lncRNA-mRNA-miRNA Networks in Arabidopsis thaliana Exposed to Micro-Nanoplastics

Long non-coding RNAs (lncRNAs) are key regulators of genetic networks in numerous biological processes. Micro-nanoplastics represent a novel abiotic stress, having a direct xenobiotic impact on plant cells, while the regulation of lncRNAs in Arabidopsis thaliana under this kind of abiotic stress remains largely unclear. We explored RNA-seq data sets of A. thaliana roots treated with two types of micro-nanoplastics: transparent polyethylene terephthalate (Tr-PET) and blue polyethylene terephthalate (Bl-PET) to reveal known and new unannotated lncRNAs. Our findings showed that the Tr-PET changed the expression of 104 lncRNAs, while the Bl-PET changed the expression of just 19. We speculate on the possible significance of the differential expressions for plant tolerance and resistance to micro-nanoplastic stress. A key finding of this work is that the studied lncRNAs tend to regulate their neighboring protein-coding genes. Consistent with this regulatory role, their promoters were found to contain cis-acting regulatory elements responsive to abscisic acid, light, MeJA, MYC/MYB, and other stress-related signals. Furthermore, some of the miRNAs that participate in plant development and defense were also predicted to be sponged by the differentially expressed lncRNAs. In summary, this study adds to our knowledge of A. thaliana lncRNAs through the discovery of new transcripts, describing their expression under micro-nanoplastic stress, and revealing their possible roles in post-transcriptional gene regulation.