From Understudied to Understood: Multi-Omics Analysis with MiniENCODE Exemplified by Zebrafish

The ENCODE project has revolutionized our understanding of functional genomic elements, yet its exhaustive approach remains inaccessible to smaller communities studying non-model organisms. To address this challenge, we developed the miniENCODE framework -a resource-efficient strategy combining carefully selected experimental assays with an integrated computational platform. Using zebrafish as a model, we implemented this framework through three core assays: RNA-seq, ATAC-seq, and H3K27ac CUT&Tag, spanning six developmental stages and 11 adult tissues. Our analysis identified 52,350 candidate enhancer-like signatures, characterized their spatiotemporal activity patterns, and experimentally validated tissue-specific enhancers. We developed the mini Omics Data Portal (miniODP) to facilitate multi-omics data reuse, integration, visualization, and analysis. Through this platform, we characterized key transcription factors and their regulatory networks in various developmental stages and adult tissues. Extending this approach to additional model organisms (cattle, lancelet, Mexican tetra, and polyp), we demonstrated its broad applicability for understanding gene regulation in diverse species. The miniENCODE framework provides a practical solution for comprehensive regulatory element characterization, enabling smaller research communities to advance genomic studies in understudied organisms without overextending their resources. This approach not only provides a valuable resource for zebrafish but also establishes a scalable model for accelerating genomic research in diverse species.