Serin is a senior at Drexel University, majoring in Biology. She is currently working in Dr. Joel Boerckel’s developmental mechanobiology lab. Through the UEXB program, she will be working on using gene ontology analysis to characterize the differential gene expression of YAP/TAZ depleted ECFCs and trying to identify potential candidate genes that are associated with the transcriptional regulators, YAP and TAZ. After graduation, Serin plans to matriculate into Drexel Univeristy’s College of Medicine as a part of the school’s accelerated BS/MD program.
Nonbiased Transcriptomic Analysis Reveals that YAP and TAZ co-Transcriptional Activators Regulate Survival
Yes-associated protein (YAP) and transcriptional co-activator with PDZ-binding motif (TAZ) are two mechanically activated transcriptional regulators that have been found to play a significant role in osteoprogenitor proliferation and differentiation during embryonic bone development and fracture healing. However, the specific gene interactions and pathways by which YAP and TAZ activate or repress these processes remains unclear. Therefore, the goal of this project was to analyze the differential expression of genes in YAP/TAZ depleted cells, and to use a non-biased gene ontology approach to identify which cellular processes these genes were involved with. In order to study gene expression changes in the absence of YAP and TAZ, we analyzed an existing data set generated in our laboratory in which bulk RNA expression profiles were measured in endothelial colony forming cells (ECFCs) transfected with siRNA to deplete YAP and TAZ. A differential gene expression analysis using this bulk RNA sequencing data identified 2,241 downregulated genes and 2,508 upregulated genes in YAP/TAZ siRNA samples. The gene expression profile of the YAP/TAZ siRNA samples reveals a relatively equal distribution of up and downregulated genes, suggesting that YAZ and TAZ may interact directly or indirectly with signaling pathways to either promote or suppress certain biological processes in the cell. To investigate these findings further, a gene ontology (GO) analysis was conducted in order to classify these up or downregulated genes into clusters based on the cellular processes they are involved in. The results of this analysis showed that YAP/ TAZ knockdown significantly reduced expression of several processes associated with cell cycle and functional protein synthesis, both of which play an integral role in cell proliferation and differentiation, respectively. A GO term analysis of genes that were upregulated in samples with YAP/ TAZ knocked down revealed an enrichment of genes associated with the positive regulation of apoptotic processes. Taken together, these results indicate that when YAP/TAZ is absent, cells are not only experiencing decreased proliferation, but they are also actively undergoing cell death, suggesting that YAP and TAZ play a significant role in regulating the survival of the cell. By classifying differentially expressed genes based on their involvement in specific biological processes, these gene ontology results have provided us with a streamlined set of candidates YAP/TAZ associated genes that can be investigated in future experiments to determine the specific mechanisms that underly proliferation and apoptosis.