Investigating Evolutionarily Conserved Molecular Mechanisms Controlling Gene Expression in the Notochord

  • Julie E. Maguire
  • Aakarsha Pandey
  • Yushi Wu
  • Anna Di Gregorio
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 1029)


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.


Ascidian Brachyury Ciona cis-Regulatory Module Electroporation Enhancer Notochord T-Box Tbx2/3 Transcription factor 



Base pair(s)


Complementary DNA


Chromatin immunoprecipitation


cis-regulatory module




fluorescence-activated cell sorting


Green fluorescent protein


Gene regulatory network


Notochord enhancer


Orphan binding site


prolyl 3-hydroxylase1


Short hairpin RNA



Thanks to all present and past laboratory members and collaborators. We are particularly indebted to Drs. Diana José-Edwards, Lavanya Katikala, Izumi Oda-Ishii, and Yale Passamaneck for their original microphotographs. Research in our laboratory is supported by the National Institute of General Medical Sciences of the National Institutes of Health under award number R01GM100466.


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Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Julie E. Maguire
    • 1
  • Aakarsha Pandey
    • 1
  • Yushi Wu
    • 1
  • Anna Di Gregorio
    • 1
  1. 1.Department of Basic Science and Craniofacial BiologyNew York University College of DentistryNew YorkUSA

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