Prenatal Acoustic Programming of the Developing Hypothalamus: A Multi-Omic Analysis of Heat Call Exposure in Zebra Finch Embryos

Author

• Prakrit Subba, Clemson UniversityFollow

Date of Award

8-2026

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Biological Sciences

Committee Chair/Advisor

Julia George

Committee Member

David Clayton

Committee Member

Susan Chapman

Committee Member

William Baldwin

Abstract

Climate change is intensifying thermal stress on wildlife globally, yet the developmental mechanisms by which embryos use prenatal cues to adjust to predicted environments remain unclear. In Australian zebra finches (Taeniopygia guttata), incubating parents produce distinctive heat call vocalizations at high ambient temperatures, and embryos exposed to these calls during late incubation develop altered growth trajectories, thermoregulatory capacity, and reproductive outcomes, suggesting a form of anticipatory developmental programming triggered by sound alone. To investigate the molecular basis of this response, I initially hypothesized that prenatal heat call exposure would act primarily through hypothalamic neuroendocrine reprogramming, given the central role of the hypothalamus in integrating environmental signals, coordinating thermoregulatory and metabolic programs. Bulk RNA-sequencing of the embryonic hypothalamus, however, indicated a coordinated downregulation vascular smooth muscle contractile programs in endothelial, smooth muscle, and ependymal cells, pointing to anticipatory cerebrovascular remodeling rather than the neuroendocrine reprogramming initially predicted. To ask whether these transcriptional differences were accompanied by any epigenetic modifications, I then performed genome-wide DNA methylation profiling, which revealed locus-specific changes in genes associated with nuclear receptor signaling, synaptic organization, inhibitory transmission, and RNA processing, including a robust signal at the splicing regulator RBFOX2, suggesting that the acoustic developmental programming response becomes embedded within a broader epigenetic regulatory architecture.

Building on these bulk-tissue findings, I next used single-nucleus RNA/ATAC sequencing to resolve which specific cell types within the heterogeneous hypothalamus were most responsive to prenatal heat call exposure, and through what regulatory mechanisms. These analyses revealed that heat call-associated chromatin remodeling was strongly concentrated in astrocytes and involved NFIC-, ASCL1-, and Notch-linked transcriptional regulatory programs, together with extensive enhancer-promoter rewiring at gliogenic developmental hubs. Notably, this chromatin reorganization was largely decoupled from immediate transcriptional output, consistent with a model in which regulatory landscapes are epigenetically primed ahead of downstream transcriptomic activation. Pseudotemporal analyses further suggested that these astrocyte-associated regulatory changes were accompanied by condition-associated shifts in developmental-state trajectories and altered expression dynamics of gliogenic genes, supporting the interpretation that prenatal heat calls are associated not only with altered chromatin accessibility, but also with changes in the timing or progression of astrocyte developmental programs. In parallel, sex-dependent regulation of transthyretin in paraventricular nucleus neurons pointed to a possible thyroid-related neuroendocrine interface through which acoustic experience may interact with developmental timing in a sex-specific manner. Together, these findings suggest that prenatal heat calls engage coordinated vascular, epigenetic, and glial regulatory responses in the embryonic hypothalamus, and they identify non-neuronal cell types, particularly astrocytes, as important and previously underappreciated contributors to acoustic developmental programming in the context of a warming world.

Recommended Citation

Subba, Prakrit, "Prenatal Acoustic Programming of the Developing Hypothalamus: A Multi-Omic Analysis of Heat Call Exposure in Zebra Finch Embryos" (2026). All Dissertations. 4400.
https://open.clemson.edu/all_dissertations/4400

Author ORCID Identifier

0000-0002-1160-7305