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

Gene ID: 114825, updated on 5-Mar-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 chromatin binding activity and histone binding activity. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in colon (RPKM 1.9), skin (RPKM 1.8) and 25 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (160044316..160119450, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (160572113..160648036, complement)
105.20220307 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 (26) 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)

Genotypes

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_2023_10

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

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