Opportunities and challenges in studying non-coding RNAs using neural organoid models

Recent advancements in whole-genome sequencing have identified non-coding RNAs (ncRNAs) as pivotal regulators in biological systems. However, investigating neural-related ncRNAs in vitro remains challenging due to their complex spatial expression patterns and regulatory networks, which are inadequately captured in traditional two-dimensional cultures. The three-dimensional (3D) neural organoids have recently evolved from stochastic assemblies to engineered, region-specific, and integrated systems, providing a high-fidelity platform to overcome these limitations. This review summarizes the current landscape of ncRNA research within neural organoid systems, including miRNAs, lncRNAs, circRNAs, and snRNAs. By highlighting key findings in neurodevelopmental modeling and disease simulation, we discuss the implications of using these 3D models to decode the non-coding genome and their potential for preclinical applications. These advancements collectively solidify neural organoids as an essential platform, linking the high complexity of the non-coding genome to the functional reality of human brain development and pathology.