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

    Gene ID: 80119, updated on 27-Dec-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
    mouse all
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    Genomic context

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    See PIF1 in Genome Data Viewer
    Location:
    15q22.31
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (64815632..64827062, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (62624916..62636352, complement)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. The Helicase PIF1 Facilitates Resection over Sequences Prone to Forming G4 Structures. Jimeno S, et al. Cell Rep, 2018 Sep 18. PMID 30232007
    2. A genomewide screen for suppressors of Alu-mediated rearrangements reveals a role for PIF1. Chisholm KM, et al. PLoS One, 2012. PMID 22347400, Free PMC Article
    3. Suppression of apoptosis by PIF1 helicase in human tumor cells. Gagou ME, et al. Cancer Res, 2011 Jul 15. PMID 21616935
    4. Determination of the biochemical properties of full-length human PIF1 ATPase. Gu Y, et al. Prion, 2013 Jul-Aug. PMID 23924759, Free PMC Article
    5. Human PIF1 helicase supports DNA replication and cell growth under oncogenic-stress. Gagou ME, et al. Oncotarget, 2014 Nov 30. PMID 25359767, Free PMC Article

    See all (32) 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)

    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 ATP-dependent H2AZ histone chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent H3-H4 histone complex chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA clamp loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables G-quadruplex DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables chromatin extrusion motor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cohesin loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables double-stranded DNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables forked DNA-dependent helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables four-way junction helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables magnesium ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables single-stranded 3'-5' DNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 recombination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin looping IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mitochondrial genome maintenance IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of telomere maintenance via telomerase IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein-DNA-RNA complex disassembly 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 mitochondrial nucleoid 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
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    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_2024_08

    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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