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MECP2 methyl-CpG binding protein 2 [ Homo sapiens (human) ]

Gene ID: 4204, updated on 5-Jul-2020

Summary

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Official Symbol
MECP2provided by HGNC
Official Full Name
methyl-CpG binding protein 2provided by HGNC
Primary source
HGNC:HGNC:6990
See related
Ensembl:ENSG00000169057 MIM:300005
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
RS; RTS; RTT; PPMX; MRX16; MRX79; MRXSL; AUTSX3; MRXS13
Summary
DNA methylation is the major modification of eukaryotic genomes and plays an essential role in mammalian development. Human proteins MECP2, MBD1, MBD2, MBD3, and MBD4 comprise a family of nuclear proteins related by the presence in each of a methyl-CpG binding domain (MBD). Each of these proteins, with the exception of MBD3, is capable of binding specifically to methylated DNA. MECP2, MBD1 and MBD2 can also repress transcription from methylated gene promoters. In contrast to other MBD family members, MECP2 is X-linked and subject to X inactivation. MECP2 is dispensible in stem cells, but is essential for embryonic development. MECP2 gene mutations are the cause of most cases of Rett syndrome, a progressive neurologic developmental disorder and one of the most common causes of cognitive disability in females. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2015]
Expression
Ubiquitous expression in ovary (RPKM 10.4), brain (RPKM 8.2) and 25 other tissues See more
Orthologs
mouse all

Genomic context

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See MECP2 in Genome Data Viewer
Location:
Xq28
Exon count:
10
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (154021573..154097717, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153287025..153363188, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene NFE2L2 motif-containing MPRA enhancer 190/191 Neighboring gene interleukin 1 receptor associated kinase 1 Neighboring gene microRNA 718 Neighboring gene opsin locus control region Neighboring gene opsin 1, long wave sensitive Neighboring gene testis expressed 28 pseudogene 2

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. Methyl-CpG-binding protein 2 (MECP2) mutation type is associated with bone disease severity in Rett syndrome. Caffarelli C, et al. BMC Med Genet, 2020 Jan 31. PMID 32005172, Free PMC Article
  2. Two novel mutations in the MECP2 gene in patients with Rett syndrome. Khalili Alashti S, et al. Gene, 2020 Mar 30. PMID 31958484
  3. Plasticity at the DNA recognition site of the MeCP2 mCG-binding domain. Lei M, et al. Biochim Biophys Acta Gene Regul Mech, 2019 Sep. PMID 31356990
  4. Characterization of large deletions of the MECP2 gene in Rett syndrome patients by gene dosage analysis. Vidal S, et al. Mol Genet Genomic Med, 2019 Aug. PMID 31206249, Free PMC Article
  5. [Rett Syndrome: MECP2 gene molecular analysis in Chilean patients]. Aron W C, et al. Rev Chil Pediatr, 2019 Apr. PMID 31095231

See all (610) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The deletions detected by multiplex ligation-dependent probe amplification (MLPA) in the gene MECP2 of 21 Rett syndrome patients.
    Title: Characterization of large deletions of the MECP2 gene in Rett syndrome patients by gene dosage analysis.
  2. As a result, genomic copy numbers of MECP2 were rapidly and precisely detected by the dPCR system established in this study. This method can be widely applied as a diagnostic method to confirm CNVs on other chromosomal regions
    Title: Establishment of a simple and rapid method to detect MECP2 duplications using digital polymerase chain reaction.
  3. miR-212-3p may be involved in infection-induced preterm labor through MeCP2, and it is a promoting molecule and novel target for the diagnosis and treatment of preterm labor in the future.
    Title: Pro-inflammatory cytokine-induced microRNA-212-3p expression promotes myocyte contraction via methyl-CpG-binding protein 2: a novel mechanism for infection-related preterm parturition.
  4. our results suggest that MeCP2 promotes Endothelial-to-mesenchymal transition by epigenetically silencing BMP7 in endothelial cells and MeCP2 may be a target for diseases driven by Endothelial-to-mesenchymal transitio
    Title: MeCP2 promotes endothelial-to-mesenchymal transition in human endothelial cells by downregulating BMP7 expression.
  5. the evolution and molecular features of MeCP2, CDKL5, and FOXG1 and their binding partners, were analyzed.
    Title: In Silico Study of Rett Syndrome Treatment-Related Genes, <i>MECP2</i>, <i>CDKL5</i>, and <i>FOXG1</i>, by Evolutionary Classification and Disordered Region Assessment.
  6. DNA topology can shape non-CG DNA methylation across the genome to dictate MeCP2-mediated enhancer regulation in the brain.
    Title: MeCP2 Represses Enhancers through Chromosome Topology-Associated DNA Methylation.
  7. In males, mutations in MECP2 are compatible with life and result in a spectrum of neurodevelopmental features.
    Title: The array of clinical phenotypes of males with mutations in Methyl-CpG binding protein 2.
  8. This study confirms that MECP2 mutation type is a strong predictor of disease severity in subjects with Rett syndrome. In particular, the subjects with more severe mutation present a greater deterioration of bone status, and a higher prevalence of scoliosis and inability to walk.
    Title: Methyl-CpG-binding protein 2 (MECP2) mutation type is associated with bone disease severity in Rett syndrome.
  9. about 70% of mutations are found in exon 3 and 4 of the MECP2 gene, and mutations in exon 4 are more common than other exons. Therefore, it is recommended that exon 4 to be a priority for screening the genetic analysis of RTT patients
    Title: Two novel mutations in the MECP2 gene in patients with Rett syndrome.
  10. High MECP2 expression is associated with epithelial-mesenchymal transition in glioma.
    Title: A central role for MeCP2 in the epigenetic repression of miR-200c during epithelial-to-mesenchymal transition of glioma.
Submit: New GeneRIF Correction See all GeneRIFs (464)

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

Copy number response

Description
Copy number response
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-05)

ClinGen Genome Curation Page
Triplosensitivity

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-05)

ClinGen Genome Curation Page

NHGRI GWAS Catalog

Description
Common variants on Xq28 conferring risk of schizophrenia in Han Chinese.
NHGRI GWA Catalog
Genetics of rheumatoid arthritis contributes to biology and drug discovery.
NHGRI GWA Catalog
Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network.
NHGRI GWA Catalog

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 MECP2 mRNA is selectively retained in HIV-1 Nef-expressing cellular exosomes, and eight miRNAs (miR-19a, miR-29b, miR-34a*, miR-146b, miR-181a, miR181c, miR-195, and let-7c) which target MECP2 mRNA are selectively secreted in exosomes from these cells 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

Clone Names

  • DKFZp686A24160

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
DNA-binding transcription repressor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
  
RNA binding HDA PubMed 
chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
double-stranded methylated DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
double-stranded methylated DNA binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
mRNA binding IEA
Inferred from Electronic Annotation
more info
  
methyl-CpG binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
protein N-terminus binding IPI
Inferred from Physical Interaction
more info
 PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
protein domain specific binding IPI
Inferred from Physical Interaction
more info
 PubMed 
siRNA binding IEA
Inferred from Electronic Annotation
more info
  
transcription corepressor activity TAS
Traceable Author Statement
more info
 PubMed 
transcription factor binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
adult locomotory behavior IEA
Inferred from Electronic Annotation
more info
  
behavioral fear response IEA
Inferred from Electronic Annotation
more info
  
cardiolipin metabolic process IEA
Inferred from Electronic Annotation
more info
  
catecholamine secretion IEA
Inferred from Electronic Annotation
more info
  
cellular biogenic amine metabolic process IEA
Inferred from Electronic Annotation
more info
  
cerebellum development IEA
Inferred from Electronic Annotation
more info
  
chromatin silencing IEA
Inferred from Electronic Annotation
more info
  
dendrite development IEA
Inferred from Electronic Annotation
more info
  
excitatory postsynaptic potential IEA
Inferred from Electronic Annotation
more info
  
glucocorticoid metabolic process IEA
Inferred from Electronic Annotation
more info
  
glutamine metabolic process IEA
Inferred from Electronic Annotation
more info
  
histone acetylation IEA
Inferred from Electronic Annotation
more info
  
histone methylation IEA
Inferred from Electronic Annotation
more info
  
inositol metabolic process IEA
Inferred from Electronic Annotation
more info
  
long-term memory IEA
Inferred from Electronic Annotation
more info
  
long-term synaptic potentiation IEA
Inferred from Electronic Annotation
more info
  
mitochondrial electron transport, ubiquinol to cytochrome c IEA
Inferred from Electronic Annotation
more info
  
mitotic spindle organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
negative regulation of angiogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
negative regulation of blood vessel endothelial cell migration IDA
Inferred from Direct Assay
more info
 PubMed 
negative regulation of gene expression IDA
Inferred from Direct Assay
more info
 PubMed 
negative regulation of neuron apoptotic process IEA
Inferred from Electronic Annotation
more info
  
negative regulation of smooth muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
  
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
  
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
 PubMed 
neurological system process involved in regulation of systemic arterial blood pressure IEA
Inferred from Electronic Annotation
more info
  
neuron maturation IEA
Inferred from Electronic Annotation
more info
  
pathogenesis IEA
Inferred from Electronic Annotation
more info
  
phosphatidylcholine metabolic process IEA
Inferred from Electronic Annotation
more info
  
positive regulation of DNA methylation IDA
Inferred from Direct Assay
more info
 PubMed 
positive regulation of G2/M transition of mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
 PubMed 
positive regulation of cell proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
positive regulation of histone H3-K9 trimethylation IEA
Inferred from Electronic Annotation
more info
  
positive regulation of microtubule nucleation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
positive regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
  
post-embryonic development IEA
Inferred from Electronic Annotation
more info
  
proprioception IEA
Inferred from Electronic Annotation
more info
  
protein localization IEA
Inferred from Electronic Annotation
more info
  
regulation of gene expression by genetic imprinting IEA
Inferred from Electronic Annotation
more info
  
regulation of respiratory gaseous exchange by neurological system process IEA
Inferred from Electronic Annotation
more info
  
respiratory gaseous exchange IEA
Inferred from Electronic Annotation
more info
  
response to hypoxia IEA
Inferred from Electronic Annotation
more info
  
sensory perception of pain IEA
Inferred from Electronic Annotation
more info
  
social behavior IEA
Inferred from Electronic Annotation
more info
  
startle response IEA
Inferred from Electronic Annotation
more info
  
synapse assembly IEA
Inferred from Electronic Annotation
more info
  
transcription initiation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
  
ventricular system development IEA
Inferred from Electronic Annotation
more info
  
visual learning IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
centrosome IMP
Inferred from Mutant Phenotype
more info
 PubMed 
cytosol IEA
Inferred from Electronic Annotation
more info
  
extracellular space HDA PubMed 
heterochromatin IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
heterochromatin IDA
Inferred from Direct Assay
more info
 PubMed 
host cell nucleus IEA
Inferred from Electronic Annotation
more info
  
mitochondrion IEA
Inferred from Electronic Annotation
more info
  
nucleoplasm IDA
Inferred from Direct Assay
more info
  
nucleoplasm TAS
Traceable Author Statement
more info
  
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
postsynapse IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
methyl-CpG-binding protein 2
Names
meCp-2 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_007107.2 RefSeqGene

    Range
    44391..120315
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001110792.2 → NP_001104262.1  methyl-CpG-binding protein 2 isoform 2

    See identical proteins and their annotated locations for NP_001104262.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), also known as MECP2B, lacks exon 2. Translation is reported to initiate in the first exon resulting in a protein isoform (2) with a distinct N-terminus. This transcript is reported to be abundant in the central nervous system (PMID: 15034579, 17171659).
    Source sequence(s)
    AF030876, BC011612, BX538060, U52112
    Consensus CDS
    CCDS48193.1
    UniProtKB/Swiss-Prot
    P51608
    UniProtKB/TrEMBL
    A0A140VKC4, Q59FJ6
    Related
    ENSP00000395535.2, ENST00000453960.7
    Conserved Domains (1) summary
    smart00391
    Location:104 → 181
    MBD; Methyl-CpG binding domain

  2. NM_001316337.2 → NP_001303266.1  methyl-CpG-binding protein 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) includes exon 2 and an additional exon, resulting in the use of a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1. Variants 3-7 all encode the same isoform (3).
    Source sequence(s)
    AB209464, AF030876, BC011612, BI767019, U52112
    UniProtKB/Swiss-Prot
    P51608
    UniProtKB/TrEMBL
    Q59FJ6
    Conserved Domains (1) summary
    smart00391
    Location:1 → 76
    MBD; Methyl-CpG binding domain

  3. NM_001369391.2 → NP_001356320.1  methyl-CpG-binding protein 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) includes exon 2 and some additional exons, resulting in the use of a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1. Variants 3-7 all encode the same isoform (3).
    Source sequence(s)
    AC244097, AF030876, U52112
    Conserved Domains (1) summary
    smart00391
    Location:1 → 76
    MBD; Methyl-CpG binding domain

  4. NM_001369392.2 → NP_001356321.1  methyl-CpG-binding protein 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) includes exon 2 and an additional exon, resulting in the use of a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1. Variants 3-7 all encode the same isoform (3).
    Source sequence(s)
    AC244097, AF030876, U52112
    Conserved Domains (1) summary
    smart00391
    Location:1 → 76
    MBD; Methyl-CpG binding domain

  5. NM_001369393.2 → NP_001356322.1  methyl-CpG-binding protein 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks exon 2 and contains an additional exon, resulting in the use of a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1. Variants 3-7 all encode the same isoform (3).
    Source sequence(s)
    AC244097, AF030876, U52112
    Conserved Domains (1) summary
    smart00391
    Location:1 → 76
    MBD; Methyl-CpG binding domain

  6. NM_001369394.2 → NP_001356323.1  methyl-CpG-binding protein 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR and coding sequence, compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1. Variants 3-7 all encode the same isoform (3).
    Source sequence(s)
    AC244097, AF030876, U52112
    Conserved Domains (1) summary
    smart00391
    Location:1 → 76
    MBD; Methyl-CpG binding domain

  7. NM_004992.4 → NP_004983.1  methyl-CpG-binding protein 2 isoform 1

    See identical proteins and their annotated locations for NP_004983.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1), also known as MECP2A, includes exon 2. Translation is reported to initiate in exon 2 resulting in a protein isoform (1) with a distinct N-terminus.
    Source sequence(s)
    AC244097, AF030876, U52112
    Consensus CDS
    CCDS14741.1
    UniProtKB/Swiss-Prot
    P51608
    UniProtKB/TrEMBL
    D3YJ43, Q59FJ6
    Related
    ENSP00000301948.6, ENST00000303391.11
    Conserved Domains (1) summary
    smart00391
    Location:92 → 169
    MBD; Methyl-CpG binding domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    154021573..154097717 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024452383.1 → XP_024308151.1  methyl-CpG-binding protein 2 isoform X1

    Conserved Domains (1) summary
    smart00391
    Location:1 → 76
    MBD; Methyl-CpG binding domain

  2. XM_011531166.2 → XP_011529468.1  methyl-CpG-binding protein 2 isoform X1

    See identical proteins and their annotated locations for XP_011529468.1

    Conserved Domains (1) summary
    smart00391
    Location:1 → 76
    MBD; Methyl-CpG binding domain

  3. XM_006724819.3 → XP_006724882.1  methyl-CpG-binding protein 2 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P51608.1 GenPept UniProtKB/Swiss-Prot:P51608

Gene LinkOut

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