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CHTOP chromatin target of PRMT1 [ Homo sapiens (human) ]

Gene ID: 26097, updated on 7-Apr-2024

Summary

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Official Symbol
CHTOPprovided by HGNC
Official Full Name
chromatin target of PRMT1provided by HGNC
Primary source
HGNC:HGNC:24511
See related
Ensembl:ENSG00000160679 MIM:614206; AllianceGenome:HGNC:24511
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
FOP; SRAG; SRAG-3; SRAG-5; pp7704; C1orf77; FL-SRAG; C10orf77
Summary
This gene encodes a small nuclear protein that is characterized by an arginine and glycine rich region. This protein may have an important role in the regulation of fetal globin gene expression and in the activation of estrogen-responsive genes. A recent study reported that this protein binds 5-hydroxymethylcytosine (5hmC) and associates with an arginine methyltransferase complex (methylosome), which promotes methylation of arginine 3 of histone H4 (H4R3) and activation of genes involved in glioblastomagenesis. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Nov 2015]
Expression
Ubiquitous expression in testis (RPKM 21.4), spleen (RPKM 20.4) and 25 other tissues See more
Orthologs
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Genomic context

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See CHTOP in Genome Data Viewer
Location:
1q21.3
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (153634066..153646306)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (152771330..152783570)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (153606542..153618782)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:153588740-153589240 Neighboring gene S100 calcium binding protein A14 Neighboring gene S100 calcium binding protein A13 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:153599403-153600228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:153601055-153601878 Neighboring gene S100 calcium binding protein A1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1751 Neighboring gene SNAP associated protein Neighboring gene interleukin enhancer binding factor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1343 Neighboring gene tRNA-iMet (anticodon CAT) 1-1

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. Chromatin target of protein arginine methyltransferase regulates invasion, chemoresistance, and stemness in epithelial ovarian cancer. Feng X, et al. Biosci Rep, 2019 Apr 30. PMID 30910850, Free PMC Article
  2. Chtop (Chromatin target of Prmt1) auto-regulates its expression level via intron retention and nonsense-mediated decay of its own mRNA. Izumikawa K, et al. Nucleic Acids Res, 2016 Nov 16. PMID 27683223, Free PMC Article
  3. Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation. Maron MI, et al. Elife, 2022 Jan 5. PMID 34984976, Free PMC Article
  4. Circulating unmethylated CHTOP and INS DNA fragments provide evidence of possible islet cell death in youth with obesity and diabetes. Syed F, et al. Clin Epigenetics, 2020 Jul 31. PMID 32736653, Free PMC Article
  5. Identification of the small protein rich in arginine and glycine (SRAG): a newly identified nucleolar protein that can regulate cell proliferation. Zullo AJ, et al. J Biol Chem, 2009 May 1. PMID 19254951, Free PMC Article

See all (120) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation.
    Title: Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation.
  2. Circulating unmethylated CHTOP and INS DNA fragments provide evidence of possible islet cell death in youth with obesity and diabetes.
    Title: Circulating unmethylated CHTOP and INS DNA fragments provide evidence of possible islet cell death in youth with obesity and diabetes.
  3. These findings first suggest that CHTOP, as a highly expressed protein in ovarian cancer, is closely associated with the malignant phenotypes of epithelial ovarian cancer cells, including metastasis, chemoresistance, and stemness, which highlights a promising role of CHTOP in ovarian cancer targeted therapy.
    Title: Chromatin target of protein arginine methyltransferase regulates invasion, chemoresistance, and stemness in epithelial ovarian cancer.
  4. the cellular level of Chtop is autoregulated via Int2 retention of its own mRNA, which subsequently undergoes NMD.
    Title: Chtop (Chromatin target of Prmt1) auto-regulates its expression level via intron retention and nonsense-mediated decay of its own mRNA.
  5. Results suggest that 5hmC plays a critical role in glioblastomagenesis by recruiting the CHTOP-methylosome complex to selective sites on the chromosome, where it methylates H4R3 and activates the transcription of cancer-related genes.
    Title: 5-Hydroxymethylcytosine plays a critical role in glioblastomagenesis by recruiting the CHTOP-methylosome complex.
  6. a spatial map is produced in living cells of the sites for the interaction of two TREX subunits, Alyref and Chtop, with Nxf1.
    Title: Mapping interactions between mRNA export factors in living cells.
  7. Chtop is a component of the dynamic TREX mRNA export complex that, along with Alyref, activates the ATPase and RNA helicase activities of Uap56.
    Title: Chtop is a component of the dynamic TREX mRNA export complex.
  8. The recently identified chromatin factor Friend of Prmt1 (FOP) is a critical modulator of gamma-globin gene expression.
    Title: Fetal globin expression is regulated by Friend of Prmt1.
  9. Fop is tightly associated with chromatin, and that it is modified by both asymmetric and symmetric arginine methylation in vivo. Fop plays an important role in the ligand-dependent activation of estrogen receptor target genes, including TFF1 (pS2).
    Title: Friend of Prmt1, a novel chromatin target of protein arginine methyltransferases.
  10. The reduction in SRAG protein that occurs in proliferating cells was mapped with inhibitors to the G(2)/M phase of the cell cycle. As expected, the overexpression of SRAG reduced the percentage of cells in the G(2)/M phase and increased cell death.
    Title: Identification of the small protein rich in arginine and glycine (SRAG): a newly identified nucleolar protein that can regulate cell proliferation.
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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

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

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

  • FLJ40551, MGC86949, MGC131924, DKFZp547E1010

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables methyl-CpG binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromatin remodeling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mRNA export from nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mRNA export from nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of ATP-dependent activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of helicase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in nuclear speck IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nuclear speck IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleolus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of transcription export complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
chromatin target of PRMT1 protein
Names
friend of PRMT1 protein
small protein rich in arginine and glycine

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_030030.1 RefSeqGene

    Range
    5085..17325
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001206612.2 → NP_001193541.1  chromatin target of PRMT1 protein isoform 2

    See identical proteins and their annotated locations for NP_001193541.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate, in-frame acceptor splice site in the coding region compared to variant 1. The resulting isoform (2) is 1 aa longer than isoform 1.
    Source sequence(s)
    AI929184, BC108721, BC120961, DC387712
    Consensus CDS
    CCDS72917.1
    UniProtKB/TrEMBL
    A0AA34QVV3
    Related
    ENSP00000357679.4, ENST00000368690.7
    Conserved Domains (1) summary
    pfam13865
    Location:210 → 244
    FoP_duplication; C-terminal duplication domain of Friend of PRMT1

  2. NM_001244664.2 → NP_001231593.1  chromatin target of PRMT1 protein isoform 3

    See identical proteins and their annotated locations for NP_001231593.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two consecutive exons in the coding region, which results in a translational frameshift compared to variant 1. The resulting isoform (3) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AF318362, AL162258, BC108721, BP375397, DC387712
    Consensus CDS
    CCDS72918.1
    UniProtKB/TrEMBL
    A0A087X1B7
    Related
    ENSP00000484038.1, ENST00000614256.4

  3. NM_001317077.2 → NP_001304006.1  chromatin target of PRMT1 protein isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an in-frame coding exon in the 3' region compared to variant 1. The resulting isoform (4, also known as SRAG-5) is shorter, lacking an internal protein segment compared to isoform 1.
    Source sequence(s)
    AF261137, AI929184, BC108721
    Consensus CDS
    CCDS81380.1
    UniProtKB/Swiss-Prot
    Q9Y3Y2
    Related
    ENSP00000385228.1, ENST00000403433.5
    Conserved Domains (1) summary
    pfam13865
    Location:162 → 197
    FoP_duplication; C-terminal duplication domain of Friend of PRMT1

  4. NM_015607.4 → NP_056422.2  chromatin target of PRMT1 protein isoform 1

    See identical proteins and their annotated locations for NP_056422.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AF261137, AI929184, BC108721
    Consensus CDS
    CCDS1048.1
    UniProtKB/Swiss-Prot
    D3DV55, Q0VAQ8, Q2VPI9, Q5T7Y8, Q5T7Y9, Q5T7Z0, Q6NSM4, Q6PB28, Q8WYT9, Q9BUC5, Q9H034, Q9H2L0, Q9Y3Y2
    UniProtKB/TrEMBL
    A0AA34QVV3
    Related
    ENSP00000357683.3, ENST00000368694.8
    Conserved Domains (1) summary
    pfam13865
    Location:209 → 243
    FoP_duplication; C-terminal duplication domain of Friend of PRMT1

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

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    153634066..153646306
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017000993.2 → XP_016856482.1  chromatin target of PRMT1 protein isoform X1

    Conserved Domains (1) summary
    pfam13865
    Location:163 → 198
    FoP_duplication; C-terminal duplication domain of Friend of PRMT1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    152771330..152783570
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054335899.1 → XP_054191874.1  chromatin target of PRMT1 protein isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y3Y2.2 GenPept UniProtKB/Swiss-Prot:Q9Y3Y2

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