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Smchd1 SMC hinge domain containing 1 [ Mus musculus (house mouse) ]

Gene ID: 74355, updated on 2-Nov-2024

Summary

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Official Symbol
Smchd1provided by MGI
Official Full Name
SMC hinge domain containing 1provided by MGI
Primary source
MGI:MGI:1921605
See related
Ensembl:ENSMUSG00000024054 AllianceGenome:MGI:1921605
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
MommeD1; mKIAA0650; 4931400A14Rik
Summary
Enables ATP hydrolysis activity and protein homodimerization activity. Acts upstream of or within inactivation of paternal X chromosome by genomic imprinting. Located in Barr body. Is expressed in several structures, including blastocyst and genitourinary system. Human ortholog(s) of this gene implicated in facioscapulohumeral muscular dystrophy 2. Orthologous to human SMCHD1 (structural maintenance of chromosomes flexible hinge domain containing 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 9.1), placenta adult (RPKM 7.4) and 24 other tissues See more
Orthologs
human all
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Genomic context

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See Smchd1 in Genome Data Viewer
Location:
17 E1.3; 17 41.87 cM
Exon count:
48
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (71651484..71782361, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (71344489..71475366, complement)

Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene elastin microfibril interfacer 2 Neighboring gene RIKEN cDNA 4930471L23 gene Neighboring gene STARR-seq mESC enhancer starr_43173 Neighboring gene ubiquitin specific peptidase 16 pseudogene Neighboring gene STARR-positive B cell enhancer mm9_chr17:71824608-71824909 Neighboring gene ATP synthase, H+ transporting mitochondrial F1 complex, beta subunit pseudogene Neighboring gene STARR-positive B cell enhancer ABC_E11650 Neighboring gene ubiquitin fusion degradation 1 like pseudogene Neighboring gene STARR-positive B cell enhancer ABC_E1200 Neighboring gene NDC80 kinetochore complex component

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease. Tapia Del Fierro A, et al. Nat Commun, 2023 Sep 25. PMID 37749075, Free PMC Article
  2. Transcriptional profiling of the epigenetic regulator Smchd1. Liu R, et al. Genom Data, 2016 Mar. PMID 26981392, Free PMC Article
  3. SmcHD1 underlies the formation of H3K9me3 blocks on the inactive X chromosome in mice. Ichihara S, et al. Development, 2022 Aug 1. PMID 35831949
  4. The chromosomal protein SMCHD1 regulates DNA methylation and the 2c-like state of embryonic stem cells by antagonizing TET proteins. Huang Z, et al. Sci Adv, 2021 Jan. PMID 33523915, Free PMC Article
  5. Smchd1 Targeting to the Inactive X Is Dependent on the Xist-HnrnpK-PRC1 Pathway. Jansz N, et al. Cell Rep, 2018 Nov 13. PMID 30428357

See all (62) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease.
    Title: SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease.
  2. SmcHD1 underlies the formation of H3K9me3 blocks on the inactive X chromosome in mice.
    Title: SmcHD1 underlies the formation of H3K9me3 blocks on the inactive X chromosome in mice.
  3. Maternal SMCHD1 regulates Hox gene expression and patterning in the mouse embryo.
    Title: Maternal SMCHD1 regulates Hox gene expression and patterning in the mouse embryo.
  4. Maternal SMCHD1 controls both imprinted Xist expression and imprinted X chromosome inactivation.
    Title: Maternal SMCHD1 controls both imprinted Xist expression and imprinted X chromosome inactivation.
  5. The chromosomal protein SMCHD1 regulates DNA methylation and the 2c-like state of embryonic stem cells by antagonizing TET proteins.
    Title: The chromosomal protein SMCHD1 regulates DNA methylation and the 2c-like state of embryonic stem cells by antagonizing TET proteins.
  6. Crystal structure of the hinge domain of Smchd1 reveals its dimerization mode and nucleic acid-binding residues.
    Title: Crystal structure of the hinge domain of Smchd1 reveals its dimerization mode and nucleic acid-binding residues.
  7. consistent with a role for SMCHD1 in promoting exit from the EGA1 state
    Title: SMCHD1 terminates the first embryonic genome activation event in mouse two-cell embryos and contributes to a transcriptionally repressive state.
  8. our study demonstrates preservation of XCI in arhinia and FSHD2, and implicates SMCHD1 in the regulation of the 3D organization of select autosomal gene clusters
    Title: Role of the Chromosome Architectural Factor SMCHD1 in X-Chromosome Inactivation, Gene Regulation, and Disease in Humans.
  9. This work adds Smchd1 to the PRC1 silencing pathway for X chromosome inactivation.
    Title: Smchd1 Targeting to the Inactive X Is Dependent on the Xist-HnrnpK-PRC1 Pathway.
  10. data suggest that Smchd1 is able to insulate chromatin, thereby limiting access to other chromatin-modifying proteins
    Title: Smchd1 regulates long-range chromatin interactions on the inactive X chromosome and at Hox clusters.
Submit: New GeneRIF Correction See all GeneRIFs (23)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

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 MGI

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP hydrolysis activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromosome organization IEA
Inferred from Electronic Annotation
more info
  
involved_in dosage compensation by inactivation of X chromosome ISO
Inferred from Sequence Orthology
more info
  
involved_in double-strand break repair IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within inactivation of paternal X chromosome by genomic imprinting IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of double-strand break repair via homologous recombination ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of double-strand break repair via homologous recombination ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in nose development ISO
Inferred from Sequence Orthology
more info
  
involved_in nose development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of DNA repair ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of DNA repair ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of double-strand break repair via nonhomologous end joining ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of double-strand break repair via nonhomologous end joining ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
is_active_in Barr body IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Barr body IDA
Inferred from Direct Assay
more info
 PubMed 
located_in Barr body ISO
Inferred from Sequence Orthology
more info
  
located_in chromosome, telomeric region IEA
Inferred from Electronic Annotation
more info
  
colocalizes_with chromosome, telomeric region ISO
Inferred from Sequence Orthology
more info
  
located_in site of double-strand break ISO
Inferred from Sequence Orthology
more info
  
located_in site of double-strand break ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
structural maintenance of chromosomes flexible hinge domain-containing protein 1
Names
SMC hinge domain-containing protein 1

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_028887.4 → NP_083163.3  structural maintenance of chromosomes flexible hinge domain-containing protein 1

    See identical proteins and their annotated locations for NP_083163.3

    Status: VALIDATED

    Source sequence(s)
    AC107664, AC126942
    Consensus CDS
    CCDS28958.2
    UniProtKB/Swiss-Prot
    Q6P5D8, Q6PDM8, Q6PE93, Q6ZQ78, Q811H3, Q8BP09, Q9D4M7
    Related
    ENSMUSP00000121835.2, ENSMUST00000127430.2
    Conserved Domains (2) summary
    smart00968
    Location:1721 → 1847
    SMC_hinge; SMC proteins Flexible Hinge Domain
    cl00075
    Location:143 → 275
    HATPase_c; Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000083.7 Reference GRCm39 C57BL/6J

    Range
    71651484..71782361 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030250119.1 → XP_030105979.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X1

    Conserved Domains (2) summary
    smart00968
    Location:1470 → 1596
    SMC_hinge; SMC proteins Flexible Hinge Domain
    COG1196
    Location:1368 → 1709
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6P5D8.2 GenPept UniProtKB/Swiss-Prot:Q6P5D8

Gene LinkOut

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