Variable levels of drift in tunicate cardiopharyngeal gene regulatory elements.

Background: Mutations in gene regulatory networks often lead to genetic divergence without impacting gene expression or developmental patterning. The rules governing this process of developmental systems drift, including the variable impact of selective constraints on different nodes in a gene regulatory network, remain poorly delineated. Results: Here we examine developmental systems drift within the cardiopharyngeal gene regulatory networks of two tunicate species, Corella inflata and Ciona robusta. Cross-species analysis of regulatory elements suggests that trans-regulatory architecture is largely conserved between these highly divergent species. In contrast, cis-regulatory elements within this network exhibit distinct levels of conservation. In particular, while most of the regulatory elements we analyzed showed extensive rearrangements of functional binding sites, the enhancer for the cardiopharyngeal transcription factor FoxF is remarkably well-conserved. Even minor alterations in spacing between binding sites lead to loss of FoxF enhancer function, suggesting that bound trans-factors form position-dependent complexes. Conclusions: Our findings reveal heterogeneous levels of divergence across cardiopharyngeal cis-regulatory elements. These distinct levels of divergence presumably reflect constraints that are not clearly associated with gene function or position within the regulatory network. Thus, levels of cis-regulatory divergence or drift appear to be governed by distinct structural constraints that will be difficult to predict based on network architectur

Variable Levels Of Drift In Tunicate Cardiopharyngeal Gene Regulatory Elements

Background: Mutations in gene regulatory networks often lead to genetic divergence without impacting gene expression or developmental patterning. The rules governing this process of developmental systems drift, including the variable impact of selective constraints on different nodes in a gene regulatory network, remain poorly delineated. Results: Here we examine developmental systems drift within the cardiopharyngeal gene regulatory networks of two tunicate species, Corella inflata and Ciona robusta. Cross-species analysis of regulatory elements suggests that trans-regulatory architecture is largely conserved between these highly divergent species. In contrast, cis-regulatory elements within this network exhibit distinct levels of conservation. In particular, while most of the regulatory elements we analyzed showed extensive rearrangements of functional binding sites, the enhancer for the cardiopharyngeal transcription factor FoxF is remarkably well-conserved. Even minor alterations in spacing between binding sites lead to loss of FoxF enhancer function, suggesting that bound trans-factors form position-dependent complexes. Conclusions: Our findings reveal heterogeneous levels of divergence across cardiopharyngeal cis-regulatory elements. These distinct levels of divergence presumably reflect constraints that are not clearly associated with gene function or position within the regulatory network. Thus, levels of cis-regulatory divergence or drift appear to be governed by distinct structural constraints that will be difficult to predict based on network architecture

Exploration of Left-Right Asymmetric Gene Expression within Ciona robusta

In bilateral organisms, the development of the left- right axis follows a conserved model. Although the steps of LR axial patterning are well established many mechanisms facilitating LR patterning remain poorly characterized. It is known that Nodal and ion flux signaling are necessary for the establishment of the LR asymmetric morphogenesis yet, it is unknown how these initial signaling pathways impact laterally asymmetric gene expression. Here we show how the model organism Ciona robusta can be utilized to visualize asymmetric gene expression as well as how gene expression is affected by early symmetry breaking mechanisms, Nodal and ion flux. In our research, asymmetric gene expression within Ciona, previously established by TOMOseq, was visualized with in situ hybridization. To explore the impact of Nodal and ion flux on asymmetric gene expression embryos were treated with Nodal and ion flux inhibitors and underwent in situ hybridization using genes previously identified as asymmetrically enriched. Through this process we found that our data was highly variable due to dechorionization. This being said, the research demonstrated that asymmetric gene expression is primarily localized in the mesenchyme, and trunk lateral cell lineages. I also observed interesting changes in the expression patterns of Crkl, Klhl4, FoxC, and Mef2 following inhibitor treatments