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F. Raible and P.R.H. Steinmetz
the UTRs of genes, and is speculated to comprise ultraconserved enhancer elements.
More than 3,000 of such elements have already been identified by genome comparisons among vertebrate species and seem to primarily act during development
(Pennacchio et al. 2006, Woolfe et al. 2005). The ability to assess the regulatory
potential of these elements in heterologous systems such as the mouse (Holland et al.
2008) now opens exciting possibilities to test if they might represent key regulatory
connections of pan-chordate relevance.
5.13 Ascidians: Changes and Constants in Developmental
Programmes
The ascidian Ciona intestinalis is a very interesting species for the comparison of
animal complexity. Phylogenetic analyses demonstrate that tunicates are the closest
relatives of vertebrates (Delsuc et al. 2006, 2008), implying that they are suitable
models for testing the evolution of vertebrate characters. Notably, whereas Ciona
possesses a tadpole-type larva, similar to those of chordate vertebrates like the frog,
the number of cells of this larva is only around 2,600, at least an order of magnitude less than what is found in vertebrates. In addition, the Ciona genome is only
5% of the size of the mouse genome. So, in comparison with vertebrate systems,
Ciona seems to generate a similar level of larval organizational complexity using
less non-coding DNA and cell types. Comparison of regulatory processes in Ciona
and vertebrate model systems therefore holds a lot of potential for the understanding
of regulatory complexity and developmental plasticity.
As early gene expression patterns in Ciona can be routinely mapped with cellular
resolution (Tassy et al. 2006), and functional tools also exist for Ciona, it is not only
possible to analyse and compare the expression of developmental marker genes in
Ciona, but also to systematically assess the function of Ciona genes. This combination of high-resolution gene expression data and functional techniques makes Ciona
a powerful tool for the analysis of developmental gene-regulatory networks in a
simple marine chordate, information which can then be compared with other clades
(Imai et al. 2006, Satou and Satoh 2006, Shoguchi et al. 2008). Importantly, such
comparisons have revealed different extents of conservation among chordate generegulatory networks. Some components seem to act in similar ways in both ascidian
and vertebrate embryogenesis. For instance, a fibroblast growth factor signal triggers the expression of the T-box transcription factor Brachyury and the formation of
the notochord in both systems, hinting at a conserved regulatory system orchestrating the development of this chordate character (Imai et al. 2002). Likewise,
effector genes encoding structural notochord components like type II collagen or
proteoglycans are conserved between Ciona and vertebrates (Hotta et al. 2008). In
contrast, upstream regulators of this process and their interconnections seem to differ more dramatically between the systems (Imai et al. 2006, Lemaire 2006). The
apparent contrast between conserved and divergent aspects of gene regulatory networks raises the question how “hard-wired” early developmental programmes are,
F. Raible and P.R.H. Steinmetz
the UTRs of genes, and is speculated to comprise ultraconserved enhancer elements.
More than 3,000 of such elements have already been identified by genome comparisons among vertebrate species and seem to primarily act during development
(Pennacchio et al. 2006, Woolfe et al. 2005). The ability to assess the regulatory
potential of these elements in heterologous systems such as the mouse (Holland et al.
2008) now opens exciting possibilities to test if they might represent key regulatory
connections of pan-chordate relevance.
5.13 Ascidians: Changes and Constants in Developmental
Programmes
The ascidian Ciona intestinalis is a very interesting species for the comparison of
animal complexity. Phylogenetic analyses demonstrate that tunicates are the closest
relatives of vertebrates (Delsuc et al. 2006, 2008), implying that they are suitable
models for testing the evolution of vertebrate characters. Notably, whereas Ciona
possesses a tadpole-type larva, similar to those of chordate vertebrates like the frog,
the number of cells of this larva is only around 2,600, at least an order of magnitude less than what is found in vertebrates. In addition, the Ciona genome is only
5% of the size of the mouse genome. So, in comparison with vertebrate systems,
Ciona seems to generate a similar level of larval organizational complexity using
less non-coding DNA and cell types. Comparison of regulatory processes in Ciona
and vertebrate model systems therefore holds a lot of potential for the understanding
of regulatory complexity and developmental plasticity.
As early gene expression patterns in Ciona can be routinely mapped with cellular
resolution (Tassy et al. 2006), and functional tools also exist for Ciona, it is not only
possible to analyse and compare the expression of developmental marker genes in
Ciona, but also to systematically assess the function of Ciona genes. This combination of high-resolution gene expression data and functional techniques makes Ciona
a powerful tool for the analysis of developmental gene-regulatory networks in a
simple marine chordate, information which can then be compared with other clades
(Imai et al. 2006, Satou and Satoh 2006, Shoguchi et al. 2008). Importantly, such
comparisons have revealed different extents of conservation among chordate generegulatory networks. Some components seem to act in similar ways in both ascidian
and vertebrate embryogenesis. For instance, a fibroblast growth factor signal triggers the expression of the T-box transcription factor Brachyury and the formation of
the notochord in both systems, hinting at a conserved regulatory system orchestrating the development of this chordate character (Imai et al. 2002). Likewise,
effector genes encoding structural notochord components like type II collagen or
proteoglycans are conserved between Ciona and vertebrates (Hotta et al. 2008). In
contrast, upstream regulators of this process and their interconnections seem to differ more dramatically between the systems (Imai et al. 2006, Lemaire 2006). The
apparent contrast between conserved and divergent aspects of gene regulatory networks raises the question how “hard-wired” early developmental programmes are,