Uncovering the pivotal role of lncRNAs in cortical neuron differentiation from human embryonic stem cells

This thesis presents a comprehensive computational and experimental investigation into the role of long non-coding RNAs (lncRNAs) in the differentiation of cortical neurons from human embryonic stem cells (hESCs). Utilizing a computational workflow, we initially explored the dynamic landscape of lncRNAs over-expressed at late stages of neural differentiation, focusing on their expression, subcellular localization, sequence characteristics, and regulatory interactions. Our k-mer profile analysis delineated distinct lncRNA clusters, each exhibiting unique sequence compositions and suggesting diverse functional roles in neural differentiation and brain tissue specificity. Notably, we identified clusters associated with ribosomal function, epigenetic regulation, and chromatin remodeling, underscoring the multifaceted roles of lncRNAs in neural development. Further investigations focused on 63 lncRNAs with significant regulatory potential, identified through their enhanced expression and chromatin association during critical differentiation phases. Among these, MIAT emerged as a key player, with subsequent experiments revealing its involvement in forming stable secondary structures that potentially interact with essential proteins involved in neural disease pathways. Knockout experiments of MIAT elucidated its crucial role in network formation and neural differentiation, highlighting its impact on neuroactive ligand-receptor interaction, synaptic assembly, and neurotransmitter metabolic processes. The morphological disruptions observed in MIAT knockout neurons point to its significance in maintaining the structural and functional integrity of neural networks. By advancing our understanding of lncRNA function in neural differentiation, this work opens new avenues for therapeutic interventions targeting lncRNAs in neurological diseases, offering insights into their potential as biomarkers and therapeutic targets. The findings also pave the way for future studies on the molecular mechanisms of lncRNA-mediated regulation, with the aim of elucidating the full spectrum of their roles in neural development and function.