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PIF1 PIF1 5'-to-3' DNA helicase [ Homo sapiens (human) ]

Gene ID: 80119, updated on 5-Mar-2024

Summary

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Official Symbol
PIF1provided by HGNC
Official Full Name
PIF1 5'-to-3' DNA helicaseprovided by HGNC
Primary source
HGNC:HGNC:26220
See related
Ensembl:ENSG00000140451 MIM:610953; AllianceGenome:HGNC:26220
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
PIF; C15orf20
Summary
This gene encodes a DNA-dependent adenosine triphosphate (ATP)-metabolizing enzyme that functions as a 5' to 3' DNA helicase. The encoded protein can resolve G-quadruplex structures and RNA-DNA hybrids at the ends of chromosomes. It also prevents telomere elongation by inhibiting the actions of telomerase. Alternative splicing and the use of alternative start codons results in multiple isoforms that are differentially localized to either the mitochondria or the nucleus. [provided by RefSeq, Nov 2013]
Expression
Broad expression in lymph node (RPKM 2.4), appendix (RPKM 1.6) and 19 other tissues See more
Orthologs
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Genomic context

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Location:
15q22.31
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (64815632..64827062, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (62624916..62636352, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (65107831..65117846, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903507 Neighboring gene MPRA-validated peak2370 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:65010266-65010766 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65024140-65024787 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65024788-65025436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65028357-65029336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:65034779-65035280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65042170-65043145 Neighboring gene RNA binding protein, mRNA processing factor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9577 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65055942-65056827 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:65063339-65063840 Neighboring gene microRNA 1272 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65067649-65068495 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65068496-65069341 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65091461-65092363 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65097880-65098388 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65098896-65099403 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65100927-65101434 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65102957-65103464 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:65103465-65103970 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:65111682-65112182 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:65114079-65114580 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65116122-65116789 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9578 Neighboring gene uncharacterized LOC124903508 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9579 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6540 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:65134214-65134737 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65134770-65135321 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9581 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65138202-65138761 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:65138762-65139320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65143675-65144621 Neighboring gene pleckstrin homology domain containing O2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65146039-65146607 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9582 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:65159077-65159756

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. PIF1 Promotes Autophagy to Inhibit Chronic Hypoxia Induced Apoptosis of Pulmonary Artery Endothelial Cells. Zhao Y, et al. Int J Chron Obstruct Pulmon Dis, 2023. PMID 37396201, Free PMC Article
  2. CircNEIL3 mediates pyroptosis to influence lung adenocarcinoma radiotherapy by upregulating PIF1 through miR-1184 inhibition. Zhang T, et al. Cell Death Dis, 2022 Feb 21. PMID 35190532, Free PMC Article
  3. PIF1 helicase promotes break-induced replication in mammalian cells. Li S, et al. EMBO J, 2021 Apr 15. PMID 33470420, Free PMC Article
  4. Downregulation of PIF1, a potential new target of MYCN, induces apoptosis and inhibits cell migration in neuroblastoma cells. Chen B, et al. Life Sci, 2020 Sep 1. PMID 32512012
  5. Structural and functional analysis of the nucleotide and DNA binding activities of the human PIF1 helicase. Dehghani-Tafti S, et al. Nucleic Acids Res, 2019 Apr 8. PMID 30698796, Free PMC Article

See all (31) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PIF1 Promotes Autophagy to Inhibit Chronic Hypoxia Induced Apoptosis of Pulmonary Artery Endothelial Cells.
    Title: PIF1 Promotes Autophagy to Inhibit Chronic Hypoxia Induced Apoptosis of Pulmonary Artery Endothelial Cells.
  2. CircNEIL3 mediates pyroptosis to influence lung adenocarcinoma radiotherapy by upregulating PIF1 through miR-1184 inhibition.
    Title: CircNEIL3 mediates pyroptosis to influence lung adenocarcinoma radiotherapy by upregulating PIF1 through miR-1184 inhibition.
  3. PIF1 helicase promotes break-induced replication in mammalian cells.
    Title: PIF1 helicase promotes break-induced replication in mammalian cells.
  4. Mitochondrial genetic variation is enriched in G-quadruplex regions that stall DNA synthesis in vitro.
    Title: Mitochondrial genetic variation is enriched in G-quadruplex regions that stall DNA synthesis in vitro.
  5. Dynamic regulation of Pif1 acetylation is crucial to the maintenance of genome stability.
    Title: Dynamic regulation of Pif1 acetylation is crucial to the maintenance of genome stability.
  6. Downregulation of PIF1, a potential new target of MYCN, induces apoptosis and inhibits cell migration in neuroblastoma cells.
    Title: Downregulation of PIF1, a potential new target of MYCN, induces apoptosis and inhibits cell migration in neuroblastoma cells.
  7. PIF1 has a role in DNA resection, specifically for defined DNA regions, such as those prone to form G-quadruplexes.
    Title: The Helicase PIF1 Facilitates Resection over Sequences Prone to Forming G4 Structures.
  8. The functions of human PIF1 (hPIF1) are also critical for survival of certain tumour cell lines during replication stress, making it an important target for cancer therapy. Crystal structures of hPIF1 presented here explore structural events along the chemical reaction coordinate of ATP hydrolysis at an unprecedented level of detail
    Title: Structural and functional analysis of the nucleotide and DNA binding activities of the human PIF1 helicase.
  9. Structural and functional characterization of the unwinding mechanism of Bacteroides and human Pif1 helicases has been reported.
    Title: Structural and Functional Insights into the Unwinding Mechanism of Bacteroides sp Pif1.
  10. Authors characterised a functional role for human PIF1 in DNA replication that becomes important for cell growth under oncogenic stress.
    Title: Human PIF1 helicase supports DNA replication and cell growth under oncogenic-stress.
Submit: New GeneRIF Correction See all GeneRIFs (22)

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 5'-3' DNA helicase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 5'-3' DNA helicase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables 5'-3' DNA/RNA helicase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables 5'-3' DNA/RNA helicase activity TAS
Traceable Author Statement
more info
  
enables ATP binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables ATP hydrolysis activity IEA
Inferred from Electronic Annotation
more info
  
enables G-quadruplex DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables magnesium ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables single-stranded DNA helicase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables telomerase inhibitor activity IEA
Inferred from Electronic Annotation
more info
  
enables telomeric DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA duplex unwinding IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in DNA recombination IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA repair IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA replication IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitochondrial genome maintenance IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of telomerase activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of telomere maintenance via telomerase IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of telomere maintenance IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in telomere maintenance via telomerase TAS
Traceable Author Statement
more info
  
Component Evidence Code Pubs
located_in chromosome, telomeric region IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrion IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in replication fork IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
ATP-dependent DNA helicase PIF1
Names
DNA repair and recombination helicase PIF1
PIF1 5'-to-3' DNA helicase homolog
PIF1/RRM3 DNA helicase-like protein
petite integration frequency 1
NP_001273425.1
NP_001273426.1
NP_001273428.1
NP_079325.2
XP_011520385.1
XP_011520386.1
XP_047289096.1
XP_054234875.1
XP_054234876.1
XP_054234877.1

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

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_001286496.2 → NP_001273425.1  ATP-dependent DNA helicase PIF1 isoform a

    See identical proteins and their annotated locations for NP_001273425.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. This variant can initiate translation from both an upstream and a downstream AUG start codon. The isoform represented in this variant (a, also known as alpha or alpha-1) initiates translation from the upstream AUG. This isoform localizes to the nucleus (PMID: 17827721). Variants 1 and 2 encode the same isoform (a).
    Source sequence(s)
    AB185926, BC033254, EU084033
    Consensus CDS
    CCDS10195.2
    UniProtKB/Swiss-Prot
    B2RPL7, Q1W5B6, Q330H5, Q33E24, Q9H611
    Related
    ENSP00000452792.1, ENST00000559239.2
    Conserved Domains (4) summary
    pfam05970
    Location:206 → 504
    PIF1; PIF1-like helicase
    cl26464
    Location:27 → 209
    Atrophin-1; Atrophin-1 family
    cl27278
    Location:487 → 640
    MobA_MobL; MobA/MobL family
    cl28079
    Location:551 → 599
    Herpes_Helicase; Helicase

  2. NM_001286497.2 → NP_001273426.1  ATP-dependent DNA helicase PIF1 isoform b

    See identical proteins and their annotated locations for NP_001273426.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR and contains an alternate exon structure in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (b, also known as beta) has a distinct C-terminus and is longer than isoform a. This isoform localizes to the mitochondria (PMID: 17827721).
    Source sequence(s)
    AB185927, EU084033
    Consensus CDS
    CCDS66797.1
    UniProtKB/Swiss-Prot
    Q9H611
    Related
    ENSP00000328174.6, ENST00000333425.10
    Conserved Domains (2) summary
    pfam05970
    Location:206 → 504
    PIF1; PIF1-like helicase
    pfam02689
    Location:551 → 611
    Herpes_Helicase; Helicase

  3. NM_001286499.2 → NP_001273428.1  ATP-dependent DNA helicase PIF1 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. This variant can initiate translation from both an upstream and a downstream AUG start codon. The isoform represented in this variant (c, also known as alpha-54) initiates translation from a downstream AUG. This isoform localizes to the mitochondria (PMID: 23275553).
    Source sequence(s)
    AB185926, BC033254, EU084033
    UniProtKB/Swiss-Prot
    Q9H611
    Conserved Domains (2) summary
    pfam05970
    Location:153 → 451
    PIF1; PIF1-like helicase
    pfam02689
    Location:498 → 558
    Herpes_Helicase; Helicase

  4. NM_025049.4 → NP_079325.2  ATP-dependent DNA helicase PIF1 isoform a

    See identical proteins and their annotated locations for NP_079325.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR, compared to variant 1. This variant can initiate translation from both an upstream and a downstream AUG start codon. The isoform represented in this variant (a, also known as alpha or alpha-1) initiates translation from the upstream AUG. This isoform localizes to the nucleus (PMID: 17827721). Variants 1 and 2 encode the same isoform (a).
    Source sequence(s)
    AB185926, AC091582
    Consensus CDS
    CCDS10195.2
    UniProtKB/Swiss-Prot
    B2RPL7, Q1W5B6, Q330H5, Q33E24, Q9H611
    Related
    ENSP00000268043.4, ENST00000268043.8
    Conserved Domains (4) summary
    pfam05970
    Location:206 → 504
    PIF1; PIF1-like helicase
    cl26464
    Location:27 → 209
    Atrophin-1; Atrophin-1 family
    cl27278
    Location:487 → 640
    MobA_MobL; MobA/MobL family
    cl28079
    Location:551 → 599
    Herpes_Helicase; Helicase

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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    64815632..64827062 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011522083.3 → XP_011520385.1  ATP-dependent DNA helicase PIF1 isoform X1

    See identical proteins and their annotated locations for XP_011520385.1

    UniProtKB/Swiss-Prot
    B2RPL7, Q1W5B6, Q330H5, Q33E24, Q9H611
    Conserved Domains (4) summary
    pfam05970
    Location:206 → 504
    PIF1; PIF1-like helicase
    cl26464
    Location:27 → 209
    Atrophin-1; Atrophin-1 family
    cl27278
    Location:487 → 640
    MobA_MobL; MobA/MobL family
    cl28079
    Location:551 → 599
    Herpes_Helicase; Helicase

  2. XM_011522084.3 → XP_011520386.1  ATP-dependent DNA helicase PIF1 isoform X1

    See identical proteins and their annotated locations for XP_011520386.1

    UniProtKB/Swiss-Prot
    B2RPL7, Q1W5B6, Q330H5, Q33E24, Q9H611
    Conserved Domains (4) summary
    pfam05970
    Location:206 → 504
    PIF1; PIF1-like helicase
    cl26464
    Location:27 → 209
    Atrophin-1; Atrophin-1 family
    cl27278
    Location:487 → 640
    MobA_MobL; MobA/MobL family
    cl28079
    Location:551 → 599
    Herpes_Helicase; Helicase

  3. XM_047433140.1 → XP_047289096.1  ATP-dependent DNA helicase PIF1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    62624916..62636352 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054378901.1 → XP_054234876.1  ATP-dependent DNA helicase PIF1 isoform X1

  2. XM_054378900.1 → XP_054234875.1  ATP-dependent DNA helicase PIF1 isoform X1

  3. XM_054378902.1 → XP_054234877.1  ATP-dependent DNA helicase PIF1 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H611.2 GenPept UniProtKB/Swiss-Prot:Q9H611

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