Snake venom systems as a model for inferring the structure and evolution of regulatory networks underlying organism-level physiological traits

How new traits arise, how organism-level phenotypes manifest through variation at the cellular level, and how trait variation is impacted by genomic changes that modify gene regulatory networks are fundamental questions for understanding the genomic basis of organismal phenotype. This collaborative project links these topics through studies of snake venom systems and the genomic, regulatory, physiological, cellular, and evolutionary mechanisms that drive variation in venom composition. The research aims to transform current understanding of gene regulatory mechanisms by integrating inferences across scales of biological organization, from single cells to whole organisms, and from within populations to distantly related species, and by applying new predictive frameworks to link genetic and phenotypic variation. New statistical approaches that leverage both cellular and evolutionary variation to generate, test, and refine hypotheses for how gene regulatory networks function – innovations that are broadly applicable to any eukaryotic system – will be developed and disseminated. The research will advance fundamental understanding of how natural selection acts to evolve, maintain, and finely tune complex traits. Mentoring and research training in integrative biology will be provided for 22 undergraduate and 8 graduate students across four institutions, and a course-based undergraduate research experience (CURE) will be implemented. In addition, the project includes workshops and online modules to enhance training in state-of-the-art genomics and biological data science. By providing new insights into how snake venom variation is regulated, the project will have broad ramifications for improving global treatment of snakebite, with potential to impact millions globally. The overarching goal of this research program is to advance the ability to understand and predict how new gene regulatory networks arise and how variation in these networks shape complex physiological traits, using snake venom as a model system. This research aims to understand how complex physiological traits are controlled, how these regulatory networks arise and subsequently re-wire existing physiological systems, and to identify the mechanisms that shape cellular and evolutionary variation in organismal phenotypes. This project will formulate, refine, and test mechanistic hypotheses for gene regulatory networks underlying venom composition by integrating across biological and evolutionary scales, and by leveraging emerging statistical frameworks to link genomic variation and gene regulatory variation with cellular and evolutionary trait variation. New methods developed will integrate predictive approaches and diverse functional genomic data to test mechanistic hypotheses and predict the roles of regulatory elements, trans-acting factors and other features that govern venom composition, and to test how cellular and evolutionary heterogeneity together shape organismal-level phenotypes. Key products of this work include novel approaches and software that leverage both single-cell variation and evolutionary variation to explicitly test hypotheses for the roles of gene regulatory components (e.g., cis-regulatory elements and trans-regulatory factors) that will be broadly applicable for developing and testing hypotheses for gene regulatory mechanisms in any eukaryotic system. The proposed research includes methodological and theoretical scientific innovation, development of new tools and software for understanding and testing hypotheses of regulatory networks and their evolution, training, establishment of collaborative networks, and impactful outreach. This project is jointly funded by BIO-IOS-Physiological Mechanisms and Biomechanics, BIO-DEB-Evolutionary Processes, and BIO-DEB-Systematics and Biodiversity Science. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.