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    HPF1 histone PARylation factor 1 [ Homo sapiens (human) ]

    Gene ID: 54969, updated on 12-Nov-2024

    Summary

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    Official Symbol
    HPF1provided by HGNC
    Official Full Name
    histone PARylation factor 1provided by HGNC
    Primary source
    HGNC:HGNC:26051
    See related
    Ensembl:ENSG00000056050 MIM:616614; AllianceGenome:HGNC:26051
    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
    C4orf27
    Summary
    Enables chromatin binding activity; histone binding activity; and protein ADP-ribosyltransferase-substrate adaptor activity. Involved in DNA repair-dependent chromatin remodeling and double-strand break repair. Located in chromatin and nucleus. Is active in site of DNA damage. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in brain (RPKM 6.3), endometrium (RPKM 6.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HPF1 in Genome Data Viewer
    Location:
    4q33
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (169729470..169757944, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (173089586..173118075, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (170650621..170679095, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22137 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15793 Neighboring gene NIMA related kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15794 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22140 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22141 Neighboring gene chloride voltage-gated channel 3 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:170581329-170582201 Neighboring gene Sharpr-MPRA regulatory region 12659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22145 Neighboring gene uncharacterized LOC107986240 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:170696269-170696769 Neighboring gene prostaglandin E synthase 3 pseudogene 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. SERious Surprises for ADP-Ribosylation Specificity: HPF1 Switches PARP1 Specificity to Ser Residues. Leung AK. Mol Cell, 2017 Mar 2. PMID 28257697
    2. Dispensability of HPF1 for cellular removal of DNA single-strand breaks. Hrychova K, et al. Nucleic Acids Res, 2024 Oct 14. PMID 39162207, Free PMC Article
    3. Germline HPF1 retrogene insertion in RB1 gene involved in cancer predisposition. Le Gall J, et al. J Med Genet, 2023 Dec 21. PMID 37541786
    4. Bridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1. Gaullier G, et al. PLoS One, 2020. PMID 33141820, Free PMC Article
    5. HPF1 and nucleosomes mediate a dramatic switch in activity of PARP1 from polymerase to hydrolase. Rudolph J, et al. Elife, 2021 Mar 8. PMID 33683197, Free PMC Article

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Dispensability of HPF1 for cellular removal of DNA single-strand breaks.
      Title: Dispensability of HPF1 for cellular removal of DNA single-strand breaks.
    2. Germline HPF1 retrogene insertion in RB1 gene involved in cancer predisposition.
      Title: Germline HPF1 retrogene insertion in RB1 gene involved in cancer predisposition.
    3. HPF1 and nucleosomes mediate a dramatic switch in activity of PARP1 from polymerase to hydrolase.
      Title: HPF1 and nucleosomes mediate a dramatic switch in activity of PARP1 from polymerase to hydrolase.
    4. HPF1 dynamically controls the PARP1/2 balance between initiating and elongating ADP-ribose modifications.
      Title: HPF1 dynamically controls the PARP1/2 balance between initiating and elongating ADP-ribose modifications.
    5. Dual function of HPF1 in the modulation of PARP1 and PARP2 activities.
      Title: Dual function of HPF1 in the modulation of PARP1 and PARP2 activities.
    6. The regulatory landscape of the human HPF1- and ARH3-dependent ADP-ribosylome.
      Title: The regulatory landscape of the human HPF1- and ARH3-dependent ADP-ribosylome.
    7. Serine-linked PARP1 auto-modification controls PARP inhibitor response.
      Title: Serine-linked PARP1 auto-modification controls PARP inhibitor response.
    8. HPF1 remodels the active site of PARP1 to enable the serine ADP-ribosylation of histones.
      Title: HPF1 remodels the active site of PARP1 to enable the serine ADP-ribosylation of histones.
    9. Bridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1.
      Title: Bridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1.
    10. Bridging of DNA breaks activates PARP2-HPF1 to modify chromatin.
      Title: Bridging of DNA breaks activates PARP2-HPF1 to modify chromatin.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    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
    Biological insights from 108 schizophrenia-associated genetic loci.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ20534, FLJ33423, FLJ42042

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables poly-ADP-D-ribose binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein ADP-ribosyltransferase-substrate adaptor activity 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 DNA damage response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in DNA repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA repair-dependent chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA repair-dependent chromatin remodeling IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in double-strand break repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in double-strand break repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of protein ADP-ribosylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in site of DNA damage IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in site of DNA damage IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    histone PARylation factor 1
    Names
    UPF0609 protein C4orf27

    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_017867.3 → NP_060337.2  histone PARylation factor 1

      See identical proteins and their annotated locations for NP_060337.2

      Status: VALIDATED

      Source sequence(s)
      AC106878, AK000541, BM905677, CB141427, DN990093
      Consensus CDS
      CCDS3813.1
      UniProtKB/Swiss-Prot
      Q9NWY4
      Related
      ENSP00000406598.1, ENST00000393381.3
      Conserved Domains (1) summary
      pfam10228
      Location:78 → 328
      DUF2228; Uncharacterized conserved protein (DUF2228)

    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
      169729470..169757944 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      173089586..173118075 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NWY4.2 GenPept UniProtKB/Swiss-Prot:Q9NWY4

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
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