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FLASH GENE
Symbol PRDM9 contributors: mct/pgu - updated : 12-07-2017
HGNC name PR domain containing 9
HGNC id 13994
Location 5p14.2      Physical location : 23.507.723 - 23.528.704
Synonym name
  • PR-domain containing protein 9
  • positive regulatory domain family protein 9
  • PR domain zinc finger protein 9
    • Synonym symbol(s) PFM6, MEISETZ
    EC.number 2.1.1.43
    DNA
    TYPE functioning gene
    STRUCTURE 20.98 kb     11 Exon(s)
    10 Kb 5' upstream gene genomic sequence study
    MAPPING cloned Y linked N status provisional
    RNA
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    11 - 3691 103.25 894 - 2010 20044539
    EXPRESSION
    Type
       expressed in (based on citations)
    organ(s)
    cell lineage
    cell lines
    fluid/secretion
    at STAGE
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • an N-terminal KRAB domain
  • an SSX repression domain
  • a SET domain, that might be responsible for activating hotspots by chromatin remodelling
  • a zinc finger array that can recognize a short sequence motif associated with hot spots, with binding to this motif possibly triggering hot-spot activity via chromatin remodeling , a highly variable tandem-repeat zinc finger (ZF) DNA-binding domain that plays a key role in determining sequence-specific hotspots of meiotic recombination genome wide
  • a C-terminal DNA binding domain consisting of 12 C2H2-type zinc fingers , C-terminal tandem-repeat zinc-finger (ZnF) array encoded by a variable minisatellite
    • HOMOLOGY
    interspecies homolog to murine Prdm9 (73.8pc)
    Homologene
    FAMILY
  • PR-domain protein family
    • CATEGORY enzyme , regulatory
    SUBCELLULAR LOCALIZATION     intracellular
    intracellular,nucleus
    basic FUNCTION
  • involved in transcriptional regulation
  • histone methyltransferase that specifically trimethylates histone H3 during meiotic prophase
  • eseential for proper meiotic progression
  • plays a central role in the transcriptional activation of gene during early meiotic prophase
  • meiosis-specific histone methyltransferase with a tandem-repeat zinc finger (ZnF) domain encoded by a minisatellite-like sequence
  • major specifier of hotspots in the human and mouse genome
  • binding of PRDM9 to specific DNA sequences targets the initiation of recombination at specific locations in the genome
  • major determinant of meiotic recombination hotspots
  • implicated as a risk factor for some pathological genome rearrangements
  • key regulator of meiotic recombination (22643917)
  • plays a key role in specifying meiotic recombination hotspot locations via recognition of hotspot sequence motifs by a variable tandem-repeat zinc finger domain
  • autoregulation of PRDM9 is unusual in its ability to eliminate any protein variants that strongly stimulate instability, resulting in the curious phenomenon of diversity being largely driven by the least, not most, unstable variants in a population
  • PRDM9 binding organizes hotspot nucleosomes and limits Holliday junction migration
  • a meiosis-specific protein that trimethylates H3K4 and controls the activation of recombination hot spots
  • is a major regulator of the localization of meiotic recombination hotspots in the human and mouse genomes
  • PRDM9 and axis-associated cohesin complexes together coordinate and facilitate meiotic recombination by recruiting key proteins for initiation of DSBs, thereby associating activated hotspots with DSB-initiating complexes on the axis
    • CELLULAR PROCESS nucleotide, transcription, regulation
    PHYSIOLOGICAL PROCESS
    PATHWAY
    metabolism
    signaling
    a component
    INTERACTION
    DNA binding
    RNA
    small molecule metal binding,
  • Zn2+
    • protein
  • binds to DNA in hotspots and subsequently uses its SET domain to locally trimethylate histone H3 at lysine 4 (H3K4me3)
  • may play critical roles through H3K36 trimethylation in cells
  • CXXC1 interact with the KRAB domain of PRDM9
  • PRDM9 interacts with STAG3 and REC8 in cooperative relationships that promote normal levels of meiotic DSBs at recombination hotspots in spermatocytes
    • cell & other
    REGULATION
    ASSOCIATED DISORDERS
    corresponding disease(s)
    Susceptibility
    Variant & Polymorphism SNP
  • mutations (17353G>T (Gly433Val) and 18109C>G (Thr685Arg)) in PRDM9 may cause idiopathic infertility in human males
    • Candidate gene
    Marker
    Therapy target
    ANIMAL & CELL MODELS