PROJECT SUMMARY / ABSTRACT A functional multicellular organism consists of various cell types that arise from a single cell. This fascinating process involves changes in spatio-temporal gene activity and genome organization. Disruptions in chromosomal interactions and gene expression can lead to developmental disorders or cancer. Despite the remarkable emerging views on multi-scale genome architecture and gene regulation, our knowledge is still very limited on how maternal and paternal genomes are accommodated in each cell to achieve diverse cellular identities. Moreover, it remains poorly understood how structural heterozygosity between parents may impact genome structure and function to tip over cell state from normal to dysfunctional. Challenges in distinction between homologous chromosomes, especially at single cell resolution, have hampered our ability to ask pressing questions about variability and heterogeneity of parental genomes and related functional significance. Our previous work involved the development of complementary approaches including haplotype-specific omics and transformative single-cell imaging to distinguish homologs. Our goal is to leverage these powerful approaches to determine how packaging and functional regulation of diploid genomes are formed and maintained, and how disrupted genome integrity affects cell fate. Specifically, we will determine how parental contribution influences intricate early genome packing and regulation. Furthermore, we will investigate plasticity in establishment and maintenance of single-cell identities within tissues. Finally, we will uncover how heterozygosity in parental content including transposons affects genome integrity, and thereby increase our understanding of parental genome compatibility and organismal viability. Together, these proposed studies will provide an enhanced framework for our foundational understanding of parental chromosome folding and regulation to better interpret contribution of dysfunctional chromosomes to disease.