Architecture and evolution of the cis-regulatory system of the echinoderm kirrelL gene

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Abstract

The gene regulatory network (GRN) that underlies echinoderm skeletogenesis is a prominent model of GRN architecture and evolution. KirrelL is an essential downstream effector gene in this network and encodes an Ig-superfamily protein required for the fusion of skeletogenic cells and the formation of the skeleton. In this study, we dissected the transcriptional control region of the kirrelL gene of the purple sea urchin, Strongylocentrotus purpuratus. Using plasmid- and BAC-based transgenic reporter assays, we identified key cis-regulatory elements (CREs) and transcription factor inputs that regulate Sp-kirrelL, including direct, positive inputs from two key transcription factors in the skeletogenic GRN, Alx1 and Ets1. We next identified kirrelL cis-regulatory regions from seven other echinoderm species that together represent all classes within the phylum. By introducing these heterologous regulatory regions into developing sea urchin embryos we provide evidence of their remarkable conservation across ~500 million years of evolution. We dissected in detail the kirrelL regulatory region of the sea star, Patiria miniata, and demonstrated that it also receives direct inputs from Alx1 and Ets1. Our findings identify kirrelL as a component of the ancestral echinoderm skeletogenic GRN. They support the view that GRN sub-circuits, including specific transcription factor-CRE interactions, can remain stable over vast periods of evolutionary history. Lastly, our analysis of kirrelL establishes direct linkages between a developmental GRN and an effector gene that controls a key morphogenetic cell behavior, cell-cell fusion, providing a paradigm for extending the explanatory power of GRNs.

Data availability

All raw numerical data used in this study are contained in the manuscript.

The following previously published data sets were used

(2018) Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling
NCBI Gene Expression Omnibus, GSE96927.

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4542-z
(2021) Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling
NCBI Gene Expression Omnibus, GSE169227.

https://genome.cshlp.org/content/early/2021/08/24/gr.275684.121.long
(2019) Genome-wide identification of binding sites and gene targets of Alx1, a pivotal regulator of echinoderm skeletogenesis
NCBI Gene Expression Omnibus, GSE131370.

https://journals.biologists.com/dev/article/146/16/dev180653/224197/Genome-wide-identification-of-binding-sites-and

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Jian Ming Khor

Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-1428-6770
Charles A Ettensohn

Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, United States

For correspondence
ettensohn@cmu.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-3625-0955

Funding

National Institutes of Health (R24-OD023046)

Charles A Ettensohn

National Science Foundation (IOS2004952)

Charles A Ettensohn

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

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This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.