Affinage

HFM1

Probable ATP-dependent DNA helicase HFM1 · UniProt A2PYH4

Length
1435 aa
Mass
162.6 kDa
Annotated
2026-06-10
26 papers in source corpus 14 papers cited in narrative 14 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

HFM1 (yeast Mer3) is a germline-specific DEXH-box DNA helicase that drives the progression of meiotic recombination toward crossover formation (PMID:10523314, PMID:17286053). The purified enzyme has DNA-stimulated ATPase activity, unwinds duplex DNA in the 3'→5' direction, and resolves Holliday-junction and overhang substrates, with replication protein A (RPA) preventing reannealing of displaced single strands to enable processive unwinding (PMID:11376001, PMID:12039965). Mechanistically it does not initiate strand pairing but stimulates 3'→5' heteroduplex extension by Rad51 to stabilize nascent joint molecules and permit second-end capture, the committed step for crossover products (PMID:15066281); mutations that abolish helicase or ATPase activity reduce crossing over and crossover interference (PMID:11971962). Beyond its catalytic role, Mer3 physically recruits the MutLβ (Mlh1–Mlh2) complex to recombination hotspots in a manner independent of its helicase activity, limiting gene conversion tract lengths (PMID:28051769), and binds RPA through a conserved interface required for helicase processivity and efficient recruitment to double-strand-break sites (PMID:41851108). In mammals, HFM1 is a ZMM-class factor essential for class I crossover formation and complete synapsis: loss causes reduced MLH1 crossover foci, altered MSH4 localization, defective synaptonemal complex extension, and meiotic arrest, and biallelic human variants cause non-obstructive azoospermia with metaphase-I arrest (PMID:23555294, PMID:35526155). In oocytes and early embryos HFM1 has additional roles, localizing to spindle poles with the Golgi marker GM130 to organize the meiotic spindle (PMID:32606310), mediating intercellular-bridge transport for primordial follicle formation via RAC1/ANLN/E-cadherin signaling (PMID:39725823), restraining FBXW11-mediated FUS degradation (PMID:38822414), and supporting nuclear functions required for zygotic genome activation (PMID:41423819).

Mechanistic history

Synthesis pass · year-by-year structured walk · 11 steps
  1. 1999 High

    Established that the helicase ortholog is needed to convert early meiotic DSBs into productive recombination intermediates and to control crossover number and distribution.

    Evidence Genetic and recombination-intermediate analysis of mer3 deletion mutants in S. cerevisiae

    PMID:10523314

    Open questions at the time
    • Did not establish the biochemical activity of the protein
    • Did not identify physical partners or substrates
  2. 2001 High

    Defined the core enzymology, showing the protein is a DNA-stimulated ATPase and 3'→5' helicase whose product displacement depends on RPA.

    Evidence In vitro ATPase, helicase directionality, and RPA-stimulation assays with purified MER3

    PMID:11376001

    Open questions at the time
    • Did not define the RPA-contact interface
    • Did not link helicase activity to a specific recombination step in vivo
  3. 2002 High

    Demonstrated that catalytic helicase activity, not merely DNA binding, is required for crossover formation and interference, and that the enzyme can unwind Holliday junctions.

    Evidence Active-site mutagenesis (G166D, K167A) with purified-protein biochemistry and meiotic genetics; helicase assays on synthetic Holliday-junction substrates

    PMID:11971962 PMID:12039965

    Open questions at the time
    • Did not show how unwinding promotes joint-molecule stability
    • Physiological substrate during recombination not identified
  4. 2004 High

    Resolved the recombination-step function, showing Mer3 stabilizes Rad51-generated joint molecules by directionally extending heteroduplex rather than initiating pairing.

    Evidence In vitro DNA strand-exchange and directional heteroduplex-extension assays with purified Mer3 and Rad51

    PMID:15066281

    Open questions at the time
    • Direct demonstration of second-end capture in vivo not shown
    • Regulation of the Mer3–Rad51 interplay unresolved
  5. 2006 Medium

    Identified human HFM1 as the Mer3 ortholog with conserved DEXH-box and zinc-finger architecture and germline-restricted expression.

    Evidence cDNA cloning, sequence/domain analysis, and RT-PCR tissue profiling of human HFM1

    PMID:17286053

    Open questions at the time
    • No functional assay on the human protein
    • Subcellular localization and partners not addressed
  6. 2013 High

    Established the mammalian meiotic requirement, defining HFM1 as a ZMM-class factor for class I crossovers and complete synapsis.

    Evidence Conditional knockout mouse spermatocytes with MSH4/MLH1 foci, chiasma, and synaptonemal complex cytology

    PMID:23555294

    Open questions at the time
    • Did not test helicase-activity dependence in mammals
    • Did not identify mammalian protein partners
  7. 2017 High

    Uncovered a non-catalytic scaffolding function: Mer3 recruits MutLβ to hotspots to constrain gene conversion tract length independent of helicase activity.

    Evidence Reciprocal Co-IP/MS, D-loop binding assays, genome-wide gene-conversion sequencing, and helicase-dead mutant analysis in yeast

    PMID:28051769

    Open questions at the time
    • Structural basis of Mer3–MutLβ contact unknown
    • Conservation of the MutLβ-recruitment role in mammals untested
  8. 2020 Medium

    Revealed a non-recombination oocyte role, placing HFM1 at spindle poles where it supports Golgi-associated spindle organization.

    Evidence Oocyte-specific conditional knockout with GM130/p-MAPK co-localization and spindle/chromosome phenotyping

    PMID:32606310

    Open questions at the time
    • Molecular link between HFM1 and GM130 retention unknown
    • Cytoplasmic mechanism not reconstituted
  9. 2022 High

    Connected HFM1 to human disease, showing biallelic variants cause non-obstructive azoospermia via impaired crossover formation, validated in dose-dependent mouse knock-ins.

    Evidence Patient whole-exome sequencing, testicular histology/immunofluorescence, and patient-equivalent mouse knock-in models

    PMID:35526155

    Open questions at the time
    • Genotype–phenotype severity determinants incompletely defined
    • Female-fertility consequences in humans not addressed here
  10. 2024 Medium

    Extended oocyte function to gene-regulatory and intercellular-transport pathways, implicating an FBXW11–FUS–BRCA1 axis and RAC1/ANLN/E-cadherin-dependent intercellular-bridge transport.

    Evidence Oocyte conditional knockouts with Co-IP, ubiquitination assays, FUS localization, gene-expression analysis, and live imaging of intercellular bridges

    PMID:38822414 PMID:39725823

    Open questions at the time
    • Directness of HFM1 action on FUS/RAC1 pathways unresolved
    • Single-lab findings not independently replicated
  11. 2026 High

    Defined the molecular RPA interface and demonstrated its in vivo importance, and showed nuclear HFM1 is required for zygotic genome activation.

    Evidence Cross-linking MS, AlphaFold2 modelling, single-molecule magnetic tweezers, ChIP-seq-equivalent localization, and RPA-binding-deficient mutant genetics; minigene splicing, RNA-seq, H3K27me3 profiling, and mouse mRNA rescue

    PMID:41423819 PMID:41851108

    Open questions at the time
    • Mechanism connecting nuclear HFM1 to ZGA transcription not fully defined
    • ZGA findings rest on a single clinical case with limited embryos

Open questions

Synthesis pass · forward-looking unresolved questions
  • How HFM1's canonical recombination helicase activity relates mechanistically to its diverse cytoplasmic, transport, and embryonic functions remains unresolved.
  • No unified model linking helicase catalysis to spindle, intercellular-bridge, and ZGA roles
  • Direct physical substrates/partners for the non-meiotic roles not established

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003677 DNA binding 3 GO:0140097 catalytic activity, acting on DNA 3 GO:0016787 hydrolase activity 2 GO:0140657 ATP-dependent activity 2 GO:0060090 molecular adaptor activity 1
Localization
GO:0005694 chromosome 2 GO:0005634 nucleus 1 GO:0005815 microtubule organizing center 1 GO:0005829 cytosol 1
Pathway
R-HSA-1474165 Reproduction 2 R-HSA-73894 DNA Repair 2 R-HSA-1640170 Cell Cycle 1

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1999 MER3 (yeast ortholog of HFM1) encodes a DExH-box type helicase required for the transition of meiotic double-strand breaks (DSBs) to later recombination intermediates and for crossover control; mer3 mutants show hyperresected DSBs persisting late in meiosis, reduced crossover frequencies, and random crossover distribution leading to non-disjunction. Genetic analysis of mer3 deletion mutants in S. cerevisiae, meiotic DSB and recombination intermediate analysis The EMBO journal High 10523314
2001 Purified MER3 protein is a DNA helicase with ATPase activity stimulated by single- or double-stranded DNA (kcat ~500/min); it unwinds DNA in the 3' to 5' direction and requires RPA (replication protein A) to displace long DNA fragments by preventing re-annealing of single-stranded products. In vitro biochemical assays with purified MER3 protein: ATPase assay, DNA helicase displacement assay, directionality assay with ssDNA circular substrates, RPA stimulation assay The Journal of biological chemistry High 11376001
2002 Mer3 helicase activity is required for meiotic crossing over: the mer3G166D mutation reduces helicase activity to <1% of wild-type without affecting DNA binding, while mer3K167A eliminates ATPase activity; both mutations cause defects in DSB transition, decreased crossing over, and reduced crossover interference. Site-directed mutagenesis of conserved helicase motif residues, purified mutant protein biochemical assays (ATPase, helicase, DNA binding), genetic analysis in S. cerevisiae meiosis Molecular and cellular biology High 11971962
2002 Purified MER3 helicase can unwind Holliday junctions (with 25-bp arms and blunt ends) as well as blunt-ended and 5'-overhang dsDNA substrates; unwinding of the 3'-overhang substrate requires ≥6 unpaired bases for initiation, and Holliday junction unwinding efficiency is influenced by Mg2+ concentration. In vitro helicase assays with purified MER3 and defined DNA substrates including synthetic Holliday junctions, varying Mg2+ conditions The Journal of biological chemistry High 12039965
2004 Mer3 helicase stimulates 3'→5' heteroduplex extension by Rad51 during DNA strand exchange, but blocks 5'→3' heteroduplex extension; Mer3 does not initiate DNA pairing but stabilizes nascent joint molecules to permit capture of the second processed end of a DSB, a step required for crossover product formation. In vitro DNA strand exchange assays with purified Mer3 and Rad51 proteins, directional heteroduplex extension assays Cell High 15066281
2006 Human HFM1 encodes a predicted 172 kDa protein with seven consecutive DEXH-box helicase motifs at the N-terminus and a single putative zinc finger motif at the C-terminus, sharing domain architecture with yeast Mer3; its transcript is preferentially expressed in testis and ovary (germ-line specific). cDNA cloning, sequence analysis, RT-PCR tissue expression analysis DNA sequence : the journal of DNA sequencing and mapping Medium 17286053
2013 Mouse HFM1 is required for normal crossover formation and complete synapsis during meiosis: Hfm1−/− spermatocytes show altered MSH4 chromosomal localization, drastically reduced MLH1 foci (crossover markers), reduced chiasmata, and incomplete synaptonemal complex extension, with arrest and apoptosis at diakinesis. Conditional knockout mouse model, cytological analysis, immunofluorescence for MSH4 and MLH1 foci, chiasma counting, synaptonemal complex analysis PLoS genetics High 23555294
2017 Mer3 helicase physically interacts with the MutLβ complex (Mlh1-Mlh2) and recruits it to meiotic recombination hotspots independently of mismatch recognition; this recruitment limits gene conversion tract lengths genome-wide without affecting crossover formation. Both purified Mer3 and MutLβ preferentially recognize D-loop structures. Surprisingly, Mer3 helicase catalytic activity does not influence gene conversion tract length, revealing a non-catalytic role of Mer3. Co-immunoprecipitation, mass spectrometry, genome-wide sequencing of gene conversion tracts, in vitro binding assays with purified proteins and D-loop substrates, helicase-dead mutant analysis eLife High 28051769
2020 In mouse oocytes, Hfm1 localizes not only to the cytoplasm but also accumulates at spindle poles where it co-localizes with the Golgi marker GM130; conditional knockout of Hfm1 in oocytes causes loss of GM130 and p-MAPK from spindle poles, abnormal spindle assembly, misaligned chromosomes, loss of cortical actin cap, and failed polar body extrusion. Conditional knockout mouse model (cKO from primordial follicle stage), immunofluorescence co-localization with GM130 and p-MAPK, spindle and chromosome analysis Cell death & disease Medium 32606310
2022 Biallelic HFM1 variants in humans cause non-obstructive azoospermia with meiotic arrest at metaphase I due to impaired crossover formation; mouse models carrying equivalent variants recapitulate the meiotic defects, showing reduced HFM1 foci on chromosome axes and varying degrees of synapsis and crossover formation defects in a dose-dependent manner. Whole-exome sequencing in patients, histological and immunofluorescence analysis of testicular sections, mouse knock-in models carrying patient-equivalent variants, HFM1 foci quantification on chromosome spreads Human reproduction (Oxford, England) High 35526155
2024 HFM1 deficiency in mouse oocytes promotes ubiquitination and FBXW11-mediated degradation of FUS protein, alters intranuclear localization of FUS, and modulates expression of meiotic and oocyte development-related genes through BRCA1; Hfm1 KO oocytes arrest at the pachytene stage with impaired DSB repair and disrupted synapsis. Conditional knockout mouse model, co-immunoprecipitation, ubiquitination assay, immunofluorescence for FUS localization and synapsis markers, gene expression analysis Biological research Medium 38822414
2024 HFM1 is involved in intercellular directional transport through germ cell intercellular bridges via the RAC1/ANLN/E-cadherin signaling pathway during oocyte differentiation; this function is required for organelle enrichment from sister germ cells and primordial follicle formation in mice. Conditional knockout mouse model, immunofluorescence, live imaging of intercellular bridge transport, pathway analysis of RAC1/ANLN/E-cad signaling Cellular and molecular life sciences : CMLS Medium 39725823
2026 RPA directly interacts with Mer3 (HFM1 in humans) through a conserved and specific interface identified by cross-linking mass spectrometry and AlphaFold2 structural modelling; this interaction is conserved between yeast Mer3 and human HFM1. Direct RPA interaction is required for Mer3 helicase processivity under low DNA tension conditions (demonstrated by single-molecule magnetic tweezers). A mer3 mutant deficient in RPA binding shows reduced crossover frequencies, accumulation of unresolved recombination intermediates, and weakened recruitment to DSB sites. Co-immunoprecipitation (yeast and human), cross-linking mass spectrometry, AlphaFold2 structural modelling, single-molecule magnetic tweezers assays, genome-wide localization (ChIP-seq equivalent), genetic analysis of RPA-binding-deficient mer3 mutant Nature communications High 41851108
2026 A pathogenic homozygous HFM1 mutation causes aberrant mRNA splicing producing a protein variant that fails to localize to the nucleus; nuclear exclusion of HFM1 leads to widespread transcriptional dysregulation, failure of zygotic genome activation (ZGA), aberrant retention of H3K27me3, and consequent embryonic arrest. Wild-type but not mutant HFM1 mRNA rescued embryonic defects in a mouse knockdown model. Minigene splicing assay, immunofluorescence and confocal imaging for protein localization, RNA-seq, epigenetic profiling (H3K27me3), functional rescue experiments in mouse embryos with WT vs. mutant HFM1 mRNA Human reproduction (Oxford, England) Medium 41423819

Source papers

Stage 0 corpus · 26 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1999 The Saccharomyces cerevisiae MER3 gene, encoding a novel helicase-like protein, is required for crossover control in meiosis. The EMBO journal 118 10523314
2013 Mouse HFM1/Mer3 is required for crossover formation and complete synapsis of homologous chromosomes during meiosis. PLoS genetics 93 23555294
2009 MER3 is required for normal meiotic crossover formation, but not for presynaptic alignment in rice. Journal of cell science 92 19470578
2004 Saccharomyces cerevisiae Mer3 helicase stimulates 3'-5' heteroduplex extension by Rad51; implications for crossover control in meiotic recombination. Cell 90 15066281
2017 Concerted action of the MutLβ heterodimer and Mer3 helicase regulates the global extent of meiotic gene conversion. eLife 57 28051769
2002 Saccharomyces cerevisiae Mer3 is a DNA helicase involved in meiotic crossing over. Molecular and cellular biology 53 11971962
2001 The MER3 helicase involved in meiotic crossing over is stimulated by single-stranded DNA-binding proteins and unwinds DNA in the 3' to 5' direction. The Journal of biological chemistry 50 11376001
2006 HFM1, the human homologue of yeast Mer3, encodes a putative DNA helicase expressed specifically in germ-line cells. DNA sequence : the journal of DNA sequencing and mapping 38 17286053
2019 A novel heterozygous splice-altering mutation in HFM1 may be a cause of premature ovarian insufficiency. Journal of ovarian research 35 31279343
2002 The MER3 DNA helicase catalyzes the unwinding of holliday junctions. The Journal of biological chemistry 33 12039965
2016 Association analysis between HFM1 variation and primary ovarian insufficiency in Chinese women. Clinical genetics 28 26679638
2020 Hfm1 participates in Golgi-associated spindle assembly and division in mouse oocyte meiosis. Cell death & disease 26 32606310
2012 Genetic interactions of hypomorphic mutations in the m7G cap-binding pocket of yeast nuclear cap binding complex: an essential role for Cbc2 in meiosis via splicing of MER3 pre-mRNA. RNA (New York, N.Y.) 26 23002122
2022 Biallelic HFM1 variants cause non-obstructive azoospermia with meiotic arrest in humans by impairing crossover formation to varying degrees. Human reproduction (Oxford, England) 25 35526155
2008 Coprinus cinereus Mer3 is required for synaptonemal complex formation during meiosis. Chromosoma 19 18841377
2023 Novel deleterious splicing variant in HFM1 causes gametogenesis defect and recurrent implantation failure: concerning the risk of chromosomal abnormalities in embryos. Journal of assisted reproduction and genetics 13 36864181
2022 Novel pathogenic splicing variants in helicase for meiosis 1 (HFM1) are associated with diminished ovarian reserve and poor pregnancy outcomes. Journal of assisted reproduction and genetics 8 35881270
2024 The crucial role of HFM1 in regulating FUS ubiquitination and localization for oocyte meiosis prophase I progression in mice. Biological research 7 38822414
2022 Identification of a new splice-acceptor mutation in HFM1 and functional analysis through molecular docking in nonobstructive azoospermia. Journal of assisted reproduction and genetics 6 35486194
2016 Transposon Tagging of a Male-Sterility, Female-Sterility Gene, St8, Revealed that the Meiotic MER3 DNA Helicase Activity Is Essential for Fertility in Soybean. PloS one 5 26930200
2024 HFM1 is essential for the germ cell intercellular bridge transport in primordial follicle formation in mice. Cellular and molecular life sciences : CMLS 3 39725823
2025 Novel biallelic HFM1 variants cause severe oligozoospermia with favorable intracytoplasmic sperm injection outcome. Asian journal of andrology 1 40320820
2026 A homozygous variant in HFM1 causes preimplantation embryo developmental arrest by disrupting zygotic genome activation. Human reproduction (Oxford, England) 0 41423819
2026 Mild defects in follicular development and reproductive performance in the heterozygous Hfm1 female mouse. Reproduction (Cambridge, England) 0 41575512
2026 RPA directly stimulates Mer3 helicase processivity to ensure normal crossover formation in meiosis. Nature communications 0 41851108
2025 Case Report and Literature Review: A 46,XX Infant with Atypical Genitalia Diagnosed with Primary Ovarian Insufficiency Caused by HFM1 Gene Variants. Hormone research in paediatrics 0 39929154

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