Enhancer RNA-mediated transcriptional regulation of TDP-43 during early neural lineage specification

TAR DNA-binding protein 43 (TDP-43) is a DNA- and RNA-binding protein that regulates gene expression by modulating transcription and RNA processing. It plays pivotal roles in neuronal development and function, and its mislocalization and aggregation are major pathological features of several neurodegenerative diseases. However, the regulatory mechanisms that control Tdp-43 expression and activity during the transition from embryonic stem cells (ESCs) to neural progenitor cells (NPCs) remain poorly understood. Through integrative epigenomic and transcriptomic analyses, we identified multiple intergenic and intragenic enhancers within and around the Tdp-43 locus that generate enhancer RNAs (eRNAs). These eRNAs exhibit dynamic, region-specific expression changes and modulate Tdp-43 transcription in a stage- and context-dependent manner. Specifically, a subset of eRNAs was highly expressed in ESCs and downregulated upon differentiation, while others were selectively retained or induced in NPCs, paralleling changes in enhancer usage and histone modification states. Targeted knockdown of these eRNAs decreased Tdp-43 expression and was accompanied by changes in the expression of pluripotency- and lineage-associated markers, without implying direct control over full differentiation trajectories. These findings uncover a previously unrecognized aspect of Tdp-43 transcriptional regulation and highlight the significance of enhancer dynamics in the epigenetic regulation of TDP-43 expression during early lineage specification.