A mechanistic understanding of how cell identity is established and maintained is fundamental to the precise engineering of cell fate. Here, I will present new genomic technologies developed by my lab to permit single-cell lineage tracing throughout reprogramming, accompanied by recording of TF-binding and chromatin accessibility profiling. Integrating this information using our unique computational tools for interrogating gene regulatory networks delivers a systems-level understanding of how cell identity can be manipulated via lineage reprogramming. We also apply these methods to understand how cell identity is naturally programmed during differentiation and development. The deconstruction of cell identity via these approaches supports precision engineering of cell fate.