Project Summary/Abstract The precise spatial and temporal patterning mechanisms that coordinate early embryonic development represent a fundamental question in developmental biology. While such complex regulation is ultimately determined at the genotypic level, the molecular mechanisms that connect genotype to phenotype remain poorly understood. Elucidation of these mechanisms is of critical importance to human health, as errors in these processes often lead to various developmental defects and diseased states. In this proposal, I will study the formation of periodic pigment patterns (e.g., stripes and spots) to uncover the mechanisms by which positional information is encoded in mammalian skin during embryogenesis. Periodic pigment patterns arise from nonrandom developmental processes that are programmed to be spatially constrained, and thereby represent an excellent model for understanding how a tissue acquires positional information. Specifically, I will take advantage of the naturally evolved pigment pattern seen in the African striped mouse (Rhabdomys pumilio), an emerging mammalian model system. I will combine a variety of genomic, transcriptomic, and functional approaches to dissect the molecular and developmental mechanisms by which positional information is acquired and interpreted in developing tissues, a long-standing question in developmental biology. First, I will use novel chromatin profiling strategies coupled to functional approaches to identify the cis-regulatory regions and their associated factors that control the spatially restricted expression of pigmentation genes. Second, I will use single-cell RNA sequencing to reconstruct the developmental trajectories of the different cell types of the embryonic skin and identify the signal(s) that establish the pattern boundary early in embryogenesis. I will then modulate candidate gene expression to functionally test their effects on pigment pattern formation. Taken together, this work will substantially advance our understanding of the mechanisms that both establish and implement spatial patterns during early mammalian development. Through the combined use of a novel mammalian model system and innovative, cutting-edge approaches, these mechanisms will be investigated in a level of detail non-existent in the current literature. This work will generate insights into the basic processes governing the development of mammalian skin, will provide a framework for understanding the mechanistic basis of developmental disorders, and generate a more comprehensive overview of the mechanisms regulating differential gene expression, a process at the forefront of various human diseases and dysfunctions. Furthermore, the combined expertise of my advisor and co-advisor, coupled with the abundant resources available at Princeton University (e.g., flow cytometry core and advanced genomics core), will allow me to substantially expand my scientific training; from learning new skillsets (e.g., advanced genomic/transcriptomic techniques and bioinformatics) to career development.

Project Narrative Mis-regulation of the mechanisms controlling spatial patterning during embryogenesis can lead to a number of congenital and postnatal malformations. In the work proposed here, I will study the formation of periodic stripes in an emerging mammalian model system, African striped mice, to dissect the molecular mechanisms by which the mammalian skin acquires, interprets, and executes positional information during development. The results from this work will provide mechanistic insights into the developmental processes by which embryonic patterning takes place, a pressing question in developmental biology and biomedical sciences.