Study of Cis-regulatory Elements in the Ascidian Ciona intestinalis

Abstract

The ascidian (sea squirt) C. intestinalis has become an important model organism for the study of cis-regulation. This is largely due to the technology that has been developed for assessing cis-regulatory activity through the use of transient reporter transgenes introduced into fertilized eggs. This technique allows the rapid and inexpensive testing of endogenous or altered DNA for regulatory activity in vivo. This review examines evidence that C. intestinalis cis-regulatory elements are located more closely to coding regions than in other model organisms. I go on to compare the organization of cis-regulatory elements and conserved non-coding sequences in Ciona, mammals, and other deuterostomes for three representative C.intestinalis genes, Pax6, FoxAa, and the DlxA-B cluster, along with homologs in the other species. These comparisons point out some of the similarities and differences between cis-regulatory elements and their study in the various model organisms. Finally, I provide illustrations of how C. intestinalis lends itself to detailed study of the structure of cis-regulatory elements, which have led, and promise to continue to lead, to important insights into the fundamentals of transcriptional regulation.

Brachyury controlsCionanotochord fate as part of a feedforward network and not as a unitary master regulator

“…We focused again on genes enriched at least two-fold in notochord during neurulation (stage 16) as well as early tailbud (stage 19). Ciona enhancers tend to be near to the transcriptional start site (Irvine, 2013), so we used a window 1500 bp upstream and downstream from the transcription start site of each gene model from which we subtracted predicted exons (see methods for full details). Putative regulatory regions of notochord enriched genes were tested for overrepresented TFBSs using the 2018 JASPAR vertebrate TFBS profile set (Khan et al, 2018) and the oPOSSUM 3.0 Single-Site Analysis algorithm (Kwon et al, 2012), with the enhancers from the 1000 most notochord depleted genes at each stage as the control set.…”

Single-cell analysis of cell fate bifurcation in the chordateCiona

“…TFBS enrichment analysis uses statistical models to determine if the binding site sequence for a particular transcription factor (TF) is overrepresented in a set of target DNA sequences compared to a set of control DNA sequences [57]. In Ciona, most enhancers and other cis-regulatory modules are thought to be relatively close to the transcription start site [58]. We used the 1.5 kB of DNA upstream of the transcription start site to test for enrichment of Ets sites in the putative regulatory regions of genes that are upregulated versus downregulated in FGF-dependent cell types as compared to their sibling cell types.…”

An organismal perspective on C. intestinalis development, origins and diversification

“…The total genome size of C. intestinalis , however, is less than one twenty-fifth that of the human genome because of the reduction in non-coding gene sequence, such as introns, and because of the organization of about one fifth of its genes into operons (see Glossary; Satou et al, 2008 ). This small, compact genome offers various advantages to the researcher ( Wang and Christiaen, 2012 ; Irvine, 2013 ).…”