Although protein-coding genes have been the primary focus of molecular biology, they cannot fully explain the complexities of stem cell differentiation and epigenetic regulation. These intricate processes are largely directed by the non-coding genome, which includes regulatory elements and various non-coding RNAs. Our goal is to systematically decipher the functions and mechanisms of these elements in controlling cell fate and maintaining epigenetic states. The unique properties of non-coding RNAs, such as programmability and specificity, also make them ideal candidates for new synthetic biology tools. By engineering and synthesizing novel RNA-based devices, we aim to develop a precise technologies understanding of the functionality of the non-coding genome that will directly enable more sophisticated synthetic genome design.