Circadian-Controlled Phase Separation of BMAL1/YAP Complexes Drives Inflammatory Enhancer Hijacking in Aging

Prof. Anya Ogawa (PhD)· Mar 21, 2026

Mechanism: Aging reduces NAD+ and SIRT1 activity, leading to hyper-acetylated BMAL1 and increased YAP, which forms stable, pro-inflammatory condensates at NF-κB enhancers. Readout: Readout: These condensates shift from transient to immobile, decreasing DNA repair and increasing inflammatory gene bursts, while NMN intervention restores transient dynamics, boosts DNA repair, and extends healthspan.

Hypothesis

The circadian clock regulates biomolecular condensate formation through rhythmic BMAL1/YAP interactions; aging shifts this equilibrium toward stable, pro‑inflammatory transcriptional condensates that sequester co‑repressors and suppress DNA‑repair gene bursting, thereby converting temporal coherence loss into a gain‑of‑function inflammatory program.

Mechanistic Rationale

Phase separation premise: BMAL1 possesses intrinsically disordered regions (IDRs) that promote liquid‑liquid phase separation (LLPS) when acetylated; YAP provides a transcriptional co‑activator surface that stabilizes these condensates at enhancers.
Aged shift: Declining NAD+ reduces SIRT1 activity, leading to hyper‑acetylated BMAL1 that favors LLPS; concurrently, YAP nuclear accumulation increases with senescence, driving BMAL1/YAP co‑condensation at NF‑κB‑linked enhancers (as seen in epidermis)[https://doi.org/10.1101/2025.04.22.649967].
Functional outcome: Within these condensates, RNA polymerase II pausing and Mediator recruitment are altered, favoring burst‑like transcription of IL‑6, CXCL1 while inhibiting nucleotide excision repair (NER) genes whose promoters require rhythmic, low‑density TF binding.

Testable Predictions

In young mouse liver, BMAL1/YAP co‑localizes in transient, fast‑recovering condensates (FRAP t½ < 5 s) at E‑box sites; in aged liver, condensates become immobile (t½ > 20 s) and enrich at H3K27ac‑marked inflammatory enhancers.
Pharmacological NAD+ boost (e.g., NMN) or timed SR9009 (REV‑ERB agonist) administered at circadian peak will dissolve aged condensates, restore rapid FRAP dynamics, and increase nascent RNA signal of Per2/NER genes while decreasing IL‑6 transcriptional bursts.
Genetic disruption of BMAL1’s IDR (ΔIDR) or YAP’s TEAD‑binding domain will prevent pathogenic condensate formation without abolishing core clock oscillations, leading to improved DNA‑repair capacity and extended healthspan despite arrhythmic feeding.

Experimental Approach

Live‑cell imaging: Generate BMAL1‑mCherry and YAP‑GFP knock‑in mice; perform intravital two‑photon imaging of hepatocytes across the circadian cycle in young (3 mo) vs aged (24 mo) mice; quantify condensate size, number, and FRAP recovery.
ChIP‑seq & CUT&Tag: Map BMAL1 and YAP occupancy with and without NMN/SR9009 treatment; look for loss of YAP peaks at inflammatory enhancers and gain at circadian repair loci.
RNA‑FISH & intron probes: Measure transcriptional bursting kinetics of Per2, Xpc, and Il6 in single cells; correlate bursting frequency with condensate state.
Functional assays: Comet assay for DNA damage, LC3‑II flux for autophagy, and ELISA for serum IL‑6 after interventions; assess grip strength and frailty index over 6 months.

Potential Implications

If proven, this hypothesis reframes the circadian firewall as a regulator of biomolecular phase separation, offering a druggable node: small molecules that modulate BMAL1/YAP IDR interactions (e.g., peptidomimetics or hydrophobic patches) could prevent pathological condensate formation, thereby converting circadian enhancement from a passive timing cue into an active anti‑aging therapy that directly restores the transcriptional chromatin landscape.

Hypothesis

Mechanistic Rationale

Phase separation premise: BMAL1 possesses intrinsically disordered regions (IDRs) that promote liquid‑liquid phase separation (LLPS) when acetylated; YAP provides a transcriptional co‑activator surface that stabilizes these condensates at enhancers.

Aged shift: Declining NAD+ reduces SIRT1 activity, leading to hyper‑acetylated BMAL1 that favors LLPS; concurrently, YAP nuclear accumulation increases with senescence, driving BMAL1/YAP co‑condensation at NF‑κB‑linked enhancers (as seen in epidermis)[https://doi.org/10.1101/2025.04.22.649967].

Functional outcome: Within these condensates, RNA polymerase II pausing and Mediator recruitment are altered, favoring burst‑like transcription of IL‑6, CXCL1 while inhibiting nucleotide excision repair (NER) genes whose promoters require rhythmic, low‑density TF binding.

Testable Predictions

In young mouse liver, BMAL1/YAP co‑localizes in transient, fast‑recovering condensates (FRAP t½ < 5 s) at E‑box sites; in aged liver, condensates become immobile (t½ > 20 s) and enrich at H3K27ac‑marked inflammatory enhancers.

Pharmacological NAD+ boost (e.g., NMN) or timed SR9009 (REV‑ERB agonist) administered at circadian peak will dissolve aged condensates, restore rapid FRAP dynamics, and increase nascent RNA signal of Per2/NER genes while decreasing IL‑6 transcriptional bursts.

Genetic disruption of BMAL1’s IDR (ΔIDR) or YAP’s TEAD‑binding domain will prevent pathogenic condensate formation without abolishing core clock oscillations, leading to improved DNA‑repair capacity and extended healthspan despite arrhythmic feeding.

Experimental Approach

Live‑cell imaging: Generate BMAL1‑mCherry and YAP‑GFP knock‑in mice; perform intravital two‑photon imaging of hepatocytes across the circadian cycle in young (3 mo) vs aged (24 mo) mice; quantify condensate size, number, and FRAP recovery.

ChIP‑seq & CUT&Tag: Map BMAL1 and YAP occupancy with and without NMN/SR9009 treatment; look for loss of YAP peaks at inflammatory enhancers and gain at circadian repair loci.

RNA‑FISH & intron probes: Measure transcriptional bursting kinetics of Per2, Xpc, and Il6 in single cells; correlate bursting frequency with condensate state.

Functional assays: Comet assay for DNA damage, LC3‑II flux for autophagy, and ELISA for serum IL‑6 after interventions; assess grip strength and frailty index over 6 months.

Potential Implications