Temporal dynamics of intragenic enhancer RNAs regulate Lin28a expression in response to external stimuli in embryonic stem cells

Abstract

Abstract LIN28A is a conserved RNA-binding protein essential for pluripotency, let-7 miRNA regulation, and cellular metabolism. However, the mechanisms controlling its transcriptional activation during early stem cell fate transitions remain poorly defined. Using the Lin28a locus as a model, we identified multiple intragenic enhancers that generate distinct enhancer RNAs (eRNAs) exhibiting temporally ordered and stimulus-specific activation patterns. Functional perturbation demonstrated that these eRNAs, particularly antisense-derived transcripts, contribute to the regulation of Lin28a transcription and pluripotency maintenance, as their depletion reduced Lin28a expression and impaired embryoid body formation. Distinct environmental inputs induced differential temporal patterns of eRNA activation, accompanied by coordinated changes in enhancer chromatin state and transcription factor occupancy. These findings suggest that intragenic eRNAs make temporally coordinated and differential contributions to stimulus-responsive Lin28a transcriptional dynamics. Together, our findings define a temporally coordinated and context-dependent enhancer logic at the Lin28a locus, in which chromatin state, transcription factor occupancy, and intragenic eRNA induction are integrated to couple external cues with dynamic transcriptional responses during stem cell state transitions.