Kane, Alexander: Reverse Genetic Approaches for Finding Fertility Genes in C. Elegans
Title: Reverse Genetic Approaches for Finding Fertility Genes in C. Elegans
Name: Alexander Kane
School affiliation: School of Arts and Sciences
Programs: Division of Life Sciences Summer Undergraduate Research Fellowship (DLS-SURF)
Other contributors: Andrew Singson, Xue Mei and Ben Lambert
Abstract: Fertilization is an essential process in all sexually reproducing species. It involves the fusion of an egg and a sperm cell to create an embryo. While a lot of the genes that encode sperm surface proteins have been identified, much less is known on the egg side of the equation. In order to discover some of these genes that encode potential egg-surface receptors for the sperm, I used a candidate genes approach to look for paralogous gene pairs that have potentially redundant functions.
This was done using Tzur’s 2018 RNA-seq analysis. We used his S11 oogenesis enriched gene list for our work, which was entered into WormBase to convert it to a list of protein sequences. These protein sequences were then used in multiple online tools in order to find any proteins that are transmembrane, secreted, or GPI-anchored. Each output was filtered using a custom-made python program. We also used the DIOPT website to find relevant paralogs for the genes on the S11 list.
The resulting candidate list contained any gene that was flagged by at least one of the websites and had a paralog on the S11 list. These genes were sorted into rows based on their paralogs, and manually reviewed for their relevancy to our lab’s interests. We then color-coded the genes based on their potential. Many genes were marked as green which indicates that they have potential. Moving forward we will analyze more datasets to find additional promising candidate genes, and eventually use gene knockout or knockdown in order to test their functions.