Conserved m6A sites in Arabidopsis thaliana and Sorghum bicolor mRNA

RNA bases can be modified in many ways. These modifications can influence stability, translation, and structure. N6-methyladenosine (m6A) is one of the most common and well-studied mRNA modifications in terms of function, but less well-known is the extent to which these marks are conserved. This project analyzed m6A modifications in two different plant species, Arabidopsis, a dicot, and Sorghum, a monocot. Tissue specificity of m6A modifications in Arabidopsis flower and seedling were also considered. After filtering for high-quality m6A predictions, m6A-methylated transcripts were compared to find genes methylated across species and tissues. This project went even further and compared individual m6A sites on orthologous transcripts to determine if the position in the transcript is similar between species. A few sites predicted to be in the same location on an ortholog were manually verified using genome browsers. This project found 45% of genes expressed in Sorghum seedling, Arabidopsis seedling, and Arabidopsis flower were also consistently m6A methylated in all three samples. These sites were found to almost entirely in the 3’-UTR or in the CDS close to the stop codon. 3,647 distinct m6A sites in Arabidopsis were predicted to have an m6A site in the same relative transcript location on the Sorghum ortholog. Because these sites are consistently methylated in two species and tissues, they likely have some important effect on the mRNA, perhaps improving stability, or moderating RNA-protein interactions and may be good targets for future research into the effects of m6A modifications.

Thanks to Kyle’s teaching, I became comfortable using R to extract the answers to research questions from our data. I know this skill will be very valuable for my future research endeavors. I also had the opportunity to meet many scientists working on a wide variety of projects in plant science. Whether it was in Nelson lab meetings, after BTI seminars, or even among my fellow REU students, the people I have talked with have increased my appreciation and interest in the field. In addition to all this, the waterfalls and trails around Ithaca are beautiful, and I enjoyed time outside of the lab exploring the town, walking through the gorges, and hanging out with the REU students. This summer research experience has provided me with skills, connections and experiences that are invaluable.