Crosstalk between transcripts, proteins, and regulatory elements controlling circadian rhythms and development in .

The () gene encodes a transcriptional repressor required for development as well as circadian behavior in adults. Alternate first exons produce transcripts predicted to produce a short VRI isoform during development and long VRI in adults. A mutant ( ) lacking long VRI transcripts is viable, confirming that short VRI is sufficient for developmental functions, yet behavioral rhythms in flies persist, showing that short VRI is sufficient for clock output. E-box regulatory elements that drive rhythmic long VRI transcript expression are required for developmental expression of short VRI transcripts. Surprisingly, long VRI transcripts primarily produce short VRI in adults, apparently due to a poor Kozak sequence context, demonstrating that short VRI drives circadian behavior. Thus, E-box-driven long VRI transcripts primarily control circadian rhythms via short VRI, whereas the same E-boxes drive short VRI transcripts that control developmental functions using short VRI.