Tissue-Specific RNA Expression Marks Distant Acting Developmental Enhancers

In this study, we explored the in vivo expression dynamics of tissue-specific non-coding RNAs in embryonic mouse tissues via in-depth transcriptome profiling. Overall, approximately 80% of validated in vivo enhancers show tissue-specific RNA expression that correlates with tissue-specific enhancer activity. Globally, we identified thousands of tissue-specifically transcribed non-coding regions (TSTRs) displaying various genomic hallmarks of bona fide enhancers. Together, our results demonstrate that tissue-specific eRNA expression is a common feature of in vivo enhancers, as well as a major source of extragenic transcription, and that eRNA expression signatures can be used to predict tissue-specific enhancers independent of known epigenomic enhancer marks. Examimation of total RNA expression in mouse heart and limb tissues collected at mouse embryonic day 11.5.