Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis

Abstract

The draft genome of the primitive chordate, Ciona intestinalis, was published three years ago. Since then, significant progress has been made in utilizing Ciona's genomic and morphological simplicity to better understand conserved chordate developmental processes. Extensive annotation and sequencing of staged EST libraries make the Ciona genome one of the best annotated among those that are publicly available. The formation of the Ciona tadpole depends on simple, well-defined cellular lineages, and it is possible to trace the lineages of key chordate tissues such as the notochord and neural tube to the fertilized egg. Electroporation methods permit the targeted expression of regulatory genes and signaling molecules in defined cell lineages, as well as the rapid identification of regulatory DNAs underlying cell-specific gene expression. The recent sequencing of a second Ciona genome (C. savignyi) permits the use of simple alignment algorithms for the identification of conserved noncoding sequences, including microRNA genes and enhancers. Detailed expression profiles are now available for almost every gene that encodes a regulatory protein or cell-signaling molecule. The combination of gene-expression profiles, comparative genome analysis, and gene-disruption assays should permit the determination of high-resolution genomic regulatory networks underlying the specification of basic chordate tissues such as the heart, blood, notochord, and neural tube.

Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques

“…The availability of genomic sequence from a closely related species, Ciona savignyi, provides opportunities to identify additional candidate regulatory elements through interspecies comparisons. A summary of Web resources and experimental data available for Ciona is provided in Shi et al (2005).…”

A spectroscopic assessment of cellulose and the molecular mechanisms of cellulose biosynthesis in the ascidian Ciona intestinalis

“…The draft genome sequence and a large amount of expressed sequence tag/cDNA information are available, and experimental techniques to incorporate foreign genes using electroporation or to inhibit gene function using antisense oligonucleotides have been established (reviewed in Shi et al, 2005). These resources may facilitate gain-or loss-of-function analyses to evaluate if and how any predicted gene in the genome is involved in cellulose biosynthesis.…”

Snail2 controls mesodermal BMP/Wnt induction of neural crest

“…twist encodes a basic helix-loop-helix (bHLH)-type transcription factor; these proteins typically act as dimers (Barnes and Firulli, 2009). Both snail-and twist-like genes are found in the primitive chordate Ciona intestinalis (Shi et al, 2005) and in the jellyfish Podocoryne carnea (Spring et al, 2002;Spring et al, 2000). A BLAST analysis indicates that both the Ciona and Podocoryne Snail proteins more closely resemble mammalian Snail2 (Slug) than Snail1 proteins (our unpublished observation).…”