Non-Covalent Poly(ADP-ribose) Signaling Organizes a Circadian E3 Ligase Network in the Brain

Abstract

Although PAR biology has traditionally been studied through covalent PARylation, non-covalent PAR-binding proteins provide an additional mechanism for interpreting transient PAR signals and converting them into downstream regulatory programs. Among these effectors, E3 ubiquitin ligases are uniquely positioned to couple PAR sensing to selective ubiquitination, thereby integrating stress signaling with proteostatic control. Because circadian systems depend heavily on temporally coordinated protein turnover, we hypothesized that PAR-binding E3 ligases may form a circadian-structured regulatory layer within the brain. To test this, we integrated GTEx v10 brain transcriptomics, GWAS Catalog gene-mapped associations, CIRCA circadian phase annotations, and Human Protein Atlas single-cell transcriptomic resources to characterize the organization of PAR-binding E3 ubiquitin ligases across neural tissues. Across the brain, the E3 ligase repertoire was broadly deployed yet regionally structured, with cerebellar and cortical enrichment patterns preserved within the PAR-binding subset. Representative ligases spanning circadian regulation, DNA repair, and neurodegeneration-relevant pathways displayed distinct abundance and regional-variability archetypes across GTEx brain regions. Human genetic analyses demonstrated that E3 ligases associated with cognition-, neurodegeneration-, and sleep/circadian-related phenotypes were disproportionately PAR-binding, supporting convergence between PAR-responsive ubiquitin regulation and disease-relevant biology. Circadian phase analyses further revealed that PAR-binding ligases occupy structured, non-random circadian windows within the broader E3 background, including distinct co-phasing relationships with BMAL1 and CRY1. Finally, cell-type enrichment analyses identified microglia as the dominant compartment for circadian-linked and PAR-binding circadian E3 weighting within the brain E3 program. Together, these findings support a systems-level framework in which non-covalent PAR-binding E3 ubiquitin ligases constitute a brain-deployed, circadian-organized regulatory layer that couples PAR signaling to time-dependent ubiquitin control in neural systems.