Studying Gene Expression in Whole Embryos by in situ Hybridization: A Peer-to-Peer Laboratory Guide

Abstract

The extracellular matrix (ECM) plays an important role in cell to cell signaling pathways. Our goal is to provide a full laboratory guide for students to study gene expression in zebrafish embryos by in situ hybridization. Prior to our study, the laboratory had observed disorganized and shortened cilia in cells that are important for cell signaling in the pronephric duct and neural tube floor plate of the zebrafish embryo. Ciliogenesis depends on a master transcriptional regulator, foxj1a, whose mRNA expression can be monitored through in situ hybridization and microscopic imaging. Knockdown morpholino-injected, control mismatched morpholino-injected, and uninjected embryos were fixed to determine if foxj1a transcription is qualitatively affected by ECM gene knockdown. Our results showed that the knockdown embryos portrayed an inconsistent foxj1a signal strength along the length of the pronephric duct, when compared to analysis of control mismatched and wild-type uninjected embryos. We created this manuscript for other students to observe how ECM gene knockdown can affect foxj1a mRNA expression, but also to give them a guide to the tools they would need to explore their own genes of interest, in zebrafish or in many other organisms and tissues.