RNAs are detectable in both Arabidopsis and rice, suggesting that these non-coding molecules are conserved. Taken together, this work proposes an efficient strategy to analyze intronic RNAs, and provides an unprecedented view of this essential component in biological pathways.
Supplemental Data
Publication
Han Li, Yimai Zhang, Jianhao Bing, Jinyu Han, Jiming Hu, Hongwei Zhao, Xiaoyong Sun. Intron-capture RNA-seq reveals the landscape of intronic RNAs in Arabidopsis. Plant Physiology and Biochemistry, Volume 196, 2023, Pages 75-88, ISSN 0981-9428, https://doi.org/10.1016/j.plaphy.2023.01.040.( Download link )
Data availability
All raw sequence data can be found at NCBI BioProject database (BioProject ID: PRJNA789586).
R source code