Variable levels of drift in tunicate cardiopharyngeal gene regulatory elements

Abstract

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.

Conservation of peripheral nervous system formation mechanisms in divergent ascidian embryos

“…The newly identified Msx CRM from A. mentula actually contains a region dense in Otx and Smad binding sites like their counterparts in Ciona and Phallusia (not shown). This phenomenon has been described for other CRMs between C. intestinalis and other species and outside ascidians ( Buffry et al, 2016 ; Colgan et al, 2019 ; Oda-Ishii et al, 2005 ).…”

“…between C. intestinalis and P. mammillata ) ( Supplementary file 2 and 5 ). There are previous examples in ascidians that clearly show that such conserved activity relies on conserved upstream regulators but that extensive binding site turnover explains the lack of sequence conservation ( Roure et al, 2014 ; Madgwick et al, 2019 ; Colgan et al, 2019 ). We thus reasoned that the CRMs with conserved activity that we have isolated from C. intestinalis and P. mammillata could help in identifying conserved TFBS and shared TF regulating CRM activity.…”

“…A few CRMs (Ciinte.Nkxtun3-up7, Phmamm.Nkxtun3-A1 and Ciinte.Tox-int1) had weak activity, below 30%, in one or the other species. However, most tested regions were active in VDML in over 40- show that such conserved activity relies on conserved upstream regulators but that extensive binding site turnover explains the lack of sequence conservation (14,27,28). We thus reasoned that the CRMs with conserved activity that we have isolated from C. intestinalis and P. mammillata could help in identifying conserved TFBS and shared TF regulating CRM activity.…”

“…Yet, their embryos are virtually identical. This paradoxical situation represents an excellent case to study the evolution and diversification of developmental mechanisms, CRMs and DSD (12,14,(26)(27)(28)(29)(30)(31)(32)(33)(34).…”

“…Yet, their embryos are virtually identical. This paradoxical situation represents an excellent case to study the evolution and diversification of developmental mechanisms, CRMs and DSD ( José-Edwards et al, 2015 ; Roure et al, 2014 ; Stolfi et al, 2014 ; Madgwick et al, 2019 ; Colgan et al, 2019 ; Takahashi et al, 1999 ; Hudson et al, 2011 ; Racioppi et al, 2017 ; Johnson et al, 2004 ; Brown et al, 2007 ; Oda-Ishii et al, 2005 ). Ascidians are simple tractable organisms and are excellent models for functional genomics, in particular with plasmid DNA electroporation that allows the easy generation of thousands of transient transgenic embryos.…”