Combine Evidence, Keep Provenance

 Quick Analysis Plan Copied

 Long Analysis Plan

Scope check: what the supplied evidence can and cannot support

Polη (POLH) UBZ loss-of-function: The only relevant record is Yoon, Unk, Haracska & Prakash, PNAS 2008. Using XPV (XP30R0) human fibroblasts complemented with GST-hPolη mutants (C635A, H650A, D652A, H654A, F655A) plus PIP1 (F443A/L444A) and PIP2 (F707A/F708A) mutants, the authors report four independent MTT UV-cytotoxicity experiments per construct, in vitro DNA synthesis assays with PCNA/RFC/RPA/Ub-PCNA, and replication-foci microscopy. Key reported findings: UBZ mutations disrupt ubiquitin binding but do not abolish PCNA binding, nuclear foci, PCNA-stimulated activity, or TLS function; single PIP mutations cause partial defects; the PIP1/PIP2 double mutant abolishes PCNA binding and TLS; Ub-PCNA did not stimulate hPolη beyond unmodified PCNA, implying ubiquitinated PCNA acts via polymerase exchange rather than direct UBZ-mediated recruitment Yoon et al. 2008 PNAS Polη PIP/UBZ study.

Polι (POLI) UBM loss-of-function: No supplied record contains any Polι UBM data. The two other records (nanobubbles for ultrasound/drug delivery; yeast Yra1-S8 mRNA-export phosphorylation) are topically unrelated to TLS polymerase domains and cannot contribute claims to this meta-analysis. A valid Polη-UBZ vs Polι-UBM meta-analysis therefore requires additional primary studies not present here.

Known blindspot: the Yoon et al. findings derive from overexpressed constructs in fibroblast lines; endogenous regulation and other fork-associated proteins were not exhaustively explored, limiting generalization Study limitations from PNAS 2008 record.

Meta-analysis execution plan

• Step 1 — Systematic retrieval: Search PubMed/Scopus for Polη UBZ (C635A/H650A etc.) and Polι UBM (UBL/UBM domain deletions or point mutants) loss-of-function studies; register inclusion criteria a priori (mutant type, cell model, TLS readout, UV survival vs bypass-fidelity endpoints).
• Step 2 — Effect-size extraction: Standardize outcomes as log-transformed UV survival ratios (mutant/WT rescue in XPV cells) and in vitro bypass efficiencies; extract n, SE, and replicate counts (the supplied record gives four independent experiments per construct but no per-experiment values — individual-level data would be required).
• Step 3 — Pooling: Random-effects models (DerSimonian-Laird or REML) in Python (statsmodels + custom DerSimonian-Laird, or PyMeta); assess heterogeneity (I², τ²); subgroup by construct class (UBZ-only vs PIP vs combined) and species.
• Step 4 — Structural annotation: Map mutations onto AlphaFold structures of POLH and POLI to correlate domain-level loss-of-function magnitude with domain position.
• Step 5 — Bias control: Funnel plots/Egger tests for publication bias; flag overexpression-system studies separately from endogenous-expression knock-in data.

Falsification criteria for the pooled model: a meta-analytic conclusion that UBZ/UBM ubiquitin-binding is dispensable for TLS would be falsified if pooled effect sizes show significant loss of UV survival or bypass fidelity upon UBZ/UBM mutation independent of PIP damage, or if Ub-PCNA enhances polymerase activity beyond PCNA in pooled in vitro data Falsification criteria from record.