UniProt functional annotation for Q8VDF2



	UniProt functional annotation for Q8VDF2

UniProt code: Q8VDF2.

Organism: Mus musculus (Mouse).

Taxonomy: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus.

Function: Multidomain protein that acts as a key epigenetic regulator by bridging DNA methylation and chromatin modification. Specifically recognizes and binds hemimethylated DNA at replication forks via its YDG domain and recruits DNMT1 methyltransferase to ensure faithful propagation of the DNA methylation patterns through DNA replication. In addition to its role in maintenance of DNA methylation, also plays a key role in chromatin modification: through its tudor-like regions and PHD-type zinc fingers, specifically recognizes and binds histone H3 trimethylated at 'Lys-9' (H3K9me3) and unmethylated at 'Arg-2' (H3R2me0), respectively, and recruits chromatin proteins. Enriched in pericentric heterochromatin where it recruits different chromatin modifiers required for this chromatin replication. Also localizes to euchromatic regions where it negatively regulates transcription possibly by impacting DNA methylation and histone modifications. Has E3 ubiquitin-protein ligase activity by mediating the ubiquitination of target proteins such as histone H3 and PML. It is still unclear how E3 ubiquitin-protein ligase activity is related to its role in chromatin in vivo. May be involved in DNA repair. {ECO:0000269|PubMed:12058012, ECO:0000269|PubMed:12084726, ECO:0000269|PubMed:14993289, ECO:0000269|PubMed:15361834, ECO:0000269|PubMed:17673620, ECO:0000269|PubMed:17994007, ECO:0000269|PubMed:21268065, ECO:0000269|PubMed:21489993}.

Catalytic activity: Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L- cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.; EC=2.3.2.27;

Pathway: Protein modification; protein ubiquitination.

Subunit: Interacts with DNMT3A and DNMT3B. Interacts with DNMT1; the interaction is direct. Interacts with USP7; leading to its deubiquitination. Interacts with HDAC1, but not with HDAC2. Interacts with UHRF1BP1. Interacts with PML. Interacts with EHMT2. Binds hemimethylated CpG containing oligonucleotides (PubMed:15361834, PubMed:17994007, PubMed:18772888, PubMed:18772891, PubMed:19056828, PubMed:19798101, PubMed:21268065). Interacts with PRAMEL7 (PubMed:28604677). Interacts with ZNF263; recruited to the SIX3 promoter along with other proteins involved in chromatin modification and transcriptional corepression where it contributes to transcriptional repression (By similarity). {ECO:0000250|UniProtKB:Q96T88, ECO:0000269|PubMed:14993289, ECO:0000269|PubMed:15361834, ECO:0000269|PubMed:17994007, ECO:0000269|PubMed:18772888, ECO:0000269|PubMed:18772891, ECO:0000269|PubMed:19056828, ECO:0000269|PubMed:19798101, ECO:0000269|PubMed:21268065, ECO:0000269|PubMed:28604677}.

Subcellular location: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00358, ECO:0000269|PubMed:10984098, ECO:0000269|PubMed:11161719, ECO:0000269|PubMed:14993289, ECO:0000269|PubMed:17994007, ECO:0000269|PubMed:21489993, ECO:0000269|PubMed:8634372}. Note=Localizes to replication foci. Enriched in pericentric heterochromatin. Also localizes to euchromatic regions.

Tissue specificity: Expressed in thymus, testis, spleen and lung. Within testis, expressed in almost all cells except elongated spermatids. {ECO:0000269|PubMed:10984098, ECO:0000269|PubMed:9880673}.

Induction: Up-regulated in proliferating cells, and down-regulated in quiescent or differentiated cells. Early induced by E1A in postmitotic cells. Down-regulated by aphidicolin. {ECO:0000269|PubMed:10984098, ECO:0000269|PubMed:11161719, ECO:0000269|PubMed:12058012, ECO:0000269|PubMed:8634372}.

Domain: The tudor-like regions specifically recognize and bind histone H3 unmethylated at 'Arg-2' (H3R2me0), while the PHD-type zinc finger specifically recognizes and binds histone H3 trimethylated at 'Lys-9' (H3K9me3). The tudor-like regions simultaneously recognizes H3K9me3 through a conserved aromatic cage in the first tudor-like subdomain and unmodified H3K4 (H3K4me0) within a groove between the tandem subdomains (PubMed:21489993). The linker region plays a role in the formation of a histone H3-binding hole between the reader modules formed by the tudor- like regions and the PHD-type zinc finger by making extended contacts with the tandem tudor-like regions. {ECO:0000269|PubMed:21489993}.

Domain: The YDG domain (also named SRA domain) specifically recognizes and binds hemimethylated DNA at replication forks (DNA that is only methylated on the mother strand of replicating DNA) (PubMed:17994007). The YDG domain contains a binding pocket that accommodates the 5- methylcytosine that is flipped out of the duplex DNA. 2 specialized loops reach through the resulting gap in the DNA from both the major and the minor grooves to read the other 3 bases of the CpG duplex. The major groove loop confers both specificity for the CpG dinucleotide and discrimination against methylation of deoxycytidine of the complementary strand (PubMed:18772888). The YDG domain also recognizes and binds 5-hydroxymethylcytosine (5hmC). {ECO:0000269|PubMed:17994007, ECO:0000269|PubMed:18772888}.

Domain: The RING finger is required for ubiquitin ligase activity.

Ptm: Phosphorylation at Ser-303 of the linker region decreases the binding to H3K9me3. Phosphorylation at Ser-639 by CDK1 during M phase impairs interaction with USP7, preventing deubiquitination and leading to degradation by the proteasome (By similarity). {ECO:0000250}.

Ptm: Ubiquitinated; which leads to proteasomal degradation. Autoubiquitinated; interaction with USP7 leads to deubiquitination and prevents degradation. Ubiquitination and degradation takes place during M phase, when phosphorylation at Ser-639 prevents interaction with USP7 and subsequent deubiquitination. Polyubiquitination may be stimulated by DNA damage. {ECO:0000269|PubMed:21268065}.

Disruption phenotype: Mice display a sensitization to DNA damage and replication block, and die in mid-gestation. {ECO:0000269|PubMed:12084726}.

Annotations taken from UniProtKB at the EBI.


Organism:		Mus musculus (Mouse).
Taxonomy:		Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus.



Function:		Multidomain protein that acts as a key epigenetic regulator by bridging DNA methylation and chromatin modification. Specifically recognizes and binds hemimethylated DNA at replication forks via its YDG domain and recruits DNMT1 methyltransferase to ensure faithful propagation of the DNA methylation patterns through DNA replication. In addition to its role in maintenance of DNA methylation, also plays a key role in chromatin modification: through its tudor-like regions and PHD-type zinc fingers, specifically recognizes and binds histone H3 trimethylated at 'Lys-9' (H3K9me3) and unmethylated at 'Arg-2' (H3R2me0), respectively, and recruits chromatin proteins. Enriched in pericentric heterochromatin where it recruits different chromatin modifiers required for this chromatin replication. Also localizes to euchromatic regions where it negatively regulates transcription possibly by impacting DNA methylation and histone modifications. Has E3 ubiquitin-protein ligase activity by mediating the ubiquitination of target proteins such as histone H3 and PML. It is still unclear how E3 ubiquitin-protein ligase activity is related to its role in chromatin in vivo. May be involved in DNA repair. {ECO:0000269\|PubMed:12058012, ECO:0000269\|PubMed:12084726, ECO:0000269\|PubMed:14993289, ECO:0000269\|PubMed:15361834, ECO:0000269\|PubMed:17673620, ECO:0000269\|PubMed:17994007, ECO:0000269\|PubMed:21268065, ECO:0000269\|PubMed:21489993}.


Catalytic activity:		Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L- cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.; EC=2.3.2.27;
Pathway:		Protein modification; protein ubiquitination.
Subunit:		Interacts with DNMT3A and DNMT3B. Interacts with DNMT1; the interaction is direct. Interacts with USP7; leading to its deubiquitination. Interacts with HDAC1, but not with HDAC2. Interacts with UHRF1BP1. Interacts with PML. Interacts with EHMT2. Binds hemimethylated CpG containing oligonucleotides (PubMed:15361834, PubMed:17994007, PubMed:18772888, PubMed:18772891, PubMed:19056828, PubMed:19798101, PubMed:21268065). Interacts with PRAMEL7 (PubMed:28604677). Interacts with ZNF263; recruited to the SIX3 promoter along with other proteins involved in chromatin modification and transcriptional corepression where it contributes to transcriptional repression (By similarity). {ECO:0000250\|UniProtKB:Q96T88, ECO:0000269\|PubMed:14993289, ECO:0000269\|PubMed:15361834, ECO:0000269\|PubMed:17994007, ECO:0000269\|PubMed:18772888, ECO:0000269\|PubMed:18772891, ECO:0000269\|PubMed:19056828, ECO:0000269\|PubMed:19798101, ECO:0000269\|PubMed:21268065, ECO:0000269\|PubMed:28604677}.
Subcellular location:		Nucleus {ECO:0000255\|PROSITE-ProRule:PRU00358, ECO:0000269\|PubMed:10984098, ECO:0000269\|PubMed:11161719, ECO:0000269\|PubMed:14993289, ECO:0000269\|PubMed:17994007, ECO:0000269\|PubMed:21489993, ECO:0000269\|PubMed:8634372}. Note=Localizes to replication foci. Enriched in pericentric heterochromatin. Also localizes to euchromatic regions.
Tissue specificity:		Expressed in thymus, testis, spleen and lung. Within testis, expressed in almost all cells except elongated spermatids. {ECO:0000269\|PubMed:10984098, ECO:0000269\|PubMed:9880673}.
Induction:		Up-regulated in proliferating cells, and down-regulated in quiescent or differentiated cells. Early induced by E1A in postmitotic cells. Down-regulated by aphidicolin. {ECO:0000269\|PubMed:10984098, ECO:0000269\|PubMed:11161719, ECO:0000269\|PubMed:12058012, ECO:0000269\|PubMed:8634372}.
Domain:		The tudor-like regions specifically recognize and bind histone H3 unmethylated at 'Arg-2' (H3R2me0), while the PHD-type zinc finger specifically recognizes and binds histone H3 trimethylated at 'Lys-9' (H3K9me3). The tudor-like regions simultaneously recognizes H3K9me3 through a conserved aromatic cage in the first tudor-like subdomain and unmodified H3K4 (H3K4me0) within a groove between the tandem subdomains (PubMed:21489993). The linker region plays a role in the formation of a histone H3-binding hole between the reader modules formed by the tudor- like regions and the PHD-type zinc finger by making extended contacts with the tandem tudor-like regions. {ECO:0000269\|PubMed:21489993}.
Domain:		The YDG domain (also named SRA domain) specifically recognizes and binds hemimethylated DNA at replication forks (DNA that is only methylated on the mother strand of replicating DNA) (PubMed:17994007). The YDG domain contains a binding pocket that accommodates the 5- methylcytosine that is flipped out of the duplex DNA. 2 specialized loops reach through the resulting gap in the DNA from both the major and the minor grooves to read the other 3 bases of the CpG duplex. The major groove loop confers both specificity for the CpG dinucleotide and discrimination against methylation of deoxycytidine of the complementary strand (PubMed:18772888). The YDG domain also recognizes and binds 5-hydroxymethylcytosine (5hmC). {ECO:0000269\|PubMed:17994007, ECO:0000269\|PubMed:18772888}.
Domain:		The RING finger is required for ubiquitin ligase activity.
Ptm:		Phosphorylation at Ser-303 of the linker region decreases the binding to H3K9me3. Phosphorylation at Ser-639 by CDK1 during M phase impairs interaction with USP7, preventing deubiquitination and leading to degradation by the proteasome (By similarity). {ECO:0000250}.
Ptm:		Ubiquitinated; which leads to proteasomal degradation. Autoubiquitinated; interaction with USP7 leads to deubiquitination and prevents degradation. Ubiquitination and degradation takes place during M phase, when phosphorylation at Ser-639 prevents interaction with USP7 and subsequent deubiquitination. Polyubiquitination may be stimulated by DNA damage. {ECO:0000269\|PubMed:21268065}.
Disruption phenotype:		Mice display a sensitization to DNA damage and replication block, and die in mid-gestation. {ECO:0000269\|PubMed:12084726}.