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FLASH GENE

Symbol

PRDM9

contributors: mct/pgu - updated : 12-07-2017

HGNC name	PR domain containing 9
HGNC id	13994

FLASH GENE DNA RNA EXPRESSION PROTEIN DISORDER ANIMAL & CELL MODELS

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

identification nb exons type bp product Protein kDa AA specific expression Year Pubmed NM_020227 11 - 3691 NP_064612 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