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

    Gene ID: 26097, updated on 3-Nov-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (153634066..153646306)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (152771330..152783570)
    RS_2024_09 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 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 (139) 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.
    Submit: New GeneRIF Correction

    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_2024_08

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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