UC Santa Cruz

The developmental process through which a single cell gives rise to a complex multicellular organism is orchestrated by precisely coordinated molecular programs that integrate both intrinsic and extrinsic cues. At the cellular level, this process requires cell fate specification and differentiation across multiple tissue types. At the molecular level, transcriptional activity must be precisely regulated to control timing and level of gene expression. The spatiotemporal regulation of gene expression ensures that specific sets of genes are activated or repressed at the appropriate developmental stage, location, and duration. Genomic approaches developed throughout the past decade enable a comprehensive view of transcriptional regulation, capturing not only gene expression profiles but also chromatin architecture, regulatory elements, and epigenetic modifications. Importantly, these regulatory elements encompass a wide range of macromolecules, including RNAs, proteins, and DNA cis-regulatory elements. The C. elegans protein NHR-23 serves as a perfect model to study tissue-specific transcriptional regulation, as it controls molting in epidermal cells (seam cells and hypodermis) and spermatogenesis in the gonad. In Chapter 3, I detail my work using Nanodam sequencing (Nanodam-seq) to determine NHR-23-occupied genomic regions in the germline, seam cells, and the hypodermis. Spermatogenesis requires coordination of a series of meiotic events and organelle biogenesis. In Chapter 4, I described work screening for transcriptional regulators of spermatogenesis, as well as work characterizing SPE-54, a newly identified gene required for spermatogenesis. In Chapter 5, I evaluated modern transgenesis methods, as a recombinase approach appeared prone to germline silencing of transgenes. I detailed my experience generating germline transgenes, including experiments aimed at finding approaches to circumvent transgene silencing.