The environmental cues that regulate diapause have been well defined, and there is also a fairly good understanding of the downstream hormonal signals that serve to coordinate diapause. But, the molecular underpinning of diapause remains poorly understood. Is diapause simply a shutdown in gene expression or does it represent the expression of a unique set of genes? An examination of the synthesis of brain proteins in flesh flies suggests that far fewer proteins are synthesized in the brain during diapause but, in addition, the brains of diapausing flies synthesize a set of proteins not observed in brains of nondiapausing flies. This suggests that diapause represents both a shutdown in gene expression and the expression of a unique set of genes.
One of the most conspicuous groups of genes that are diapause upregulated is that of the heat-shock proteins. Both heat-shock protein 70 (Hsp70) and one of the small heat-shock proteins (Hsp23) are upregulated in flesh flies during diapause. The Hsps are upregulated upon entry into diapause, remain elevated throughout diapause, and then drop sharply at diapause termination. When expression of the Hsps is knocked down using RNA interference, cold tolerance of the diapausing pupae is lost, suggesting that the Hsps offer protection from environmental stresses during diapause.
Genes that are diapause downregulated are potentially of equal interest. Among the genes in this category is the gene that encodes proliferating cell nuclear antigen, a cell-cycle regulator. The downregu-lation of this gene during diapause may be important in bringing about the cell-cycle arrest. As more genes are examined, it is evident that certain genes are expressed throughout diapause, others are turned off during diapause, while still others are expressed only during early or late diapause or may be expressed intermittently during diapause.
It is still too early to know if common sets of genes are expressed during diapause in different species and different life stages, but preliminary data suggest that the expression patterns of at least some of the genes, those that encode Hsp70, may be shared across species and life stages. Likewise, insulin signaling is emerging as a signaling pathway that is likely to be commonly involved in insect diapause as well as in dormancies of other invertebrates.
Ecdysone is a steroidal prohormone of the major insect molting hormone 20-hydroxyecdysone , which is secreted from the prothoracic glands . Insect molting hormones (ecdysone and its homologues) are generally called ecdysteroids . Ecdysteroids act as moulting hormones of arthropods but also occur in other related phyla where they can play different roles. In Drosophila melanogaster , an increase in ecdysone concentration induces the expression of genes coding for proteins that the larva requires, and it causes chromosome puffs (sites of high expression) to form in polytene chromosomes. Recent findings in Chris Q. Doe lab have found a novel role of this hormone in regulating temporal gene transitions within neural stem cells.  Ecdysone and other ecdysteroids also appear in many plants mostly as a protection agent (toxins or antifeedants) against herbivorous insects. These phytoecdysteroids have been reputed to have medicinal value and are part of herbal adaptogenic remedies like Cordyceps , yet an ecdysteroid precursor in plants has been shown to have cytotoxic properties.  A pesticide sold with the name MIMIC has ecdysteroid activity, although its chemical structure has little resemblance to the ecdysteroids.