Hypothesis

We propose that the circadian clock directly times the assembly and disassembly of the primary cilium in stem cells, thereby gating Hedgehog (Hh) pathway activity to synchronize DNA damage response (DDR) with the metabolic cycle. In young tissue, BMAL1/CLOCK drive rhythmic expression of intraflagellar transport genes (e.g., IFT88, KIF3A) that produce oscillating cilium length; peak cilium presence during the active phase enhances SMO‑GLI signaling, which in turn promotes transcription of DDR factors such as BRCA1 and XPC. When the clock weakens with age, cilium oscillations flatten, Hh signaling becomes constitutively low or arrhythmic, and DDR falls out of phase with replication stress, leading to accumulated mutations and stem cell exhaustion.

Mechanistic rationale

• Clock‑cilium link: BMAL1 binds enhancers of IFT88 and tubulin genes, a relationship shown in liver where GLI knockdown disrupts PER2::LUC rhythms [6]. We extend this to suggest that BMAL1/CLOCK heterodimers drive daily pulses of ciliogenesis, creating a temporal window for Hh pathway activation.
• Hh‑DDR coupling: GLI transcription factors directly regulate promoters of nucleotide excision repair (NER) genes; prior work shows BMAL1/CLOCK regulate NER efficiency in a gene‑specific manner [1]. Thus, rhythmic GLI activity could impose a circadian schedule on NER capacity.
• Feedback from damage: DNA lesions trigger PER2 degradation and BMAL1 promoter activation [2]; loss of cilium‑mediated Hh signaling would blunt this feedback, further destabilizing the clock.
• Stem cell niche: In muscle satellite cells, disrupted BMAL1/CLOCK oscillations impair regeneration [3]; we predict that rescuing cilium rhythm (e.g., by timed overexpression of IFT88) restores both Hh signaling and repair capacity, mitigating sarcopenia.

Testable predictions

1. Cilium length oscillates in young mouse satellite cells with a ~24 h period, peaking at ZT6‑ZT10; this rhythm is blunted in >2‑year‑old mice.
2. Pharmacological lengthening of cilia (e.g., with cilia‑stabilizing agents) during the rest phase amplifies GLI‑dependent transcription of XPC and reduces γH2AX foci after UV exposure.
3. Conditional knockout of IFT88 in satellite cells abolishes the protective effect of timed feeding or exercise on DDR markers, despite intact BMAL1/CLOCK expression.
4. Small‑molecule enhancement of REV‑ERBα activity (which suppresses CXCL5) restores cilium oscillations in aged fibroblasts, linking inflammatory control to the cilium‑clock axis.

Falsifiable outcomes

If any of the following are observed, the hypothesis is weakened:

• Cilium length shows no circadian variation in young stem cells.
• Manipulating cilium length does not alter the phase or amplitude of GLI‑driven DDR gene expression.
• Restoring circadian feeding fails to improve DNA repair in IFT88‑deficient cells.