In the negative feedback loops, CK1ε periodically binds to and phosphorylates the PER proteins (PER1, PER2, and PER3), which form heterodimers with each other and interact with CRY1 and CRY2. The effects of phosphorylation are two-fold. It has been shown in Drosophila that phosphorylation of the PER proteins increase their ubiquitination, which leads to degradation. Phosphorylation of the PER proteins also leaves them unable to enter the nucleus, where they suppress transcription of clock genes. The blocking of nuclear translocation occurs via phosphorylation of PER at the nuclear localization signal, which masks the signal and prevents nuclear entry. However, this CK1ε-mediated constraint to the cytoplasm can be overcome when the PER protein complex is bound to CRY. CK1ε has been shown to phosphorylate CRY when both CK1ε and CRY are complexed with PER in vitro, but the functional significance of this remains undetermined.
CK1ε may also have a role in positive feedback; the transcription factor BMAL1 is a CK1ε substrate in vitro, and increased CK1ε activity has been shown to positively regulate transcription of genes under the influence of BMAL1-dependent circadian gene promoters. This has not yet been studied in vivo.