Affinage

SHOC1

Protein shortage in chiasmata 1 ortholog · UniProt Q5VXU9

Length
1444 aa
Mass
165.2 kDa
Annotated
2026-06-10
23 papers in source corpus 12 papers cited in narrative 12 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

SHOC1 (MZIP2/C9orf84) is a ZMM-class meiotic recombination factor required for class I, interference-dependent crossover formation during meiotic prophase I (PMID:18812090, PMID:30272023). It is the structural homolog of XPF/MUS81-family nucleases, carrying a conserved ERCC4-(HhH)2 core, and its XPF-like domain mediates preferential binding to branched (recombination intermediate) DNA structures, yet the purified protein lacks detectable in vitro endonuclease activity (PMID:29742103, PMID:42258546). SHOC1 partners with the ERCC1-like protein SPO16 and with TEX11 to form the trimeric ZZS complex; SPO16 stabilizes SHOC1 protein and SHOC1 in turn is required to recruit downstream recombination factors including TEX11, MSH4, and M1AP to recombination intermediates, with this branched-DNA-binding activity essential for crossover formation (PMID:29742103, PMID:30272023, PMID:30746471, PMID:42258546). Loss of SHOC1 abolishes crossovers, leaves meiotic double-strand breaks unrepaired, and produces incomplete or aberrant synapsis with arrest at a zygotene-like stage in mice and early meiotic arrest in men (PMID:30272023, PMID:40374915). The XPF-like domain additionally protects autosomes from meiotic silencing of unsynapsed chromatin by preventing autosome intrusion into the sex body (PMID:42258546). Biallelic loss-of-function SHOC1 variants cause non-obstructive azoospermia in human males (PMID:35485979, PMID:42258546, PMID:40374915).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 2008 High

    Established that SHOC1 acts specifically in the class I crossover pathway rather than in early recombination, defining its position downstream of strand invasion.

    Evidence Genetic mutant and double-mutant epistasis analysis with cytological DMC1 quantification in Arabidopsis

    PMID:18812090

    Open questions at the time
    • Did not identify the biochemical substrate or interacting proteins
    • XPF-family role inferred from sequence similarity only
  2. 2011 High

    Identified the heterodimeric architecture by showing the XPF-like domain mediates interaction with an ERCC1-like partner (PTD), framing SHOC1 as half of an XPF-ERCC1-like module for class I crossovers.

    Evidence Yeast two-hybrid domain mapping and genetic epistasis in Arabidopsis

    PMID:21771883

    Open questions at the time
    • Interaction shown in plant ortholog; mammalian complex not directly tested
    • No demonstration of catalytic activity
  3. 2018 High

    Defined the biochemical activity of human SHOC1 as branched-DNA binding without detectable nuclease activity, and connected it in mammals to TEX11, crossover maturation, and proper synapsis.

    Evidence In vitro DNA binding and endonuclease assays with recombinant human protein, plus cytology and Co-IP in SHOC1 hypomorphic mice

    PMID:29742103

    Open questions at the time
    • Reason for absent nuclease activity despite conserved catalytic domain unresolved
    • Whether a partner subunit confers catalysis untested
  4. 2018 High

    Demonstrated that SHOC1/MZIP2 is essential for recruiting TEX11 and MSH4 to recombination intermediates, establishing it as an upstream organizer of the ZMM module in mammalian meiosis.

    Evidence Complete mouse knockout with chromosome spreads and immunofluorescence of downstream factors

    PMID:30272023

    Open questions at the time
    • Mechanism of branched-DNA recognition coupling to recruitment not resolved
    • Female versus male requirement detail limited
  5. 2019 High

    Completed the trimeric ZZS complex by showing reciprocal SHOC1-SPO16 interaction and that SPO16 stabilizes SHOC1, separating its crossover function from synapsis.

    Evidence Co-IP, mouse knockout, and cytological localization of ZMM proteins

    PMID:30746471

    Open questions at the time
    • Stoichiometry and structure of the ZZS complex not determined
    • How SPO16 stabilizes SHOC1 mechanistically unknown
  6. 2022 Medium

    Placed M1AP within the ZZS network downstream of SHOC1 localization, showing M1AP loss reduces TEX11 recruitment and crossovers without disturbing SHOC1.

    Evidence Co-IP, mouse knockout, and chromosome spread immunofluorescence

    PMID:36440627

    Open questions at the time
    • Direct versus indirect SHOC1-M1AP contact not resolved
    • Sex-specific differences in M1AP requirement not fully explained
  7. 2022 Medium

    Extended SHOC1 function to a presynaptic role by linking biallelic loss to abnormal DMC1/RAD51/RPA2 dynamics and pairing/synapsis defects in azoospermic men and mice.

    Evidence Whole-exome sequencing of NOA patients, mouse knockout, and meiotic spread immunofluorescence

    PMID:35485979

    Open questions at the time
    • Presynaptic mechanism is a single-lab inference
    • Molecular link between SHOC1 and strand-exchange protein loading undefined
  8. 2024 Medium

    Positioned SHOC1 downstream of the RNF212B E3 ligase in the crossover maturation pathway by showing reduced SHOC1 focus formation in RNF212B mutants.

    Evidence RNF212B knockout mouse with cytological MZIP2 focus quantification

    PMID:38865271

    Open questions at the time
    • SHOC1 was not the primary subject
    • Whether RNF212B acts on SHOC1 directly is untested
  9. 2025 High

    Pinpointed the XPF-like domain via a disease missense variant (p.Q590R) as required for branched-DNA binding, factor recruitment, and protection of autosomes from MSUC, mechanistically linking domain function to chromatin architecture and disease.

    Evidence Patient variant identification, in vitro branched-DNA binding assay, cytology, and 3D chromatin analysis

    PMID:42258546

    Open questions at the time
    • Structural basis of branched-DNA recognition not resolved
    • How the domain prevents autosome intrusion into the sex body mechanistically unknown
  10. 2025 Medium

    Distinguished ZZS deficiency (early meiotic arrest with synapsis and DSB-repair failure) from M1AP deficiency (metaphase I arrest) in human males, defining SHOC1/ZZS as essential for early recombination steps leading to synapsis.

    Evidence Testicular phenotyping of men with biallelic LoF variants, meiotic spreads, immunofluorescence

    PMID:40374915

    Open questions at the time
    • Observational human characterization without manipulation
    • Molecular step distinguishing ZZS from M1AP arrest not defined

Open questions

Synthesis pass · forward-looking unresolved questions
  • Why SHOC1 retains a conserved XPF/ERCC4 catalytic architecture yet shows no detectable endonuclease activity, and whether catalysis is acquired in the assembled ZZS complex or has been functionally replaced by branched-DNA recognition, remains unresolved.
  • No structure of the ZZS complex bound to branched DNA
  • No reconstituted assay testing catalysis in complex context
  • Mechanism coupling branched-DNA binding to downstream ZMM recruitment undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003677 DNA binding 2
Localization
GO:0000228 nuclear chromosome 3
Pathway
R-HSA-1474165 Reproduction 3 R-HSA-1640170 Cell Cycle 3 R-HSA-73894 DNA Repair 3
Complex memberships
ZZS complex (SHOC1-SPO16-TEX11)

Evidence

Reading pass · 12 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2008 SHOC1 (Arabidopsis ortholog) is required for class I meiotic crossover formation; shoc1 mutants show striking reduction in CO number with normal early recombination (DMC1 foci) and synapsis completion. Double-mutant analysis showed SHOC1 acts in the same pathway as AtMSH5 (a ZMM protein). SHOC1 shows sequence similarity to the XPF endonuclease protein family, suggesting direct involvement in maturation of DNA intermediates leading to COs. Genetic mutant analysis in Arabidopsis, cytological DMC1 foci quantification, double-mutant epistasis analysis, sequence similarity analysis Current biology : CB High 18812090
2011 Arabidopsis SHOC1 interacts with PTD (an ERCC1-like protein) through its XPF-like nuclease-(HhH)2 domain to form an XPF-ERCC1-like heterodimer required for class I interfering crossovers. Both SHOC1 and PTD are required for class-I-interfering COs alongside MSH4, MSH5, MER3, and MLH3. The authors propose that the human ortholog C9orf84 (SHOC1) forms an analogous heterodimer with Zip2 in yeast. Yeast two-hybrid assay, genetic mutant analysis, double-mutant epistasis Journal of cell science High 21771883
2018 Purified recombinant human SHOC1 (an XPF/MUS81 family member with conserved ERCC4-(HhH)2 core structure) preferentially binds branched DNA molecules in vitro but apparently lacks in vitro endonuclease activity despite conserved catalytic domain. In SHOC1 hypomorphic mice, MLH1 chromosomal localization is reduced, chiasma formation is reduced, and cells arrest at metaphase I with lagging chromosomes. SHOC1 localizes to a subset of recombination sites, axial element formation and homologous pairing are normal, but synapsis is altered. SHOC1 interacts with TEX11, connecting SHOC1 to chromosome axis and crossover structure. In vitro DNA binding assay with purified recombinant protein, in vitro endonuclease assay (negative result for nuclease), cytological analysis of SHOC1 hypomorphic mice, Co-immunoprecipitation/interaction assay with TEX11 PLoS genetics High 29742103
2018 MZIP2 (SHOC1 mammalian ortholog) is the mammalian ortholog of yeast Zip2. Complete MZIP2 knockout in mice causes sterility in both males and females and defects in repairing meiotic DNA double-strand breaks. MZIP2 forms discrete foci on chromosome axes and is required for localization of TEX11 (mammalian Zip4 ortholog) and MSH4 to form crossover-prone recombination intermediates. In MZIP2-null meiocytes, crossover formation is abolished, synaptonemal complex formation is incomplete, and meiosis arrests at a zygotene-like stage. Mouse knockout, cytological analysis (foci localization, chromosome spreads), immunofluorescence Communications biology High 30272023
2019 SPO16 (mammalian ortholog of yeast Spo16) physically interacts with SHOC1 (MZIP2/mammalian Zip2 ortholog) and forms a complex. SPO16 localizes to recombination nodules alongside SHOC1 and TEX11. SPO16 is required for stabilization of SHOC1 protein levels and proper localization of other ZMM proteins. In SPO16-deleted meiocytes, DSBs are repaired without CO formation though synapsis is less affected. The SPO16-SHOC1 complex-associated recombination intermediate is a key step facilitating meiotic recombination that produces COs. Co-immunoprecipitation, mouse KO, cytological localization studies, immunofluorescence Science advances High 30746471
2022 Bi-allelic SHOC1 loss-of-function variants in NOA patients and Shoc1-knockout mice show meiotic defects including comprehensive defects in homologous pairing and synapsis, along with abnormal expression/localization of DMC1, RAD51, and RPA2 in spermatocyte spreads, suggesting SHOC1 has a presynaptic function during meiotic recombination in addition to its role in crossover formation. Whole-exome sequencing in patients, mouse KO (germ-cell-specific and general), meiotic chromosome spread analysis, immunofluorescence for DMC1/RAD51/RPA2 Molecular human reproduction Medium 35485979
2022 M1AP interacts with the mammalian ZZS complex components SHOC1, TEX11, and SPO16. M1AP localizes to chromosomal axes in a SPO16-dependent manner. Ablation of M1AP does not alter SHOC1 localization but reduces the recruitment of TEX11 to recombination intermediates and decreases crossover formation in males. Co-immunoprecipitation, mouse KO, cytological immunofluorescence, chromosome spread analysis EMBO reports Medium 36440627
2024 In RNF212B mutant mice, MZIP2 (SHOC1) localization to recombination intermediates is reduced, placing SHOC1 downstream of the RNF212B E3 ligase in the CO maturation pathway. Mouse KO of RNF212B, cytological immunofluorescence for MZIP2 foci Proceedings of the National Academy of Sciences of the United States of America Medium 38865271
2023 FLIP-FIGNL1 complex promotes RAD51/DMC1 dissociation; FLIP-null meiocytes arrest at zygotene-like stage with massive RAD51 and DMC1 foci that frequently co-localize with SHOC1 and TEX11, indicating that SHOC1-positive recombination intermediates accumulate when RAD51/DMC1 are not properly dissociated. Mouse germline-specific KO, cytological co-localization immunofluorescence Nucleic acids research Low 37439366
2025 In human SHOC1, the XPF-like domain is required for binding branched DNA structures and for CO formation. A missense variant (p.Q590R) within the XPF-like domain impairs DNA double-strand break repair by compromising branched DNA binding and recruitment of M1AP, REDIC1, and ZMM factors to recombination intermediates. The XPF-like domain also prevents autosome intrusion into the sex body, protecting autosomal loci from meiotic silencing of unsynapsed chromatin (MSUC). The variant disrupts 3D chromatin structure in pachytene spermatocytes and induces synapsis defects. Patient variant identification, in vitro DNA binding assay (branched DNA), cytological immunofluorescence, 3D chromatin analysis Nucleic acids research High 42258546
2025 Men with ZZS (SHOC1/TEX11/SPO16) deficiency show early meiotic arrest with incorrect synapsis of homologous chromosomes, unrepaired DNA double-strand breaks, and incomplete recombination, phenotypically distinct from M1AP deficiency (which causes metaphase I arrest). This establishes SHOC1/ZZS function as essential for early meiotic recombination steps leading to synapsis in humans. In-depth testicular phenotyping of men with biallelic LoF variants, meiotic spread analysis, immunofluorescence EMBO molecular medicine Medium 40374915
2023 During meiotic prophase I, SHOC1 binds to branched DNA and recruits SPO16 and other ZMM proteins to facilitate crossover formation (mechanistic model stated in context of SPO16 POI findings, consistent with prior experimental evidence from PMID:29742103 and PMID:30746471). Synthesis of experimental evidence cited in paper; SPO16 variant functional assay (minigene); prior biochemical data from referenced studies Clinical genetics Low 37270785

Source papers

Stage 0 corpus · 23 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2020 Genetic dissection of spermatogenic arrest through exome analysis: clinical implications for the management of azoospermic men. Genetics in medicine : official journal of the American College of Medical Genetics 123 32741963
2008 SHOC1, an XPF endonuclease-related protein, is essential for the formation of class I meiotic crossovers. Current biology : CB 73 18812090
2011 SHOC1 and PTD form an XPF-ERCC1-like complex that is required for formation of class I crossovers. Journal of cell science 51 21771883
2018 SHOC1 is a ERCC4-(HhH)2-like protein, integral to the formation of crossover recombination intermediates during mammalian meiosis. PLoS genetics 46 29742103
2019 SPO16 binds SHOC1 to promote homologous recombination and crossing-over in meiotic prophase I. Science advances 32 30746471
2018 Evolutionarily-conserved MZIP2 is essential for crossover formation in mammalian meiosis. Communications biology 30 30272023
2020 Bi-allelic SHOC1 loss-of-function mutations cause meiotic arrest and non-obstructive azoospermia. Journal of medical genetics 27 32900840
2024 RNF212B E3 ligase is essential for crossover designation and maturation during male and female meiosis in the mouse. Proceedings of the National Academy of Sciences of the United States of America 18 38865271
2019 OsSHOC1 and OsPTD1 are essential for crossover formation during rice meiosis. The Plant journal : for cell and molecular biology 18 30589140
2022 M1AP interacts with the mammalian ZZS complex and promotes male meiotic recombination. EMBO reports 17 36440627
2022 Bi-allelic variants in SHOC1 cause non-obstructive azoospermia with meiosis arrest in humans and mice. Molecular human reproduction 14 35485979
2023 The FLIP-FIGNL1 complex regulates the dissociation of RAD51/DMC1 in homologous recombination and replication fork restart. Nucleic acids research 12 37439366
2019 Analysis of mRNA Expression Patterns in Peripheral Blood Cells of 3 Patients With Cancer After the First Fraction of 2 Gy Irradiation: An Integrated Case Report and Systematic Review. Dose-response : a publication of International Hormesis Society 11 30833875
2023 Integration of Mendelian randomisation and systems biology models to identify novel blood-based biomarkers for stroke. Journal of biomedical informatics 10 36958462
2023 Pathogenic bi-allelic variants of meiotic ZMM complex gene SPO16 in premature ovarian insufficiency. Clinical genetics 5 37270785
2023 FANCM interacts with the MHF1-MHF2 complex to limit crossover frequency during rice meiosis. The Plant journal : for cell and molecular biology 4 37632767
2022 Achaete-scute complex-like 2 regulated inflammatory mechanism through Toll-like receptor 4 activating in stomach adenocarcinoma. World journal of surgical oncology 3 36008864
2022 Molecular characteristics of pediatric nasopharyngeal carcinoma using whole-exome sequencing. Oral oncology 3 36332446
2025 Genotype-specific differences in infertile men due to loss-of-function variants in M1AP or ZZS genes. EMBO molecular medicine 1 40374915
2024 A comprehensive study of common and rare genetic variants in spermatogenesis-related loci identifies new risk factors for idiopathic severe spermatogenic failure. Human reproduction open 1 39678461
2026 XPF-like domain in human SHOC1 is required for crossover formation and protecting autosome from MSUC. Nucleic acids research 0 42258546
2025 Establishment and clinical significance of genetic factor screening method for patients with nonobstructive azoospermia based on whole exon sequencing technology. Translational andrology and urology 0 40376536
2025 circSHOC1-SLC25A3 promotes 2-naphthylamine-induced DNA damage in bronchial epithelial cells via activation of oxidative stress. Toxicology and applied pharmacology 0 41285321

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