Investigating Evolutionarily Conserved Molecular Mechanisms Controlling Gene Expression in the Notochord

Abstract

Ascidian embryos have been employed as model systems for studies of developmental biology for well over a century, owing to their desirable blend of experimental advantages, which include their rapid development, traceable cell lineage, and evolutionarily conserved morphogenetic movements. Two decades ago, the development of a streamlined electroporation method drastically reduced the time and cost of transgenic experiments, and, along with the elucidation of the complete genomic sequences of several ascidian species, propelled these simple chordates to the forefront of the model organisms available for studies of regulation of gene expression. Numerous ascidian sequences with tissue-specific enhancer activity were isolated and rapidly characterized through systematic in vivo experiments that would require several weeks in most other model systems. These cis-regulatory sequences include a large collection of notochord enhancers, which have been used to visualize notochord development in vivo, to generate mutant phenotypes, and to knock down genes of interest. Moreover, their detailed characterization has allowed the reconstruction of different branches of the notochord gene regulatory network. This chapter describes how the use of transgenic techniques has rendered the ascidian Ciona a competitive model organism for studies of notochord development, evolution, and gene regulation.

Matrix metalloproteinase Nas15 regulates the lumen formation and expansion in Ciona notochord

“…However, the Ciona larval notochord construct an extracellular connected lumen (Dong et al, 2009), which is a special notochord structure in notochord evolution. Previous researches showed that the Ciona notochord expressed some evolutionarily conserved key molecule regulating notochord specific gene expression (Maguire et al, 2018;Raghavan et al, 2023), which suggests a key phylogenetic position of Ciona as a notochord origin class. Therefore, the notochord extracellular lumen may show the early form of vacuolate notochord.…”

Transcription Factors of the bHLH Family Delineate Vertebrate Landmarks in the Nervous System of a Simple Chordate

“…Since the beginning of the past century, studies on ascidians have provided a valuable reference for chordate development, first by informing comparative biological studies between embryos featuring different ontogenetic strategies [2][3][4][5], and, more recently, by shedding light on the molecular mechanisms underlying a variety of developmental processes, both ancestral and derived [6][7][8][9][10]. These processes include formation of the notochord [11][12][13] neural tube closure and dorsoventral patterning [14,15], regionalization of the central nervous system (CNS) [16,17], heart development [18,19], formation of the cardiopharyngeal precursors [20][21][22], biosynthesis and role of thyroid hormones [23], and specialization of the digestive tract [24,25]. The search for compartments evolutionarily related to the anatomical structures that punctuate the vertebrate brain in invertebrate chordates stretches over several decades, and started out with comparative morphological observations and immunocytochemical studies, which have been complemented, in more recent years, by phylogenomic analyses and single-cell molecular fingerprinting.…”

Quantitative analysis of the ThrbCRM1-centered gene regulatory network

“…Electroporation is one method to identify and characterize cis-regulatory elements as components of GRNs. Several studies have used this method to identify cis-regulatory elements, providing critical insights into retinal development and other developmental contexts (Bery et al, 2014; Emerson et al, 2013; Emerson and Cepko, 2011; Hsiau et al, 2007; Maguire et al, 2018; Mills et al, 2017; Uchikawa et al, 2004; Wang et al, 2014). In addition, the technique of electroporation is widely used to misexpress transcription factors, or other signaling factors (Chang et al, 2013; Cherry et al, 2011; de Melo et al, 2011; Emerson et al, 2013; La Torre et al, 2013; Matsuda and Cepko, 2007; Mattar et al, 2015; Onishi et al, 2010; Wang et al, 2014).…”