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    PWWP2A PWWP domain containing 2A [ Homo sapiens (human) ]

    Gene ID: 114825, updated on 9-Dec-2024

    Summary

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    Official Symbol
    PWWP2Aprovided by HGNC
    Official Full Name
    PWWP domain containing 2Aprovided by HGNC
    Primary source
    HGNC:HGNC:29406
    See related
    Ensembl:ENSG00000170234 MIM:617823; AllianceGenome:HGNC:29406
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MST101
    Summary
    Enables NuRD complex binding activity; chromatin binding activity; and methylated histone binding activity. Involved in chromatin remodeling. Located in nucleus. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in colon (RPKM 1.9), skin (RPKM 1.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PWWP2A in Genome Data Viewer
    Location:
    5q33.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (160044316..160119450, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (160572113..160648036, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (159502889..159546457, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene adrenoceptor alpha 1B Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 40 Neighboring gene MPRA-validated peak5555 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:159435885-159436780 Neighboring gene uncharacterized LOC124901124 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:159455528-159455695 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:159469604-159470298 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:159470299-159470993 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:159487609-159488120 Neighboring gene tetratricopeptide repeat domain 1 Neighboring gene MPRA-validated peak5557 silencer Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:159507098-159508004 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:159508005-159508910 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:159513521-159513688 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23555 Neighboring gene MPRA-validated peak5558 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:159546009-159546508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16575 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16578 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23557 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:159588248-159588903 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:159589561-159590215 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:159591897-159592496 Neighboring gene Sharpr-MPRA regulatory region 721 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:159593698-159594298 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:159602660-159603248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16579 Neighboring gene MPRA-validated peak5559 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16580 Neighboring gene FABP6 antisense RNA 1 Neighboring gene fatty acid binding protein 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16581 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:159664401-159665356 Neighboring gene ubiquinol-cytochrome c reductase binding protein pseudogene Neighboring gene cyclin J like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Dysregulation of cPWWP2A-miR-579 axis mediates dexamethasone-induced cytotoxicity in human osteoblasts. Hong H, et al. Biochem Biophys Res Commun, 2019 Sep 24. PMID 31376935
    2. PWWP2A binds distinct chromatin moieties and interacts with an MTA1-specific core NuRD complex. Link S, et al. Nat Commun, 2018 Oct 16. PMID 30327463, Free PMC Article
    3. Multivalent binding of PWWP2A to H2A.Z regulates mitosis and neural crest differentiation. Pünzeler S, et al. EMBO J, 2017 Aug 1. PMID 28645917, Free PMC Article
    4. A variant NuRD complex containing PWWP2A/B excludes MBD2/3 to regulate transcription at active genes. Zhang T, et al. Nat Commun, 2018 Sep 18. PMID 30228260, Free PMC Article
    5. High throughput RNAi screening identifies ID1 as a synthetic sick/lethal gene interacting with the common TP53 mutation R175H. Imai H, et al. Oncol Rep, 2014 Mar. PMID 24378760, Free PMC Article

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. It has been shown that dysregulation of the circular RNA PWWP2A-miR-579 axis is involved in dexamethasone-induced cytotoxicity in human osteoblasts.
      Title: Dysregulation of cPWWP2A-miR-579 axis mediates dexamethasone-induced cytotoxicity in human osteoblasts.
    2. PWWP2A is a complex chromatin-binding protein that serves to direct the deacetylase complex M1HR to H2A.Z-containing chromatin, thereby promoting changes in histone acetylation levels.PWWP2A's internal region binds H2A.Z nucleosomes and DNA.
      Title: PWWP2A binds distinct chromatin moieties and interacts with an MTA1-specific core NuRD complex.
    3. Study in HeLa, HEK293F, and mouse embryonic stem cells reveal that loss of PWWP2A/B leads to increases in histone acetylation predominantly at highly expressed genes, accompanied by decreases in Pol II elongation. Collectively, these findings suggest a role for PWWP2A/B in regulating transcription through the fine-tuning of histone acetylation dynamics at actively transcribed genes.
      Title: A variant NuRD complex containing PWWP2A/B excludes MBD2/3 to regulate transcription at active genes.
    4. Thus, PWWP2A is a novel H2A.Z-specific multivalent chromatin binder providing a surprising link between H2A.Z, chromosome segregation, and organ development.
      Title: Multivalent binding of PWWP2A to H2A.Z regulates mitosis and neural crest differentiation.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1935, MGC132770

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables NuRD complex binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin remodeling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chromatin remodeling ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of transcription elongation by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of transcriptional start site selection at RNA polymerase II promoter ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    PWWP domain-containing protein 2A
    Names
    MSTP101

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001130864.2 → NP_001124336.1  PWWP domain-containing protein 2A isoform b

      See identical proteins and their annotated locations for NP_001124336.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site at its 3'-terminal exon, compared to variant 1, which results in a protein (isoform B) with a longer and distinct C-terminus, compared to isoform A.
      Source sequence(s)
      AC008706, AI972512, AK055921, BC018680, BC105110, DB450981
      Consensus CDS
      CCDS47332.1
      UniProtKB/Swiss-Prot
      G5EA07, Q2HJJ2, Q8IYR3, Q96N64, Q96PV3
      Related
      ENSP00000305151.7, ENST00000307063.9
      Conserved Domains (1) summary
      cd05835
      Location:653 → 739
      Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...

    2. NM_001267035.3 → NP_001253964.1  PWWP domain-containing protein 2A isoform c

      See identical proteins and their annotated locations for NP_001253964.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the 3' coding region, compared to variant 1, which results in a protein (isoform C) with a shorter C-terminus, compared to isoform A.
      Source sequence(s)
      AC008706, BC039106, BC143437, BI548991, CB218424, DB450981
      Consensus CDS
      CCDS58990.1
      UniProtKB/Swiss-Prot
      Q96N64
      Related
      ENSP00000428143.1, ENST00000523662.1

    3. NM_001349732.2 → NP_001336661.1  PWWP domain-containing protein 2A isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in its 5' UTR, and its 3' terminal exon extends past a splice site that is used in variant 1. These differences cause translation initiation at a downstream start codon and results in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (d) has a shorter N-terminus and distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AC008706, AI288438, AI972512, AK055921, BC018680, BC105110, DB450981
      Conserved Domains (1) summary
      cd05835
      Location:436 → 522
      Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...

    4. NM_001349733.2 → NP_001336662.1  PWWP domain-containing protein 2A isoform e

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) contains an alternate exon in the 5' region, resulting in use of a downstream start codon compared to variant 1. The encoded isoform (e) has a shorter N-terminus than isoform a.
      Source sequence(s)
      AC008706, AI288438, AV720552, BC035076, BC039106, BC105110, CB218424, DB450981

    5. NM_001349734.2 → NP_001336663.1  PWWP domain-containing protein 2A isoform f

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) contains two consecutive alternate exons in the 5' region, and lacks an alternate in-frame exon in the 3' coding region compared to variant 1. These differences cause translation initiation at a downstream start codon and result in an isoform (f) with a shorter N-terminus and lacking an internal segment, compared to isoform a. Variants 6 and 7 encode the same protein (isoform f).
      Source sequence(s)
      AC008706, AI288438, BC039106, BC105110, BC143437, CB218424, DB450981

    6. NM_001349735.2 → NP_001336664.1  PWWP domain-containing protein 2A isoform f

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) contains an alternate exon in the 5' region, and lacks an alternate in-frame exon in the 3' coding region compared to variant 1. These differences cause translation initiation at a downstream start codon and result in an isoform (f) with a shorter N-terminus and lacking an internal segment, compared to isoform a. Variants 6 and 7 encode the same protein (isoform f).
      Source sequence(s)
      AC008706, AI288438, BC039106, BC143437, BI548991, CB218424, DB450981

    7. NM_052927.4 → NP_443159.1  PWWP domain-containing protein 2A isoform a

      See identical proteins and their annotated locations for NP_443159.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform a.
      Source sequence(s)
      AC008706, AV720552, BC035076, BC039106, BC105110, CB218424, DB450981
      Consensus CDS
      CCDS47331.1
      UniProtKB/Swiss-Prot
      Q96N64
      Related
      ENSP00000390462.2, ENST00000456329.7
      Conserved Domains (1) summary
      PTZ00121
      Location:323 → 464
      PTZ00121; MAEBL; Provisional

    RNA

    1. NR_146216.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC008706, AV720552, BC035076, BC039106, BC105110, CB218424, CN336545, DB450981

    2. NR_146217.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9) contains two alternate internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC008706, AI288438, AV720552, BC035076, BC039106, BC105110, CB218424, CN336545, DB450981

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      160044316..160119450 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011534424.4 → XP_011532726.1  PWWP domain-containing protein 2A isoform X1

    2. XM_005265812.4 → XP_005265869.2  PWWP domain-containing protein 2A isoform X3

    3. XM_005265811.4 → XP_005265868.1  PWWP domain-containing protein 2A isoform X2

      See identical proteins and their annotated locations for XP_005265868.1

      Conserved Domains (1) summary
      cd05835
      Location:436 → 522
      Dnmt3b_related; The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in ...

    RNA

    1. XR_007058578.1 RNA Sequence

    2. XR_007058579.1 RNA Sequence

    3. XR_007058580.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      160572113..160648036 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351546.1 → XP_054207521.1  PWWP domain-containing protein 2A isoform X1

    2. XM_054351548.1 → XP_054207523.1  PWWP domain-containing protein 2A isoform X3

    3. XM_054351547.1 → XP_054207522.1  PWWP domain-containing protein 2A isoform X2

    RNA

    1. XR_008487079.1 RNA Sequence

    2. XR_008487080.1 RNA Sequence

    3. XR_008487081.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96N64.2 GenPept UniProtKB/Swiss-Prot:Q96N64

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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