SHLD2: paired human–horse review notes

Biological evidence

The important distinction is shieldin-family identity versus an intact DNA-end-protection module. Human SHLD2 has experimentally distinct long/short splice products; a short product can still recruit to damage sites and assemble with shieldin while failing to suppress homologous recombination.

• PMID:30022168: The shieldin complex mediates 53BP1-dependent DNA repair. — full text cached.
• PMID:29789392: FAM35A associates with REV7 and modulates DNA damage responses of normal and BRCA1-defective cells. — full text cached.
• PMID:29656893: DNA Repair Network Analysis Reveals Shieldin as a Key Regulator of NHEJ and PARP Inhibitor Sensitivity. — full text cached.

Exact horse model

The 883-residue horse model retains the insertion absent from human canonical SHLD2, but its distal OB-domain region is divergent/gapped in the long-isoform alignment. Nuclear and damage-site recruitment are plausible; the complete NHEJ/resection-suppression mechanism is UNC for the exact model. Human Protein Atlas XML supports an additional human actin-associated pool, so the actin prediction is unresolved in horse rather than refuted as incompatible with nuclear localization.

The reproducible alignment, source paths and hashes are in the paired comparison. Current UniProt sequences have not been proven identical to the original ProtNLM input sequences. Sequence anomalies are therefore recorded as model/transfer limitations, not as proven wrong-input pipeline errors.

Evidence gaps

Obtain a transcript-supported horse C terminus and inspect the OB folds. Distinguish long/short human isoforms in any assay transfer. Inspect the HPA antibody/cell-line context before transferring secondary actin localization.

Review scope and checks

Every seeded annotation receives a current assessment. UNDECIDED marks unresolved source-specific or biological evidence; these are initial reviews rather than a claim that every original experimental assay has been independently reproduced or verified. The human Edison report is retained as a research synthesis and source-finding aid; decisive YAML excerpts cite primary publications, source records or reproducible analysis. The validator advisory to cite the deep-research file is deliberately not satisfied by citing AI prose as biological proof.

2026-10-20 — Full re-review, independent of the ProtNLM2 predictions

Scope: re-examined every GOA row, the description and core functions against the cached full texts
(PMID:30022168, PMID:29789392), the partial Gupta et al. text (PMID:29656893), the ASTE1 abstract
(PMID:34354233), the UniProt record and the PTHR14495 PAINT data. ProtNLM2 output was not consulted.

Identity of the benchmark accession

• Q86V20 is the reviewed, canonical UniProt entry for human SHLD2, so this folder is keyed to the right
  gene. It is not a fragment or an alternative gene model.
• Caveat: the UniProt displayed sequence (Q86V20-1, 835 aa) is the SHORT splice form. Q86V20-2
  (904 aa, VSP_016165, 69-residue insertion after K654) is the LONG form. Tomida et al. name them in the
  reverse order: "Isoforms 1 and 2 are the most common, encoding 904 and 835 amino acid proteins,
  respectively" and "One exon is absent in isoform 2 compared to isoform 1, deleting 69 aa from OB domain B"
  PMID:29789392.
• The biochemistry and rescue work use the long form. SHLD2C is residues 421-904 PMID:30022168, and
  the NHEJ rescue uses "FAM35A isoform 1" PMID:29789392. Noordermeer's SHLD2S is "a splice variant of
  SHLD2 that disrupts OBB" cloned from the ORFeome "short isoform". It is almost certainly the 835-aa
  UniProt displayed sequence. I infer this; the paper does not give the length. SHLD2S still localises to
  DSBs and assembles with shieldin, but "the SHLD2-m1 and SHLD2S mutants are defective in suppressing HR"
  and SHLD2C-S "displayed reduced and aberrant ssDNA-binding behaviour" PMID:30022168.
• The gene-level annotations rest on the long form. Any sequence-based predictor fed the canonical
  835-aa sequence sees a form with a disrupted OB fold B.

Evolutionary grounding

• PANTHER PTHR14495 has a single subfamily, SF2 "SHIELDIN COMPLEX SUBUNIT 2". Human, mouse (Q3UEN2) and
  horse SHLD2 all sit in SF2.
• PAINT node PTN001025652 (taxon 6072, Eumetazoa) is seeded only by human SHLD2. It carries nucleus,
  site of DSB and regulation of DSB repair via HR. The curator did not propagate NHEJ promotion, isotype
  switching or ssDNA binding. I read that as a deliberate choice: it matters for transfers to other
  species, not for the human rows, which rest on human experiments.
• The PTHR14495 family review (interpro/panther/PTHR14495/PTHR14495-review.yaml) has the same subfamily
  placement (SF2) and no disagreement. Its summary does not mention ssDNA binding; that could be added at
  family level.

Changes from the previous review

• NEW GO:0003697 single-stranded DNA binding (IDA, PMID:30022168): "We estimate the binding affinity of
  the SHLD2C-ssDNA interaction to be ~10 nM ... We conclude that SHLD2 possesses ssDNA-binding activity."
  This is now the first core MF. The adaptor (scaffold) activity is kept as a second core function.
• GO:0005515 rows now follow the protein-binding policy. SHLD1, SHLD3 and REV7 (both papers) → MODIFY
  to GO:0030674 protein-macromolecule adaptor activity, on the basis of the N-terminal SHLD3-REV7 and
  C-terminal SHLD1 mapping. TP53BP1, RIF1 and ASTE1 → REMOVE (uninformative; the interactions are not
  disputed).
• chromosome (IDA and IEA) → MODIFY to site of double-strand break (part_of chromosome; already on the gene).
• somatic diversification of immunoglobulins (NAS) → MODIFY to GO:0045190 isotype switching. The term
  note on GO:0045190 asks for gene products in the recombination mechanism, which fits shieldin's end joining.
• IBA regulation of HR → MODIFY to negative regulation (GO:2000042), unchanged from before.
• Telomere maintenance in response to DNA damage stays KEEP_AS_NON_CORE, with the caveat that the readout
  is NHEJ fusion of deprotected telomeres.
• Removed the triplicated supporting_text anchors on the NHEJ rows and gave each row its own support.

Relative for next review

• Mouse Shld2, UniProtKB:Q3UEN2 (reviewed, 891 aa, PTHR14495:SF2). It is the 1:1 ortholog in the same
  PANTHER subfamily, and is characterised in mouse cells and B cells for CSR and PARPi responses.
  There is no review in the repo (no genes/mouse/Shld2).

Modules

• No module under modules/ covers shieldin or 53BP1-dependent DSB repair pathway choice. The only grep
  hits ("shielding" in viral_factory.yaml) are unrelated.