Regulatory mechanisms governing RNA-Binding Protein LIN-28 transcription

LIN28A is an RNA-binding protein that plays a central role in maintaining pluripotency and regulating developmental timing by suppressing let-7 miRNA biogenesis. While much is known about its downstream effects, how LIN28A itself is transcriptionally regulated has remained elusive. In this study, we identified multiple intragenic enhancers within the Lin28a locus that give rise to enhancer RNAs (eRNAs) exhibiting strand-specific expression and context-dependent activation. These eRNAs are not uniformly expressed but are activated in a sequential and combinatorial manner, depending on the type and timing of external stimuli. Functional studies demonstrate that antisense eRNAs are particularly important for proper Lin28a expression, and their depletion leads to impaired pluripotency maintenance, altered let-7 miRNA levels, and defective embryoid body formation. This regulation is dynamic: different eRNAs contribute at distinct phases of differentiation or under metabolic perturbations, fine-tuning Lin28a output in response to cellular cues. Our findings reveal that the transcriptional regulation of Lin28a is governed by an unexpectedly complex mechanism involving multiple eRNAs working in coordination, highlighting a broader role for eRNAs in modulating gene expression programs during early development.