Two single MYB transcription factors, CCA1 and LHY, activate expression of PRR7 and PRR9. In turn, PRR7 and PRR9 repress CCA1 and LHY through the binding of their promoters. This interaction forms the morning loop of the repressilator of the biological clock in A. thaliana. Chromatin immunoprecipitation demonstrates that LUX binds to the PRR9 promoter to repress it. Additionally, ELF3 has been shown to activate PRR9 and repress CCA1 and LHY. PRR9 is also activated by alternative RNA splicing. When PRMT5 (a methylation factor) is prevented from methylating intron 2 of PRR9, a frameshift resulting in premature truncation occurs.
PRR7 and PRR9 also play a role in the entrainment of A. thaliana to a temperature cycle. Double-mutant plants with inactivated PRR7 and PRR9 exhibit extreme period lengthening at high temperatures but show no change in period at low temperatures. However, the inactivation of CCA1 and LHY in the PRR7/PRR9 loss-of-function mutants shows no change in period at high temperatures—this suggests that PRR7 and PRR9 are acting by overcompensation.