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EED embryonic ectoderm development [ Homo sapiens (human) ]

Gene ID: 8726, updated on 6-Jan-2019

Summary

Official Symbol
EEDprovided by HGNC
Official Full Name
embryonic ectoderm developmentprovided by HGNC
Primary source
HGNC:HGNC:3188
See related
Ensembl:ENSG00000074266 MIM:605984
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

Genomic context

See EED in Genome Data Viewer
Location:
11q14.2
Exon count:
15
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (86244384..86285420)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (85955586..85989785)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984426 Neighboring gene farnesyltransferase, CAAX box, alpha pseudogene 1 Neighboring gene immunoglobin superfamily member 21 pseudogene Neighboring gene microRNA 6755 Neighboring gene SET pseudogene 17 Neighboring gene Hikeshi, heat shock protein nuclear import factor Neighboring gene RNA, 7SL, cytoplasmic 225, pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

Related articles in PubMed

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

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 BioSystems

  • Activation of HOX genes during differentiation, organism-specific biosystem (from REACTOME)
    Activation of HOX genes during differentiation, organism-specific biosystemHox genes encode proteins that contain the DNA-binding homeobox motif and control early patterning of segments in the embryo as well as later events in development (reviewed in Rezsohazy et al. 2015)...
  • Activation of anterior HOX genes in hindbrain development during early embryogenesis, organism-specific biosystem (from REACTOME)
    Activation of anterior HOX genes in hindbrain development during early embryogenesis, organism-specific biosystemIn mammals, anterior Hox genes may be defined as paralog groups 1 to 4 (Natale et al. 2011), which are involved in development of the hindbrain through sequential expression in the rhombomeres, trans...
  • Cellular Senescence, organism-specific biosystem (from REACTOME)
    Cellular Senescence, organism-specific biosystemCellular senescence involves irreversible growth arrest accompanied by phenotypic changes such as enlarged morphology, reorganization of chromatin through formation of senescence-associated heterochr...
  • Cellular responses to stress, organism-specific biosystem (from REACTOME)
    Cellular responses to stress, organism-specific biosystemCells are subject to external molecular and physical stresses such as foreign molecules that perturb metabolic or signaling processes, and changes in temperature or pH. The ability of cells and tissu...
  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • Developmental Biology, organism-specific biosystem (from REACTOME)
    Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
  • Epigenetic regulation of gene expression, organism-specific biosystem (from REACTOME)
    Epigenetic regulation of gene expression, organism-specific biosystemEpigenetic processes regulate gene expression by modulating the frequency, rate, or extent of gene expression in a mitotically or meiotically heritable way that does not entail a change in the DNA se...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Histone Modifications, organism-specific biosystem (from WikiPathways)
    Histone Modifications, organism-specific biosystemHistones can undergo many post-translational modifications that are involved in transcription regulation. This pathway provides an overview of various modifications for histones H3 and H4 and the en...
  • Interactome of polycomb repressive complex 2 (PRC2), organism-specific biosystem (from WikiPathways)
    Interactome of polycomb repressive complex 2 (PRC2), organism-specific biosystemA proposed interactome of Polycomb repressive complex 2 (PRC2), based on proteomics.
  • Oxidative Stress Induced Senescence, organism-specific biosystem (from REACTOME)
    Oxidative Stress Induced Senescence, organism-specific biosystemOxidative stress, caused by increased concentration of reactive oxygen species (ROS) in the cell, can happen as a consequence of mitochondrial dysfunction induced by the oncogenic RAS (Moiseeva et al...
  • PKMTs methylate histone lysines, organism-specific biosystem (from REACTOME)
    PKMTs methylate histone lysines, organism-specific biosystemLysine methyltransferases (KMTs) and arginine methyltransferases (RMTs) have a common mechanism of catalysis. Both families transfer a methyl group from a common donor, S-adenosyl-L-methionine (SAM),...
  • PRC2 methylates histones and DNA, organism-specific biosystem (from REACTOME)
    PRC2 methylates histones and DNA, organism-specific biosystemPolycomb group proteins are responsible for the heritable repression of genes during development (Lee et al. 2006, Ku et al. 2008, reviewed in Simon and Kingston 2009, Margueron and Reinberg 2011, Di...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA polymerase II proximal promoter sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
contributes_to histone methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to histone methyltransferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
contributes_to histone methyltransferase activity (H3-K27 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
contributes_to histone methyltransferase activity (H3-K27 specific) IMP
Inferred from Mutant Phenotype
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
contributes_to nucleosome binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
 
chromatin silencing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone H3-K27 methylation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of G0 to G1 transition TAS
Traceable Author Statement
more info
 
negative regulation of gene expression, epigenetic TAS
Traceable Author Statement
more info
 
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
positive regulation of histone H3-K27 methylation IEA
Inferred from Electronic Annotation
more info
 
regulation of adaxial/abaxial pattern formation IEA
Inferred from Electronic Annotation
more info
 
regulation of gene expression by genetic imprinting IEA
Inferred from Electronic Annotation
more info
 
spinal cord development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
ESC/E(Z) complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ESC/E(Z) complex IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus NAS
Non-traceable Author Statement
more info
PubMed 
pronucleus IEA
Inferred from Electronic Annotation
more info
 
sex chromatin IEA
Inferred from Electronic Annotation
more info
 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_029595.1 RefSeqGene

    Range
    4621..39047
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001308007.1NP_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/Swiss-Prot
    O75530
    Related
    ENSP00000338186.5, ENST00000351625.10
    Conserved Domains (2) summary
    sd00039
    Location:96140
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:150463
    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_001330334.1NP_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:96140
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:150358
    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_003797.5NP_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
    O75530
    Related
    ENSP00000263360.6, ENST00000263360.10
    Conserved Domains (2) summary
    sd00039
    Location:96140
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:150438
    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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

    Range
    86244384..86285420
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545330.2XP_011543632.1  polycomb protein EED isoform X1

    Conserved Domains (3) summary
    COG2319
    Location:79424
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:96140
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:150423
    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_017018513.2XP_016874002.1  polycomb protein EED isoform X4

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

  4. XM_011545331.2XP_011543633.1  polycomb protein EED isoform X2

    Conserved Domains (3) summary
    COG2319
    Location:79326
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:96140
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:81264
    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 ...

RNA

  1. XR_001748022.2 RNA Sequence

  2. XR_247215.4 RNA Sequence

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.
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