Transcriptomic Profiling of DAF-7/TGFβ Pathway Mutants in <i>C. elegans</i>

• Main Authors: Muhan Hu, David Crossman, Jeevan K. Prasain, Michael A. Miller, Rosa A. Serra
• Format: Article
• Language: English
• Published: MDPI AG 2020-03-01
• Series: Genes
• Subjects: tgfβ; <i>daf-1</i>; <i>daf-3</i>; rna sequencing; <i>c. elegans</i>; gene ontology; qpcr
• Online Access: https://www.mdpi.com/2073-4425/11/3/288

The transforming growth factor beta superfamily encompasses a large family of ligands that are well conserved across many organisms. They are regulators of a number of physiological and pathological processes. The model nematode <i>Caenorhabditis elegans</i> has been instrumental in identifying key components of the transforming growth factor beta (TGF&#946;) pathway. In <i>C. elegans</i>, the TGF&#946; homolog DAF-7 signals through the DAF-1 Type I and DAF-4 Type II receptors to phosphorylate downstream R-SMADs DAF-8 and DAF-14. These R-SMADs translocate into the nucleus to inhibit Co-SMAD DAF-3. Many of the roles of the canonical DAF-7 pathway, involving both DAF-1 and DAF-3, have been identified using targeted genetic studies. Few have assessed the global transcriptomic changes in response to these genes, especially in adult animals. In this study, we performed RNA sequencing on wild type, <i>daf-1</i>, and <i>daf-1</i>; <i>daf-3</i> adult hermaphrodites. To assess the overall trends of the data, we identified differentially expressed genes (DEGs) and performed gene ontology analysis to identify the types of downstream genes that are differentially expressed. Hierarchical clustering showed that the <i>daf-1</i>; <i>daf-3</i> double mutants are transcriptionally more similar to wild type than <i>daf-1</i> mutants. Analysis of the DEGs showed a disproportionally high number of genes whose expression is increased in <i>daf-1</i> mutants, suggesting that DAF-1 acts as a general repressor of gene expression in wild type animals. Gene ontology analysis of the DEGs produced many significantly enriched terms, including Molting Cycle, Response to Topologically Incorrect Protein, and Response to Biotic Stimulus. Understanding the direct and indirect targets of the DAF-7 TGF&#946; pathway through this RNA-seq dataset can provide insight into novel roles of the multifunctional signaling pathway, as well as identify novel genes that may participate in previously reported functions of TGF&#946; signaling.