About

Dr. Charles A. Ettensohn is a Principal Investigator and Professor at Carnegie Mellon University. He holds a Ph.D. from Yale University and completed a postdoctoral appointment at Duke University. Dr. Ettensohn leads the Ettensohn Lab, which includes a team of research associates, Ph.D. students, master's students, and undergraduate students. The lab focuses on developmental biology, with research areas including developmental regulatory genomics, developmental plasticity and cellular reprogramming, and molecular mechanisms of early patterning. Dr. Ettensohn's work contributes to understanding the genetic and molecular bases of development, as reflected in the diverse expertise and projects undertaken by his lab members.

Research topics

• Biology
• Genetics
• Computer Science
• Computational biology
• Evolutionary biology
• Data science
• Cell biology
• Ecology

Selected publications

• A stage and anatomy ontology for embryogenesis in indirect-developing echinoderms

  Development · 2026-02-20

  article1st authorCorresponding

  Developmental and anatomical ontologies are fundamental tools for standardizing biological data. They facilitate the reproducibility of experiments and the integration of information across laboratories and animal species. They underpin digital curation, dissemination and analysis of diverse biological data, including gene expression patterns and phenotypes associated with pharmacological, molecular and genetic perturbations. As such, ontologies are cornerstones of model organism knowledgebases. Echinoderms have been prominent developmental biology models for more than a century and are widely used to address evolutionary questions; however, no formalized ontology has been produced for any echinoderm. Here, based on direct observations of living embryos of five species, representing euechinoids, cidaroids and sea stars, we provide developmental and anatomical ontologies for the embryogenesis of indirect-developing echinoderms. Moreover, we leverage these ontologies to create a 'pan-echinoderm' developmental and anatomical ontology, which we show will support comparative analyses across the phylum. These resources will be important for the curation of data from multiple species by Echinobase and Marimba, two public knowledgebases of echinoderm genomics and invertebrate marine models, respectively. They will greatly enhance the use and value of echinoderms as model organisms for biological research.

  PublisherDOI

• BMP signaling regulates dorsal skeletal growth in the sea urchin embryo

  Development · 2026-04-23

  articleOpen accessSenior author

  The development of the elaborate, calcified endoskeleton of sea urchin embryos is a model for understanding the dynamic nature of developmental gene regulatory networks and the control of biomineralization. While several signaling pathways have been shown to regulate gene expression and biomineral formation by sea urchin skeletogenic cells, important gaps in our understanding remain. Here, we focused on signals that regulate skeletogenesis along the dorsal-ventral axis of the late-stage embryo. We used a specific inhibitor of Type I BMP receptors, K02288, to show that BMP signaling regulates skeletal growth selectively in the dorsal region. K02288 treatment led to dorsal skeletal defects and inhibited the expression of genes typically expressed specifically in the dorsal skeletogenic cells, including biomineralization genes. Using RNA sequencing, we identified genes that were uniquely downstream of either the BMP or a ventral signaling pathway (the VEGF pathway) at late developmental stages and genes downstream of both pathways. Our findings establish BMP signaling as a key pathway regulating dorsal skeleton formation and show that BMP signaling functions in concert with VEGF signaling to define the dorsal-ventral axis of the skeleton.

  PublisherDOI

• Horizontal Transfer of <i>msp130</i> Genes and the Evolution of Metazoan Biocalcification

  Genome Biology and Evolution · 2025-02-01 · 3 citations

  articleOpen accessSenior author

  The formation of calcified skeletons is crucial for the development, physiology, and ecology of many marine metazoans. The evolutionary origins of the genetic toolkit required for biocalcification are widely debated. MSP130 proteins, originally identified through their expression specifically by sea urchin skeletal cells, have been hypothesized to have been acquired by metazoans from bacteria through horizontal gene transfer. Here, we provide support for a horizontal gene transfer-based origin of metazoan MSP130 proteins by conducting phylogenetic and in silico protein analyses utilizing high-quality genomes. We show that msp130 genes underwent duplications within almost all biocalcifying bilaterian phyla and identify highly conserved intron-exon junctions specific to bilaterian msp130 genes. The absence of MSP130 proteins in calcifying, nonbilaterian metazoans and other basal eukaryotes suggests that an ancestral msp130 gene underwent a horizontal gene transfer event that predates bilaterians, but not metazoans. We report striking structural similarities between bilaterian and bacterial MSP130 proteins, with each containing a seven-bladed, barrel-like motif that encompasses a choice-of-anchor domain, and identify highly conserved, predicted Ca2+-binding sites associated with the barrels. These findings point to a conserved, ancient function for MSP130 proteins in biocalcification and support the view that lateral transfer of bacterial genes supported the appearance of calcified animal skeletons.

  PublisherDOI

• eLife Assessment: ROCK and the actomyosin network control biomineral growth and morphology during sea urchin skeletogenesis

  2024-03-01

  peer-reviewOpen access1st authorCorresponding

  Biomineralization had apparently evolved independently in different phyla, using distinct minerals, organic scaffolds and gene regulatory networks (GRNs). However, diverse eukaryotes from unicellular organisms, through echinoderms to vertebrates, use the actomyosin network during biomineralization. Specifically, the actomyosin remodeling protein, Rho-associated coiled-coil kinase (ROCK) regulates cell differentiation and gene expression in vertebrates’ biomineralizing cells, yet, little is known on ROCK’s role in invertebrates’ biomineralization. Here we reveal that ROCK controls the formation, growth and morphology of the calcite spicules in the sea urchin larva. ROCK expression is elevated in the sea urchin skeletogenic cells downstream of the Vascular Endothelial Growth Factor (VEGF) signaling. ROCK inhibition leads to skeletal loss and disrupts skeletogenic gene expression. ROCK inhibition after spicule formation reduces spicule elongation rate and induces ectopic spicule branching. Similar skeletogenic phenotypes are observed when ROCK is inhibited in a skeletogenic cell culture, indicating that these phenotypes are due to ROCK activity specifically in the skeletogenic cells. Reduced skeletal growth and enhanced branching are also observed under direct perturbations of the actomyosin network. We propose that ROCK and the actomyosin machinery were employed independently, downstream of distinct GRNs, to regulate biomineral growth and morphology in Eukaryotes.

  PublisherDOI

• Echinobase: a resource to support the echinoderm research community

  Genetics · 2024-01-23 · 38 citations

  articleOpen accessSenior author

  Echinobase (www.echinobase.org) is a model organism knowledgebase serving as a resource for the community that studies echinoderms, a phylum of marine invertebrates that includes sea urchins and sea stars. Echinoderms have been important experimental models for over 100 years and continue to make important contributions to environmental, evolutionary, and developmental studies, including research on developmental gene regulatory networks. As a centralized resource, Echinobase hosts genomes and collects functional genomic data, reagents, literature, and other information for the community. This third-generation site is based on the Xenbase knowledgebase design and utilizes gene-centric pages to minimize the time and effort required to access genomic information. Summary gene pages display gene symbols and names, functional data, links to the JBrowse genome browser, and orthology to other organisms and reagents, and tabs from the Summary gene page contain more detailed information concerning mRNAs, proteins, diseases, and protein-protein interactions. The gene pages also display 1:1 orthologs between the fully supported species Strongylocentrotus purpuratus (purple sea urchin), Lytechinus variegatus (green sea urchin), Patiria miniata (bat star), and Acanthaster planci (crown-of-thorns sea star). JBrowse tracks are available for visualization of functional genomic data from both fully supported species and the partially supported species Anneissia japonica (feather star), Asterias rubens (sugar star), and L. pictus (painted sea urchin). Echinobase serves a vital role by providing researchers with annotated genomes including orthology, functional genomic data aligned to the genomes, and curated reagents and data. The Echinoderm Anatomical Ontology provides a framework for standardizing developmental data across the phylum, and knowledgebase content is formatted to be findable, accessible, interoperable, and reusable by the research community.

  PublisherOA PDFDOI

• eLife Assessment: ROCK and the actomyosin network control biomineral growth and morphology during sea urchin skeletogenesis

  2024-03-19

  peer-reviewOpen access1st authorCorresponding

  Biomineralization had apparently evolved independently in different phyla, using distinct minerals, organic scaffolds and gene regulatory networks (GRNs). However, diverse eukaryotes from unicellular organisms, through echinoderms to vertebrates, use the actomyosin network during biomineralization. Specifically, the actomyosin remodeling protein, Rho-associated coiled-coil kinase (ROCK) regulates cell differentiation and gene expression in vertebrates' biomineralizing cells, yet, little is known on ROCK's role in invertebrates' biomineralization. Here we reveal that ROCK controls the formation, growth and morphology of the calcite spicules in the sea urchin larva. ROCK expression is elevated in the sea urchin skeletogenic cells downstream of the Vascular Endothelial Growth Factor (VEGF) signaling. ROCK inhibition leads to skeletal loss and disrupts skeletogenic gene expression. ROCK inhibition after spicule formation reduces spicule elongation rate and induces ectopic spicule branching. Similar skeletogenic phenotypes are observed when ROCK is inhibited in a skeletogenic cell culture, indicating that these phenotypes are due to ROCK activity specifically in the skeletogenic cells. Reduced skeletal growth and enhanced branching are also observed under direct perturbations of the actomyosin network. We propose that ROCK and the actomyosin machinery were employed independently, downstream of distinct GRNs, to regulate biomineral growth and morphology in Eukaryotes.

  PublisherDOI

• eLife assessment: ROCK and the actomyosin network control biomineral growth and morphology during sea urchin skeletogenesis

  2024-04-04

  peer-reviewOpen access1st authorCorresponding
  PublisherDOI

• Molecular compartmentalization in a syncytium: restricted mobility of proteins within the sea urchin skeletogenic mesenchyme

  Development · 2023-10-30 · 4 citations

  articleOpen accessSenior author

  Multinucleated cells, or syncytia, are found in diverse taxa. Their biological function is often associated with the compartmentalization of biochemical or cellular activities within the syncytium. How such compartments are generated and maintained is poorly understood. The sea urchin embryonic skeleton is secreted by a syncytium, and local patterns of skeletal growth are associated with distinct sub-domains of gene expression within the syncytium. For such molecular compartments to be maintained and to control local patterns of skeletal growth: (1) the mobility of TFs must be restricted to produce stable differences in the transcriptional states of nuclei within the syncytium; and (2) the mobility of biomineralization proteins must also be restricted to produce regional differences in skeletal growth. To test these predictions, we expressed fluorescently tagged forms of transcription factors and biomineralization proteins in sub-domains of the skeletogenic syncytium. We found that both classes of proteins have restricted mobility within the syncytium and identified motifs that limit their mobility. Our findings have general implications for understanding the functional and molecular compartmentalization of syncytia.

  PublisherOA PDFDOI

• Referee report. For: The genome sequence of the spiny starfish, Marthasterias glacialis (Linnaeus, 1758) [version 1; peer review: 1 approved, 1 approved with reservations]

  Faculty of 1000 Research Ltd · 2023-01-01

  articleOpen access1st authorCorresponding
  PublisherDOI

• The people behind the papers – Jian Ming Khor and Charles Ettensohn

  Development · 2023-11-15

  articleOpen accessCorresponding

  Syncytia are multinucleated cells that form distinct functional compartments. In a new paper in Development, Charles Ettensohn and colleagues use the sea urchin embryonic skeleton to study how specialized compartments are generated in a syncytium to give rise to local skeletal patterns. We caught up with first author Jian Ming Khor and corresponding author Charles Ettensohn, Professor at Carnegie Mellon University, to find out more about their research.

  PublisherOA PDFDOI

Recent grants

• Cell Interactions and Cell Fate Specification

  NSF · $390k · 2002–2004

• Analysis of a Gene Regulatory Network in Early Animal Development

  NSF · $260k · 2005–2007

• Analysis of a Model Developmental Gene Regulatory Network

  NSF · $764k · 2017–2020

• Analysis of a Gene Regulatory Network in Early Animal Development

  NSF · $875k · 2010–2014

• NIH Grant R01HD024690

  NIH · $744k · 2000

Frequent coauthors

• Jonathan P. Rast

  71 shared

• R. Andrew Cameron

  California Institute of Technology

  67 shared

• Albert J. Poustka

  66 shared

• Eric H. Davidson

  65 shared

• Brian T. Livingston

  California State University, Long Beach

  62 shared

• Pedro Martı́nez

  Instituto Politécnico Nacional

  61 shared

• Richard O. Hynes

  Howard Hughes Medical Institute

  40 shared

• Gregory G. Mahairas

  40 shared

Labs

• Ettensohn LabPI

Education

• Ph.D.

  Yale University

• Other

  Duke University