Impact of a lincRNA on seedling development

Plant responses to environmental stimuli are complex, involving regulatory mechanisms at the protein and RNA levels. In this research, we are looking at transcriptional regulation mediated by long non-coding RNAs (lncRNAs). LncRNAs have been shown to regulate the transcription of other genes, both near and far, by DNA methylation, chromatin compaction, and Pol-II interference, to name a few of the more prominent mechanisms. In this study, we examined the regulatory function of the LincRNA with Germination Defects 1 (LGD1) locus. Lgd1 is believed to be linked to germination in Arabidopsis thaliana due to its pattern of expression in the Arabidopsis tissue atlas and germination defects observed in a preliminary screen of flower and seed-expressed lncRNAs. To test the role of Lgd1, we grew three different T-DNA insertion lines (lgd1-1, lgd1-2, lgd1-3) and genotyped them to ensure they were homozygous mutants. To assess the most common causes of germination defects, we screened seeds from these lines on agar plates with and without gibberellic acid (GA) and sucrose (SUC). We then measured their growth for seven days to observe the impact of disrupting this locus on seedling development. In addition, an RNA-seq analysis of germinating seedling tissue was performed to determine if disrupting Lgd1 impacted nearby genes or the transcriptome in general. Our results showed that Lgd1 T-DNA lines did not statistically significantly impact seedling development in growth media different from WT lines. In contrast, our RNA-seq analysis demonstrated that the two Lgd1 isoforms may play different roles. We observed significant differences in up-and down-regulated genes that, based on GO-term enrichment, are involved mainly in the cellular response to hypoxia and the jasmonic acid-mediated signaling pathway. These results shed light on the functioning of lincRNAs and RNA-mediated regulation of seedling establishment.

I had the incredible opportunity to work at the Nelson lab under the mentorship of Caylyn E. Rayley and other lab members, with whom I worked on understanding more about the RNA-mediated regulation of long non-coding RNAs in the Arabidopsis thaliana genome. Our study aimed to understand the functionality of the lincRNA Germination Defects 1 (LGD1) locus at the molecular and physiological level of Arabidopsis seedlings under various environmental stimuli. Before doing this research, I had minimal experience in bioinformatics and next-generation sequencing knowledge. However, after working on this project, I gained valuable skills for a plant researcher, such as performing plate assays, DNA extraction, PCRs, differential expression, and statistical data analysis. Also, it helped me to improve my critical thinking skills in developing a research hypothesis and experimental planning. I cannot be more grateful for this fantastic opportunity at Boyce Thompson Institute and for everyone who made this NSF-funded REU program a complete and fulfilling experience.