EED embryonic ectoderm development [Homo sapiens (human)] - Gene

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; 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: mouse all
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Genomic context

Location:: 11q14.2

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (86244753..86287615)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (86186227..86228460)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (85955795..85989852)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
Embryonic Ectoderm Development (EED) as a Novel Target for Cancer Treatment.
Title: Embryonic Ectoderm Development (EED) as a Novel Target for Cancer Treatment.
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.
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.
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.
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.
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.
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.
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	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables enzyme activator activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone methyltransferase activity	IDA Inferred from Direct Assay 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 chromatin remodeling	IEA Inferred from Electronic Annotation more info
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

NG_029595.2 RefSeqGene

Range

5002..39059

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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 ...
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 ...
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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

86244753..86287615

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

B4DVW7
XM_017018513.3 → XP_016874002.1 polycomb protein EED isoform X5
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 ...
XM_047427801.1 → XP_047283757.1 polycomb protein EED isoform X4
XM_047427802.1 → XP_047283758.1 polycomb protein EED isoform X6
XM_047427803.1 → XP_047283759.1 polycomb protein EED isoform X7

Alternate T2T-CHM13v2.0

Genomic

NC_060935.1 Alternate T2T-CHM13v2.0

Range

86186227..86228460

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054370359.1 → XP_054226334.1 polycomb protein EED isoform X3
XM_054370361.1 → XP_054226336.1 polycomb protein EED isoform X5
XM_054370357.1 → XP_054226332.1 polycomb protein EED isoform X1
XM_054370358.1 → XP_054226333.1 polycomb protein EED isoform X2
XM_054370360.1 → XP_054226335.1 polycomb protein EED isoform X4
XM_054370362.1 → XP_054226337.1 polycomb protein EED isoform X6
XM_054370363.1 → XP_054226338.1 polycomb protein EED isoform X7

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

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.