Peter Kohler
Year: 2017
Faculty Advisor: Zhangjun Fei

“Ethylene mediated epigenome changes in ripening climacteric melon”

Project Summary:

Ripening is a complex process that dramatically alters fruit color, flavor, firmness, and nutritional content. Improving our understanding of this process promotes the ability to optimize crop yields, disease resistance, and fruit quality. Ethylene is a natural plant hormone and is best known as a crucial regulatory component for climacteric fruit ripening. However, how ethylene controls ripening at the epigenome level is poorly understood.

To illustrate whether ethylene mediate gene expression through DNA methylation, a climacteric melon and ACC oxidase RNAi mutant with inhibited ethylene production were selected for the bisulfite sequencing (BS-Seq) analysis. By comparing the methylation level between wild-type and mutant melon, an overall demethylation patterns are observed in the mutant fruit. We identified 10,243 and 52,829 differentially methylated regions (DMRs) for CG and CHH cytosine context, representing 0.32% and 1.79% of the melon genome, respectively.

Furthermore 670 CG and 5,194 CHH DMRs intersect with 570 and 2,574 genes, respectively, of which 73% and 75% were differentially expressed based on a previous transcriptome study using the same samples. Hypo-methylation of promoters of ethylene signal transduction and biosynthesis pathway genes in the wild-type melon indicates the role of DNA methylation in the ethylene positive feedback loop. Hypo-methylated promoters and upregulated expression of some ripening-related genes in the wild-type melon, e.g. STAY-GREEN, alcohol acyl transferase, indicate ethylene regulated these ripening genes by DNA methylation.

My Experience:

Coming from a heavy computational background, this internship has been wonderful experience of learning for me, as it provided a project whose core activities catered to my strengths, while also requiring me to obtain an understanding of its biological significance. I have gotten to learn Perl, deepen my knowledge of GNU make and R, and practice analyzing the interrelated facets of biological systems, which require a different sort of consideration than the systems I am used to dealing with. I have had to learn to manage large data sets, and consequently also obtained a rare opportunity to practice performance-conscious programming.

What I appreciate most, however, is how being in BTI’s environment—listening to presentations and getting into conversations—has increased my grasp of the broader biological picture, made me aware of exciting developments and discoveries, and answered some of my long-held questions and confusion. I feel that I have been given a solid introduction to the concerns, interests, tools and mindsets of this field, which is exactly what I was hoping to obtain this summer.