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ZCCHC4 zinc finger CCHC-type containing 4 [ Homo sapiens (human) ]

Gene ID: 29063, updated on 2-Nov-2024

Summary

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Official Symbol
ZCCHC4provided by HGNC
Official Full Name
zinc finger CCHC-type containing 4provided by HGNC
Primary source
HGNC:HGNC:22917
See related
Ensembl:ENSG00000168228 MIM:611792; AllianceGenome:HGNC:22917
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ZGRF4; HSPC052
Summary
Enables S-adenosyl-L-methionine binding activity; rRNA (adenine-N6-)-methyltransferase activity; and zinc ion binding activity. Involved in positive regulation of translation and rRNA methylation. Located in cytoplasm and nucleolus. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in testis (RPKM 1.4), ovary (RPKM 1.3) and 25 other tissues See more
Orthologs
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Genomic context

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See ZCCHC4 in Genome Data Viewer
Location:
4p15.2
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (25312774..25370383)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (25294601..25352222)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (25314396..25372005)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900916 Neighboring gene phosphatidylinositol 4-kinase type 2 beta Neighboring gene uncharacterized LOC124900685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21373 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21374 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:25314050-25314926 Neighboring gene uncharacterized LOC124900686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21376 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21377 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15324 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21379 Neighboring gene anaphase promoting complex subunit 4 Neighboring gene uncharacterized LOC105374536 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15325 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:25451941-25452758 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:25458193-25458692

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. The epigenetic downregulation of LncGHRLOS mediated by RNA m6A methylase ZCCHC4 promotes colorectal cancer tumorigenesis. Chen K, et al. J Exp Clin Cancer Res, 2024 Feb 7. PMID 38326863, Free PMC Article
  2. RNA-binding protein ZCCHC4 promotes human cancer chemoresistance by disrupting DNA-damage-induced apoptosis. Zhu H, et al. Signal Transduct Target Ther, 2022 Jul 20. PMID 35853866, Free PMC Article
  3. ZCCHC4 Promotes Osteosarcoma Progression by Upregulating ITGB1. Luo L, et al. Crit Rev Eukaryot Gene Expr, 2023. PMID 37606162
  4. N(6-)Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Ma H, et al. Nat Chem Biol, 2019 Jan. PMID 30531910, Free PMC Article
  5. Structure and regulation of ZCCHC4 in m(6)A-methylation of 28S rRNA. Ren W, et al. Nat Commun, 2019 Nov 6. PMID 31695039, Free PMC Article

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The epigenetic downregulation of LncGHRLOS mediated by RNA m6A methylase ZCCHC4 promotes colorectal cancer tumorigenesis.
    Title: The epigenetic downregulation of LncGHRLOS mediated by RNA m6A methylase ZCCHC4 promotes colorectal cancer tumorigenesis.
  2. ZCCHC4 Promotes Osteosarcoma Progression by Upregulating ITGB1.
    Title: ZCCHC4 Promotes Osteosarcoma Progression by Upregulating ITGB1.
  3. RNA-binding protein ZCCHC4 promotes human cancer chemoresistance by disrupting DNA-damage-induced apoptosis.
    Title: RNA-binding protein ZCCHC4 promotes human cancer chemoresistance by disrupting DNA-damage-induced apoptosis.
  4. In summary, we establish ZCCHC4 as the enzyme responsible for m6A modification of human 28S rRNA, and demonstrate its functional significance in mRNA translation.
    Title: The human methyltransferase ZCCHC4 catalyses N6-methyladenosine modification of 28S ribosomal RNA.
  5. 3.1 A-resolution crystal structure of human CCHC zinc finger-containing protein ZCCHC4, a 28S rRNA-specific m(6)A methyltransferase, bound to S-adenosyl-L-homocysteine. Mutational and enzymatic analyses further substantiate the molecular basis for ZCCHC4-RNA recognition and a role of the stem-loop structure within substrate in governing the substrate specificity.
    Title: Structure and regulation of ZCCHC4 in m(6)A-methylation of 28S rRNA.
  6. ZCCHC4 protein is overexpressed in hepatocellular carcinoma tumors.ZCCHC4 is an m6A RNA methyltransferase.
    Title: N(6-)Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC21108

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables S-adenosyl-L-methionine binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
enables rRNA (adenine-N6-)-methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables rRNA (adenine-N6-)-methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in positive regulation of translation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in rRNA methylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in rRNA methylation IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
rRNA N6-adenosine-methyltransferase ZCCHC4
Names
DHHC domain-containing zinc finger protein
zinc finger CCHC domain-containing protein 4
zinc finger, CCHC domain containing 4
zinc finger, GRF-type containing 4
NP_001305077.1
NP_079212.2
XP_011512137.1
XP_016863618.1
XP_054205811.1
XP_054205812.1

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_001318148.2 → NP_001305077.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks several exons and includes an alternate 3' terminal exon, compared to variant 1. It encodes isoform 2 which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC108218, AK309675, BG719159, CA952098
    Conserved Domains (2) summary
    pfam06839
    Location:38 → 82
    zf-GRF; GRF zinc finger
    pfam10237
    Location:172 → 329
    N6-adenineMlase; Probable N6-adenine methyltransferase

  2. NM_024936.3 → NP_079212.2  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform 1

    See identical proteins and their annotated locations for NP_079212.2

    Status: VALIDATED

    Description
    Transcript Variant: Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK026677, AY629351, BG719159
    Consensus CDS
    CCDS43218.1
    UniProtKB/Swiss-Prot
    B2RXF6, B4DRD8, B7ZW20, Q5IW78, Q96AN7, Q9H5U6
    Related
    ENSP00000303468.4, ENST00000302874.9
    Conserved Domains (3) summary
    pfam06839
    Location:38 → 82
    zf-GRF; GRF zinc finger
    pfam10237
    Location:172 → 329
    N6-adenineMlase; Probable N6-adenine methyltransferase
    cl19890
    Location:409 → 438
    zf-DHHC; DHHC palmitoyltransferase

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    25312774..25370383
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011513835.3 → XP_011512137.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform X1

    Conserved Domains (3) summary
    pfam06839
    Location:38 → 82
    zf-GRF; GRF zinc finger
    pfam10237
    Location:166 → 294
    N6-adenineMlase; Probable N6-adenine methyltransferase
    cl19890
    Location:424 → 453
    DHHC; DHHC palmitoyltransferase

  2. XM_017008129.3 → XP_016863618.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform X2

    Conserved Domains (3) summary
    pfam06839
    Location:38 → 82
    zf-GRF; GRF zinc finger
    pfam10237
    Location:166 → 256
    N6-adenineMlase; Probable N6-adenine methyltransferase
    cl19890
    Location:325 → 354
    DHHC; DHHC palmitoyltransferase

RNA

  1. XR_925324.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    25294601..25352222
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054349836.1 → XP_054205811.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform X1

  2. XM_054349837.1 → XP_054205812.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform X2

RNA

  1. XR_008486972.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_014150.1: Suppressed sequence

    Description
    NM_014150.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H5U6.3 GenPept UniProtKB/Swiss-Prot:Q9H5U6

Gene LinkOut

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