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    NAA60 N-alpha-acetyltransferase 60, NatF catalytic subunit [ Homo sapiens (human) ]

    Gene ID: 79903, updated on 2-Nov-2024

    Summary

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    Official Symbol
    NAA60provided by HGNC
    Official Full Name
    N-alpha-acetyltransferase 60, NatF catalytic subunitprovided by HGNC
    Primary source
    HGNC:HGNC:25875
    See related
    Ensembl:ENSG00000122390 MIM:614246; AllianceGenome:HGNC:25875
    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
    HAT4; NatF; IBGC9; NAT15; hNaa60
    Summary
    This gene encodes an enzyme that localizes to the Golgi apparatus, where it transfers an acetyl group to the N-terminus of free proteins. This enzyme acts on histones, and its activity is important for chromatin assembly and chromosome integrity. Alternative splicing and the use of alternative promoters results in multiple transcript variants. The upstream promoter is located in a differentially methylated region (DMR) and undergoes imprinting; transcript variants originating from this position are expressed from the maternal allele. [provided by RefSeq, Nov 2015]
    Expression
    Ubiquitous expression in kidney (RPKM 15.2), duodenum (RPKM 14.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NAA60 in Genome Data Viewer
    Location:
    16p13.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (3443611..3486963)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (3470880..3514228)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (3493611..3536963)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:3450765-3451264 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7133 Neighboring gene zinc finger protein 174 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:3470303-3470585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3481451-3481952 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10322 Neighboring gene zinc finger protein 597 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7135 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_43328 and experimental_43330 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_43334 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_43335 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_43338 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3517275-3517812 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3519547-3520264 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_43345 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_43346 Neighboring gene Sharpr-MPRA regulatory region 11363 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:3543048-3543257 Neighboring gene microRNA 6126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10323 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3551746-3552263 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3552264-3552780 Neighboring gene chromosome 16 open reading frame 90 Neighboring gene ribosomal protein L18 pseudogene 12 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10325 Neighboring gene clusterin associated protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3580705-3581205 Neighboring gene uncharacterized LOC101929732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:3594423-3594923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10326 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3602829-3603548 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3603549-3604269 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:3604270-3604989 Neighboring gene NLR family CARD domain containing 3

    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. NAA60 (HAT4): the newly discovered bi-functional Golgi member of the acetyltransferase family. Donnarumma F, et al. Clin Epigenetics, 2022 Dec 21. PMID 36539894, Free PMC Article
    2. Biallelic NAA60 variants with impaired n-terminal acetylation capacity cause autosomal recessive primary familial brain calcifications. Chelban V, et al. Nat Commun, 2024 Mar 13. PMID 38480682, Free PMC Article
    3. Molecular determinants of the N-terminal acetyltransferase Naa60 anchoring to the Golgi membrane. Aksnes H, et al. J Biol Chem, 2017 Apr 21. PMID 28196861, Free PMC Article
    4. Holding it together: Naa60 at the Golgi. Aksnes H, et al. Oncotarget, 2015 Jun 30. PMID 26164078, Free PMC Article
    5. Methylation screening of reciprocal genome-wide UPDs identifies novel human-specific imprinted genes. Nakabayashi K, et al. Hum Mol Genet, 2011 Aug 15. PMID 21593219

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Biallelic NAA60 variants with impaired n-terminal acetylation capacity cause autosomal recessive primary familial brain calcifications.
      Title: Biallelic NAA60 variants with impaired n-terminal acetylation capacity cause autosomal recessive primary familial brain calcifications.
    2. NAA60 (HAT4): the newly discovered bi-functional Golgi member of the acetyltransferase family.
      Title: NAA60 (HAT4): the newly discovered bi-functional Golgi member of the acetyltransferase family.
    3. Results from a study on gene expression variability markers in early-stage human embryos shows that NAA60 (NAT15) is a putative expression variability marker for the 3-day, 8-cell embryo stage.
      Title: Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development.
    4. The hNaa60 protein contains an amphipathic helix following its GNAT domain that may contribute to Golgi localization of hNaa60, and the beta7-beta8 hairpin adopted different conformations in the hNaa60(1-242) and hNaa60(1-199) crystal structures.
      Title: Structure and function of human Naa60 (NatF), a Golgi-localized bi-functional acetyltransferase.
    5. analysis of the mode of cytosolic Naa60 anchoring to the Golgi apparatus, most likely occurring post-translationally and specifically facilitating post-translational N-terminal acetylation of many transmembrane proteins
      Title: Molecular determinants of the N-terminal acetyltransferase Naa60 anchoring to the Golgi membrane.
    6. Knockdown of the N-terminal acetyltransferase Naa60 compromises Golgi ribbon integrity.
      Title: Holding it together: Naa60 at the Golgi.
    7. The first crystal structure of the N-terminal acetyltransferase Naa60 reveals two elongated loops important for substrate-specific binding not found in other NAT structures.
      Title: Crystal Structure of the Golgi-Associated Human Nα-Acetyltransferase 60 Reveals the Molecular Determinants for Substrate-Specific Acetylation.
    8. Naa60 is necessary for maintenance of the Golgi ribbon through its Nt-acetylation of substrate protein(s) that is/are involved in Golgi ribbon structural and/or functional organization.
      Title: An organellar nα-acetyltransferase, naa60, acetylates cytosolic N termini of transmembrane proteins and maintains Golgi integrity.
    9. Naa60 is an N-terminal acetyltransferase defined as NatF. Human and Drosophila melanogaster Naa60 acetylate Met-Lys- and other Met-starting N-termini. In Drosophila cells, NAA60 knockdown induced chromosomal segregation defects.
      Title: NatF contributes to an evolutionary shift in protein N-terminal acetylation and is important for normal chromosome segregation.
    10. HAT4 is an important player in the organization and function of the genome and may contribute to the diversity and complexity of higher eukaryotic organisms [HAT4]
      Title: HAT4, a Golgi apparatus-anchored B-type histone acetyltransferase, acetylates free histone H4 and facilitates chromatin assembly.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association study of ancestry-specific TB risk in the South African Coloured population.
    EBI GWAS Catalog

    Variation

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    See Variation Viewer (GRCh37.p13)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Potential readthrough

    Included gene: ZNF174

    Homology

    Clone Names

    • FLJ11693, FLJ14154

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables histone H4 acetyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone acetyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables peptide alpha-N-acetyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables peptide alpha-N-acetyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables peptide-methionine-alpha-N-acetyltransferase activity 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 N-terminal peptidyl-methionine acetylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in N-terminal protein amino acid acetylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chromosome segregation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chromosome segregation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in nucleosome assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in Golgi membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    N-alpha-acetyltransferase 60
    Names
    N-acetyltransferase 15 (GCN5-related, putative)
    N-alpha-acetyltransferase F
    epididymis secretory sperm binding protein
    histone acetyltransferase type B protein 4
    NP_001077069.1
    NP_001077070.1
    NP_001304022.1
    NP_001304023.1
    NP_001304024.1
    NP_001304025.1
    NP_001304026.1
    NP_001304027.1
    NP_079121.1

    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.

    Genomic

    1. NG_045230.1 RefSeqGene

      Range
      5070..48343
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1067

    mRNA and Protein(s)

    1. NM_001083600.3 → NP_001077069.1  N-alpha-acetyltransferase 60 isoform a

      See identical proteins and their annotated locations for NP_001077069.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) represents use of an alternate promoter and differs in the 5' UTR, compared to variant 1. Variants 1, 2, and 3 encode the same isoform (a).
      Source sequence(s)
      AC004224, AC025283, AK130792, BC011267, BG472911, DC339939
      Consensus CDS
      CCDS45396.1
      UniProtKB/Swiss-Prot
      B3KRQ0, B4DLZ0, B4DPZ8, B4DYC4, D3DUC2, E7EQ65, Q6IA31, Q6UX26, Q9H7X0
      UniProtKB/TrEMBL
      A0A384NYU5
      Related
      ENSP00000458667.1, ENST00000575076.5
      Conserved Domains (1) summary
      pfam00583
      Location:23 → 155
      Acetyltransf_1; Acetyltransferase (GNAT) family

    2. NM_001083601.3 → NP_001077070.1  N-alpha-acetyltransferase 60 isoform a

      See identical proteins and their annotated locations for NP_001077070.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. This variant may be expressed predominantly from the maternal allele (PMID:21593219). Variants 1, 2, and 3 encode the same isoform (a).
      Source sequence(s)
      AC004224, AL833594, BC011267, BG472911, DC401343
      Consensus CDS
      CCDS45396.1
      UniProtKB/Swiss-Prot
      B3KRQ0, B4DLZ0, B4DPZ8, B4DYC4, D3DUC2, E7EQ65, Q6IA31, Q6UX26, Q9H7X0
      UniProtKB/TrEMBL
      A0A384NYU5
      Related
      ENSP00000385903.4, ENST00000407558.9
      Conserved Domains (1) summary
      pfam00583
      Location:23 → 155
      Acetyltransf_1; Acetyltransferase (GNAT) family

    3. NM_001317093.1 → NP_001304022.1  N-alpha-acetyltransferase 60 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains multiple differences in the 5' coding region and initiates translation at an alternate upstream start codon, compared to variant 1. The encoded isoform (b) has a longer, distinct N-terminus compared to isoform a.
      Source sequence(s)
      AC004224, AK297219, BC011267, BG472911, DC401343
      Consensus CDS
      CCDS81937.1
      UniProtKB/Swiss-Prot
      Q9H7X0
      Related
      ENSP00000401237.2, ENST00000424546.6
      Conserved Domains (2) summary
      COG0456
      Location:44 → 173
      RimI; Ribosomal protein S18 acetylase RimI and related acetyltransferases [Translation, ribosomal structure and biogenesis]
      pfam00583
      Location:86 → 163
      Acetyltransf_1; Acetyltransferase (GNAT) family

    4. NM_001317094.2 → NP_001304023.1  N-alpha-acetyltransferase 60 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) represents use of an alternate promoter and contains multiple differences in both UTRs and in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
      Source sequence(s)
      AC004224, AK311524, BC011267, DC339939
      Consensus CDS
      CCDS81940.1
      UniProtKB/TrEMBL
      I3L153
      Related
      ENSP00000461703.1, ENST00000576916.5

    5. NM_001317095.2 → NP_001304024.1  N-alpha-acetyltransferase 60 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) represents use of an alternate promoter and contains multiple differences in both UTRs and in the coding region, compared to variant 1. It initiates translation at a downstream start codon. The encoded isoform (d) has a shorter N-terminus than isoform a.
      Source sequence(s)
      AC004224, AK092005, BC011267, BU501490
      Consensus CDS
      CCDS81941.1
      UniProtKB/Swiss-Prot
      Q9H7X0
      Related
      ENSP00000354108.5, ENST00000360862.9
      Conserved Domains (1) summary
      pfam00583
      Location:12 → 90
      Acetyltransf_1; Acetyltransferase (GNAT) family

    6. NM_001317096.2 → NP_001304025.1  N-alpha-acetyltransferase 60 isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) represents use of an alternate promoter and contains multiple differences in both UTRs and in the coding region, resulting in a frameshift, compared to variant 1. The encoded isoform (e) has a distinct C-terminus and is shorter than isoform a.
      Source sequence(s)
      AC004224, AK298566, BC011267, BU501490, DC339939
      Consensus CDS
      CCDS81938.1
      UniProtKB/Swiss-Prot
      Q9H7X0
      Related
      ENSP00000405873.3, ENST00000421765.7

    7. NM_001317097.2 → NP_001304026.1  N-alpha-acetyltransferase 60 isoform f

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) represents use of an alternate promoter and contains multiple differences in both UTRs and in the coding region, resulting in a frameshift, compared to variant 1. The encoded isoform (f) has a distinct C-terminus and is shorter than isoform a. Variants 8 and 9 encode the same isoform (f).
      Source sequence(s)
      AC004224, AK302361, BC011267, BU501490, DC339939
      Consensus CDS
      CCDS81939.1
      UniProtKB/Swiss-Prot
      Q9H7X0
      Related
      ENSP00000461730.1, ENST00000572942.5

    8. NM_001317098.2 → NP_001304027.1  N-alpha-acetyltransferase 60 isoform f

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) represents use of an alternate promoter and contains multiple differences in the 5' UTR and the coding region, resulting in a frameshift, compared to variant 1. The encoded isoform (f) has a distinct C-terminus and is shorter than isoform a. Variants 8 and 9 encode the same isoform (f).
      Source sequence(s)
      AC004224, BC011267, BG472911, BG822206, DC339939
      Consensus CDS
      CCDS81939.1
      UniProtKB/Swiss-Prot
      Q9H7X0
      Related
      ENSP00000460763.1, ENST00000570819.5

    9. NM_024845.4 → NP_079121.1  N-alpha-acetyltransferase 60 isoform a

      See identical proteins and their annotated locations for NP_079121.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents use of an alternate promoter, differs in the 5' UTR, and uses an alternate splice site in the 3' UTR, compared to variant 1. Variants 1, 2, and 3 encode the same isoform (a).
      Source sequence(s)
      AC004224, AK024216, BC011267, BU501490, DC339939
      Consensus CDS
      CCDS45396.1
      UniProtKB/Swiss-Prot
      B3KRQ0, B4DLZ0, B4DPZ8, B4DYC4, D3DUC2, E7EQ65, Q6IA31, Q6UX26, Q9H7X0
      UniProtKB/TrEMBL
      A0A384NYU5
      Related
      ENSP00000393224.2, ENST00000414063.6
      Conserved Domains (1) summary
      pfam00583
      Location:23 → 155
      Acetyltransf_1; Acetyltransferase (GNAT) family

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      3443611..3486963
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      3470880..3514228
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H7X0.1 GenPept UniProtKB/Swiss-Prot:Q9H7X0

    Gene LinkOut

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

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