Rules and Constraints Shaping the Evolution of Gene Regulatory Networks

New body structures allow organisms to explore new ways of surviving and adapt to different environments. Understanding how such structures arise at the molecular level has long been a central goal in biology. Rather than inventing new genes to build new body features, evolution often works by reusing existing ones, changing when and where genes are turned on and how they interact with each other. These changes in how genes interact, known as gene regulatory networks, are now thought to be a primary driver of the emergence of new body features. However, it remains unclear whether the evolution of gene regulatory networks follows any predictable trends, underlying rules, or inherent limitations. Using the highly modified wings of beetles as a model system, this project seeks to uncover the principles that govern how gene networks change over evolutionary time to generate new structures. Beyond its scientific significance, this project advances the broader national interest in several ways. The project integrates research and education by supporting a student-driven gene annotation initiative conducted in the teaching laboratory, in which undergraduate students perform original genetic experiments and contribute their findings to a publicly accessible database, gaining real-world research experience. The project also establishes several science outreach initiatives designed to engage and recruit individuals with disabilities into scientific careers. Furthermore, insights into the principles governing gene network evolution derived from this project have relevance to biotechnology applications and bioinspired engineering, including the rational design of synthetic gene circuits and the development of adaptive biological systems, with potential applications in medical diagnostics, biologically facilitated environmental improvement, and optimized bioproduction. Morphological innovation often arises from novel uses of evolutionarily conserved genes, i.e., modifications in gene regulatory networks (GRNs). GRN modifications are often driven by changes in enhancers, which control gene expression and enable new regulatory connections, but whether their evolution follows predictable rules or constraints remains unclear. The elytron, a highly modified forewing unique to beetles, is a key morphological innovation that shields the body from environmental stresses. This project utilizes the elytron of Tribolium castaneum, a beetle with well-established genetic and genomic tools, to explore previously underexamined aspects of GRN evolution. Specific Aim 1 will explore how the wing gene network (WGN) in beetles has co-opted numerous effector genes to produce the protective surface of the elytron through genomic and enhancer analyses, examining both the extent of co-option and whether it is driven by individual gene recruitment or coordinated by an upstream regulatory gene. Specific Aims 2 and 3 will investigate how the WGN manages its pleiotropic nature and accommodates the changes required for elytron development while preserving the ancestral flight wing morphology of the hindwing. Several hypotheses regarding how the functional properties of transcription factors, acting as activators or repressors, influence the network evolution will be tested through enhancer analysis and novel RNA interference (RNAi)-based genetic interaction assays. Through these aims, this project explores the underlying principles and inherent constraints guiding WGN evolution, providing new insights into how complex gene networks evolve to produce novel morphological traits while often retaining their essential ancestral functions. 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. NSF Award ID: 2544766 | Program: 01002627DB NSF RESEARCH & RELATED ACTIVIT | Principal Investigator: Yoshinori Tomoyasu | Institution: Miami University, OXFORD, OH | Award Amount: $763,232 View on NSF Award Search: https://www.nsf.gov/awardsearch/show-award/?AWD_ID=2544766 View on Research.gov: https://www.research.gov/awardapi-service/v1/awards/2544766.html