The genetic regulatory architecture and epigenomic basis for age-related changes in rattlesnake venom

• 成果类型: Article
• 署名作者: Hogan, Michael P.; Holding, Matthew L.; Nystrom, Gunnar S.; Colston, Timothy J.; Bartlett, Daniel A.; Mason, Andrew J.; Ellsworth, Schyler A.; Rautsaw, Rhett M.; Lawrence, Kylie C.; Strickland, Jason L.; He, Bing; Fraser, Peter; Margres, Mark J.; Gilberti, David M.; Gibbse, H. Lisle; Parkinson, Christopher L.; Rokyta, Darin R.
• 署名单位: State University System of Florida; Florida State University; University of Michigan System; University of Michigan; University of Puerto Rico; University of Puerto Rico Mayaguez; Clemson University; University System of Ohio; Ohio State University; State University System of Florida; University of South Florida; Washington State University; University of South Alabama
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-9326
• DOI: 10.1073/pnas.2313440121
• 发表日期: 2024-04-16
• 关键词: evo-devo; EVOLUTION; expression; origin; pedomorphosis; adaptation; contribute; enhancers; selection; alignment

摘要

Developmental phenotypic changes can evolve under selection imposed by age- and size -related ecological differences. Many of these changes occur through programmed alterations to gene expression patterns, but the molecular mechanisms and generegulatory networks underlying these adaptive changes remain poorly understood. Many venomous snakes, including the eastern diamondback rattlesnake (Crotalus adamanteus), undergo correlated changes in diet and venom expression as snakes grow larger with age, providing models for identifying mechanisms of timed expression changes that underlie adaptive life history traits. By combining a highly contiguous, chromosome -level genome assembly with measures of expression, chromatin accessibility, and histone modifications, we identified cis -regulatory elements and transregulatory factors controlling venom ontogeny in the venom glands of C. adamanteus. Ontogenetic expression changes were significantly correlated with epigenomic changes within genes, immediately adjacent to genes (e.g., promoters), and more distant from genes (e.g., enhancers). We identified 37 candidate transcription factors (TFs), with the vast majority being up -regulated in adults. The ontogenetic change is largely driven by an increase in the expression of TFs associated with growth signaling, transcriptional activation, and circadian rhythm/biological timing systems in adults with corresponding epigenomic changes near the differentially expressed venom genes. However, both expression activation and repression contributed to the composition of both adult and juvenile venoms, demonstrating the complexity and potential evolvability of gene regulation for this trait. Overall, given that age -based trait variation is common across the tree of life, we provide a framework for understanding generegulatory -network -driven life -history evolution more broadly.