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EED embryonic ectoderm development [ Homo sapiens (human) ]

Gene ID: 8726, updated on 2-Nov-2024

Summary

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Official Symbol
EEDprovided by HGNC
Official Full Name
embryonic ectoderm developmentprovided by HGNC
Primary source
HGNC:HGNC:3188
See related
Ensembl:ENSG00000074266 MIM:605984; AllianceGenome:HGNC:3188
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HEED; COGIS; WAIT1
Summary
This gene encodes a member of the Polycomb-group (PcG) family. PcG family members form multimeric protein complexes, which are involved in maintaining the transcriptional repressive state of genes over successive cell generations. This protein interacts with enhancer of zeste 2, the cytoplasmic tail of integrin beta7, immunodeficiency virus type 1 (HIV-1) MA protein, and histone deacetylase proteins. This protein mediates repression of gene activity through histone deacetylation, and may act as a specific regulator of integrin function. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in lymph node (RPKM 3.3), appendix (RPKM 2.2) and 25 other tissues See more
Orthologs
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Genomic context

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See EED in Genome Data Viewer
Location:
11q14.2
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (86244753..86287615)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (86186227..86228460)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (85955795..85989852)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2695 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:85913252-85913752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:85913753-85914253 Neighboring gene farnesyltransferase, CAAX box, alpha pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5373 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:85955248-85955778 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:85955779-85956307 Neighboring gene Sharpr-MPRA regulatory region 11891 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5374 Neighboring gene immunoglobin superfamily member 21 pseudogene Neighboring gene microRNA 6755 Neighboring gene Sharpr-MPRA regulatory region 13347 Neighboring gene SET pseudogene 17 Neighboring gene heat shock protein nuclear import factor hikeshi Neighboring gene RNA, 7SL, cytoplasmic 225, pseudogene

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 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. EED related overgrowth: First report of multiple members in a single family. Goel H, et al. Am J Med Genet A, 2024 Feb. PMID 37840385
  2. EED-associated overgrowth in a second male patient. Cohen AS, et al. J Hum Genet, 2016 Sep. PMID 27193220
  3. An Allosteric PRC2 Inhibitor Targeting EED Suppresses Tumor Progression by Modulating the Immune Response. Dong H, et al. Cancer Res, 2019 Nov 1. PMID 31395608
  4. Novel EED mutation in patient with Weaver syndrome. Cooney E, et al. Am J Med Genet A, 2017 Feb. PMID 27868325
  5. The murine Polycomb-group gene eed and its human orthologue: functional implications of evolutionary conservation. Schumacher A, et al. Genomics, 1998 Nov 15. PMID 9806832

See all (168) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. EED related overgrowth: First report of multiple members in a single family.
    Title: EED related overgrowth: First report of multiple members in a single family.
  2. The PRC2 molecule EED is a target of epigenetic therapy for neuroblastoma.
    Title: The PRC2 molecule EED is a target of epigenetic therapy for neuroblastoma.
  3. Embryonic Ectoderm Development (EED) as a Novel Target for Cancer Treatment.
    Title: Embryonic Ectoderm Development (EED) as a Novel Target for Cancer Treatment.
  4. Methylation of microRNA-338-5p by EED promotes METTL3-mediated translation of oncogene CDCP1 in gastric cancer.
    Title: Methylation of microRNA-338-5p by EED promotes METTL3-mediated translation of oncogene CDCP1 in gastric cancer.
  5. PICOT binding to chromatin-associated EED negatively regulates cyclin D2 expression by increasing H3K27me3 at the CCND2 gene promoter.
    Title: PICOT binding to chromatin-associated EED negatively regulates cyclin D2 expression by increasing H3K27me3 at the CCND2 gene promoter.
  6. BR-001, a potent inhibitor of the EED subunit of the PRC2 complex, suppresses tumor progression by modulating the tumor microenvironment.
    Title: An Allosteric PRC2 Inhibitor Targeting EED Suppresses Tumor Progression by Modulating the Immune Response.
  7. review the PRC2 complex and clinical syndromes of overgrowth and intellectual disability associated with core components EZH2, EED, and SUZ12
    Title: PRC2-complex related dysfunction in overgrowth syndromes: A review of EZH2, EED, and SUZ12 and their syndromic phenotypes.
  8. Identification of mutations in the PRC2 components EED and SUZ12 in the majority of MPNSTs may imply noncanonical oncogenic activities of the intact component, EZH2, and provide new opportunities for therapeutic intervention.
    Title: Malignant Peripheral Nerve Sheath Tumors: From Epigenome to Bedside.
  9. Mutation in the EED gene is associated with Cohen-Gibson syndrome.
    Title: EED and EZH2 constitutive variants: A study to expand the Cohen-Gibson syndrome phenotype and contrast it with Weaver syndrome.
  10. PICOT knock-down in Jurkat T cells resulted in a reduced histone H3 lysine 27 trimethylation (H3K27me3) at the PRC2 target gene, myelin transcription factor 1 (MYT1), suggesting that PICOT binding to EED alters PRC2-regulated transcriptional repression, and potentially contributes to the epigenetic regulation of chromatin silencing and remodeling.
    Title: PICOT binding to the polycomb group protein, EED, alters H3K27 methylation at the MYT1 PRC2 target gene.
Submit: New GeneRIF Correction See all GeneRIFs (37)

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

Associated conditions

Description Tests
Cohen-Gibson syndrome
MedGen: C4479654 OMIM: 617561 GeneReviews: EED-Related Overgrowth
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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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Nef nef HIV-1 Nef antagonizes the negative effect of EED on virus production and genome encapsidation. The deletion mutant Nef(delta57) shows no EED-counteracting activity PubMed
nef Yeast two-hybrid screening and coimmunoprecipitation experiments have shown that peptides spanning from 1 to 35 and from 138 to 211 in HIV-1 Nef bind to the polycomb group protein EED, which is known as a nuclear factor and repressor of transcription PubMed
nef HIV-1 Nef induces a transient relocalization of EED from nucleus to cytoplasm and the relocalization of EED is required for HIV-1 Tat-mediated transcription PubMed
integrase gag-pol 3D structure of EED shows the binding site of the HIV-1 IN protein is mapped to position 224-232 on the linear sequence of EED PubMed
gag-pol HIV-1 integrase (amino acids 212-264) has been shown to interact with EED (amino acids 96-104 and 224-232) in both yeast and in HIV-1 infected cells PubMed
gag-pol Interaction of EED with HIV-1 integrase stimulates the activity of integrase in vitro PubMed
matrix gag EED has negative effects on virion production due to a defect in Gag assembly. Interfering RNA targeting EED increases virion production PubMed
gag 3D structure of EED shows the binding site of the HIV-1 MA protein is mapped to position 294-309 on the linear sequence of EED PubMed
gag HIV-1 Matrix and HEED co-localize in the nucleus along with HIV-1 integrase, suggesting the occurrence of multi protein complexes involving these three proteins at early steps of the HIV-1 life cycle PubMed
gag The N-terminal region of HIV-1 Matrix (amino acids 1-40) binds to HEED (amino acids 388-403 and 495-535) PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables enzyme activator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables enzyme activator activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
contributes_to nucleosome binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription corepressor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in heterochromatin formation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of DNA-templated transcription NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in spinal cord development IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of ESC/E(Z) complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of ESC/E(Z) complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in chromosome IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
polycomb protein EED
Names
WD protein associating with integrin cytoplasmic tails 1
embryonic ectoderm development protein

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.

Genomic

  1. NG_029595.2 RefSeqGene

    Range
    5002..39059
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001308007.2 → NP_001294936.1  polycomb protein EED isoform c

    See identical proteins and their annotated locations for NP_001294936.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (c).
    Source sequence(s)
    AK292120, AW263732, BC068995, DB086430
    Consensus CDS
    CCDS76463.1
    UniProtKB/TrEMBL
    A0A9L9PY60
    Related
    ENSP00000338186.5, ENST00000351625.10
    Conserved Domains (2) summary
    sd00039
    Location:96 → 140
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:150 → 463
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  2. NM_001330334.2 → NP_001317263.1  polycomb protein EED isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks three alternate in-frame exons in the 3' coding region compared to variant 3. It encodes isoform d, which is shorter than isoform c.
    Source sequence(s)
    AP003084, AW263732
    Consensus CDS
    CCDS81612.1
    UniProtKB/TrEMBL
    E9PJK2
    Related
    ENSP00000431778.1, ENST00000528180.5
    Conserved Domains (2) summary
    sd00039
    Location:96 → 140
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:150 → 358
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  3. NM_003797.5 → NP_003788.2  polycomb protein EED isoform a

    See identical proteins and their annotated locations for NP_003788.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an in-frame exon in the 3' coding region compared to variant 3. It encodes isoform a, which is shorter than isoform c.
    Source sequence(s)
    AA811323, AK292120, AL546955, AW263732, DB086430
    Consensus CDS
    CCDS8273.1
    UniProtKB/Swiss-Prot
    A8K7V5, O00149, O75530, Q6NTH2, Q7LDA5, Q7LDG8, Q86VV2, Q9UNY7
    UniProtKB/TrEMBL
    A0A9L9PY60
    Related
    ENSP00000263360.6, ENST00000263360.11
    Conserved Domains (2) summary
    sd00039
    Location:96 → 140
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:150 → 438
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    86244753..86287615
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545330.3 → XP_011543632.1  polycomb protein EED isoform X1

    UniProtKB/TrEMBL
    B4DVW7
    Conserved Domains (3) summary
    COG2319
    Location:79 → 424
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:96 → 140
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:150 → 423
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  2. XM_017018512.3 → XP_016874001.1  polycomb protein EED isoform X3

    UniProtKB/TrEMBL
    B4DVW7

  3. XM_017018513.3 → XP_016874002.1  polycomb protein EED isoform X5

  4. XM_011545331.3 → XP_011543633.1  polycomb protein EED isoform X2

    UniProtKB/TrEMBL
    B4DVW7
    Conserved Domains (2) summary
    sd00039
    Location:96 → 140
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:81 → 264
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

  5. XM_047427801.1 → XP_047283757.1  polycomb protein EED isoform X4

  6. XM_047427802.1 → XP_047283758.1  polycomb protein EED isoform X6

  7. XM_047427803.1 → XP_047283759.1  polycomb protein EED isoform X7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    86186227..86228460
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054370359.1 → XP_054226334.1  polycomb protein EED isoform X3

  2. XM_054370361.1 → XP_054226336.1  polycomb protein EED isoform X5

  3. XM_054370357.1 → XP_054226332.1  polycomb protein EED isoform X1

  4. XM_054370358.1 → XP_054226333.1  polycomb protein EED isoform X2

  5. XM_054370360.1 → XP_054226335.1  polycomb protein EED isoform X4

  6. XM_054370362.1 → XP_054226337.1  polycomb protein EED isoform X6

  7. XM_054370363.1 → XP_054226338.1  polycomb protein EED isoform X7

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_152991.2: Suppressed sequence

    Description
    NM_152991.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75530.2 GenPept UniProtKB/Swiss-Prot:O75530

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