YY1 stabilization blocks PARP‑dependent cohesin unloading and rescues enhancer‑promoter looping in aged stem cells

Ivan Klein (MD/PhD)· Mar 25, 2026

Mechanism: YY1 loss in aging leads to PARP1-mediated PARylation and unloading of cohesin from DNA, disrupting TAD boundaries and enhancer-promoter loops. Readout: Intervention with PARP inhibitors or YY1 restoration prevents cohesin unloading, preserving genomic architecture.

Hypothesis

YY1 loss in aging stem cells triggers PARP1‑mediated PARylation of cohesin subunits, leading to premature cohesin unloading, TAD boundary erosion, and decoupling of hyperactive enhancers from target promoters. Restoring YY1 or inhibiting PARP1 early in aging should preserve cohesin loading, maintain TAD insulation, and prevent the proinflammatory transcriptional drift.

Mechanistic Rationale

YY1 normally recruits cohesin loading factor NIPBL to super‑enhancers and promoters, stabilizing loops.
Inflammation‑induced NF‑kappaB signaling activates PARP1, which PARylates RAD21 and SMC3, reducing their chromatin residence.
YY1 depletion removes a protective scaffold, allowing PARP1 access to cohesin at SEs.
Result: loss of intra‑TAD insulation (observed as ~38% differential TADs in geriatric MuSCs) and enhancer‑promoter contact decay despite increased H3K27ac.
Early PARP1 activity thus couples the proinflammatory shift to architectural collapse; later SE hyperacetylation reflects compensatory enhancer activation that cannot communicate with genes.

Testable Predictions

Biochemical: In young MSCs treated with TNF‑alpha or LPS, PARP1 activity will increase and co‑immunoprecipitation will show reduced YY1‑cohesin interaction; YY1 overexpression will block PARP1‑dependent cohesin PARylation.
Genetic: MSC‑specific Yy1 knock‑in of a PARP‑resistant RAD21 mutant (e.g., K->R at PARylation sites) will preserve TAD boundaries in aged mice, as measured by Hi-C (>1B reads) and insulation scores.
Pharmacological: Short‑term PARP inhibitor (olaparib) administration to middle‑aged mice will delay the loss of YY1 at SEs, maintain H3K27ac/H3K4me1 balance, and reduce inflammatory gene expression (Il6, Tnf) without affecting global compartment A/B.
Functional: Rescued loop architecture will restore MSC osteogenic/adipogenic differentiation capacity in vitro and improve tissue repair in vivo (e.g., tibial fracture healing).

Experimental Approach (brief)

Isolate MSCs from young (3 mo) and geriatric (24 mo) mice.
Perform CUT&RUN for YY1, RAD21, PAR; Hi-C; ATAC‑seq; RNA‑seq.
Treat cohorts with vehicle, olaparib (10 mg/kg i.p. thrice weekly), or AAV‑YY1.
Compare insulation scores, loop strength at Myf5/Myf6 and MSC SE‑target genes, and lineage‑specific transcription.

Potential Outcomes & Falsification

If PARP inhibition fails to restore YY1 occupancy or TAD insulation despite reducing PARylation, the hypothesis is falsified.
If YY1 overexpression does not prevent cohesin PARylation or loop decay, alternative mechanisms (e.g., HDAC‑mediated deacetylation) must be considered.
Conversely, rescue of both architectural metrics and stem cell function would support the model.

Hypothesis

Mechanistic Rationale

YY1 normally recruits cohesin loading factor NIPBL to super‑enhancers and promoters, stabilizing loops.

Inflammation‑induced NF‑kappaB signaling activates PARP1, which PARylates RAD21 and SMC3, reducing their chromatin residence.

YY1 depletion removes a protective scaffold, allowing PARP1 access to cohesin at SEs.

Result: loss of intra‑TAD insulation (observed as ~38% differential TADs in geriatric MuSCs) and enhancer‑promoter contact decay despite increased H3K27ac.

Early PARP1 activity thus couples the proinflammatory shift to architectural collapse; later SE hyperacetylation reflects compensatory enhancer activation that cannot communicate with genes.

Testable Predictions

Biochemical: In young MSCs treated with TNF‑alpha or LPS, PARP1 activity will increase and co‑immunoprecipitation will show reduced YY1‑cohesin interaction; YY1 overexpression will block PARP1‑dependent cohesin PARylation.

Genetic: MSC‑specific Yy1 knock‑in of a PARP‑resistant RAD21 mutant (e.g., K->R at PARylation sites) will preserve TAD boundaries in aged mice, as measured by Hi-C (>1B reads) and insulation scores.

Pharmacological: Short‑term PARP inhibitor (olaparib) administration to middle‑aged mice will delay the loss of YY1 at SEs, maintain H3K27ac/H3K4me1 balance, and reduce inflammatory gene expression (Il6, Tnf) without affecting global compartment A/B.

Functional: Rescued loop architecture will restore MSC osteogenic/adipogenic differentiation capacity in vitro and improve tissue repair in vivo (e.g., tibial fracture healing).

Experimental Approach (brief)

Isolate MSCs from young (3 mo) and geriatric (24 mo) mice.

Perform CUT&RUN for YY1, RAD21, PAR; Hi-C; ATAC‑seq; RNA‑seq.

Treat cohorts with vehicle, olaparib (10 mg/kg i.p. thrice weekly), or AAV‑YY1.

Compare insulation scores, loop strength at Myf5/Myf6 and MSC SE‑target genes, and lineage‑specific transcription.

Potential Outcomes & Falsification

If PARP inhibition fails to restore YY1 occupancy or TAD insulation despite reducing PARylation, the hypothesis is falsified.

If YY1 overexpression does not prevent cohesin PARylation or loop decay, alternative mechanisms (e.g., HDAC‑mediated deacetylation) must be considered.

Conversely, rescue of both architectural metrics and stem cell function would support the model.