NON-CODING RNAS AS REGULATORS OF CORAL BIOLOGY

Author

Jill Ashey, University of Rhode IslandFollow

Date of Award

2025

Degree Type

Dissertation

Degree Name

Doctor of Philosophy in Biological and Environmental Sciences

Department

Biological Sciences

First Advisor

Hollie M. Putnam

Abstract

Coral reef ecosystems face increasing threats from climate change, yet knowledge of the molecular mechanisms that underlie coral acclimatization, resilience, and development remains incomplete. Among these mechanisms, non-coding RNAs (ncRNAs), specifically microRNAs (miRNAs), are emerging as key regulators of gene expression in response to environmental and developmental cues. This dissertation explores the diversity, function, and dynamics of ncRNAs in scleractinian corals across ecological, physiological, and developmental contexts. In Chapter 1, I present the first comprehensive analysis of ncRNAs - specifically long ncRNAs (lncRNAs), miRNAs, and piwi-RNAs (piRNAs) - in three reef-building coral species from Mo’orea, French Polynesia: Acropora pulchra, Pocillopora tuahiniensis, and Porites evermanni. Despite their differing symbiotic associations and life history strategies, I found that these species shared conserved components of ncRNA machinery. Conserved miRNAs were identified in the three species and shared and species-specific miRNAs regulated immune response and signal transduction pathways. The majority of piRNAs were found in proximity to genes involved in genome maintenance, and lncRNAs were often located near immune-related genes, suggesting potential roles in coral homeostasis and stress response. Chapter 2 investigates seasonal and thermal influences on physiology and miRNA-mediated gene expression regulation in the temperate coral Astrangia poculata. Using a long-term thermal stress experiment, I demonstrated that seasonal variation, more than warming alone, drove shifts in both physiology and gene expression. Novel miRNAs exhibited differential expression across seasons and were predicted to regulate transcripts related to nutrient uptake, apoptosis, and autophagy, highlighting the potential role of miRNAs in mediating seasonal plasticity in this facultatively symbiotic coral. In Chapter 3, I examine the maternal-to-zygotic (MZT) in the early development of the reef-building coral Montipora capitata, focusing on the role of miRNAs in maternal mRNA clearance and zygotic genome activation. Distinct waves of gene expression were observed, corresponding to Maternal, Minor Wave, and Major Wave gene expression profiles. Further, mRNA-miRNA interaction analyses suggest that miRNAs contribute to the degradation of maternal transcripts involved in developmental regulation, providing critical temporal and mechanistic insights into the MZT in corals. Collectively, this work establishes ncRNAs as central players in gene expression regulations across life stages and environmental conditions. By characterizing ncRNAs and their regulatory roles, this dissertation reveals novel regulatory layers that may underpin coral resilience, plasticity, and development, and contributes to the broader understanding of epigenetic regulation in marine invertebrates.

Creative Commons License

This work is licensed under a Creative Commons Attribution-No Derivative Works 4.0 License.

Recommended Citation

Ashey, Jill, "NON-CODING RNAS AS REGULATORS OF CORAL BIOLOGY" (2025). Open Access Dissertations. Paper 4483.
https://digitalcommons.uri.edu/oa_diss/4483