Background: Investigations of transcriptional responses during developmental transitions typically use time courses with intervals that are not commensurate with the timescales of known biological processes. Moreover, such experiments typically focus on protein-coding transcripts, ignoring the important impact of long noncoding RNAs

Results: We evaluated coding and noncoding expression dynamics at high temporal resolution (6-hourly) in differentiating mouse embryonic stem cells and report the effects of increased temporal resolution on the characterisation of the underlying molecular processes. We present a refined resolution of global transcriptional alterations, including regulatory network interactions, coding and noncoding gene expression changes as well as alternative splicing events, many of which cannot be resolved by existing coarse developmental time-courses. We describe novel short lived and cycling patterns of gene expression and temporally dissect ordered gene expression at bidirectional promoters and responses to transcription factors.

Conclusions: These findings demonstrate the importance of temporal resolution for understanding gene interactions in mammalian systems.