Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo

Enhancers control gene expression and play crucial roles in development and homeostasis^(1-3). However, the targeted de novo design of enhancers with tissue-specific activities has remained challenging. Here, we combine deep learning and transfer learning to design tissue-specific enhancers for five tissues in the Drosophila melanogaster embryo - the central nervous system (CNS), epidermis, gut, muscle, and brain. We first train convolutional neural networks (CNNs) using genome-wide …