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    POLR1A RNA polymerase I subunit A [ Homo sapiens (human) ]

    Gene ID: 25885, updated on 5-May-2024

    Summary

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    Official Symbol
    POLR1Aprovided by HGNC
    Official Full Name
    RNA polymerase I subunit Aprovided by HGNC
    Primary source
    HGNC:HGNC:17264
    See related
    Ensembl:ENSG00000068654 MIM:616404; AllianceGenome:HGNC:17264
    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
    A190; RPA1; HLD27; RPO14; AFDCIN; RPA190; RPA194; RPO1-4
    Summary
    The protein encoded by this gene is the largest subunit of the RNA polymerase I complex. The encoded protein represents the catalytic subunit of the complex, which transcribes DNA into ribosomal RNA precursors. Defects in this gene are a cause of the Cincinnati type of acrofacial dysostosis. [provided by RefSeq, May 2016]
    Expression
    Ubiquitous expression in testis (RPKM 5.9), endometrium (RPKM 5.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    2p11.2
    Exon count:
    34
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (86020216..86105886, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (86022315..86107956, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (86247339..86333009, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124906031 Neighboring gene uncharacterized LOC105374843 Neighboring gene CRISPRi-validated cis-regulatory element chr2.3134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16149 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:86239243-86239743 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16150 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:86260844-86261047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16151 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11710 Neighboring gene conserved acetylation island sequence 34 enhancer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:86272354-86273553 Neighboring gene MPRA-validated peak3776 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:86296595-86297794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:86301664-86302164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:86302165-86302665 Neighboring gene uncharacterized LOC124907852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16154 Neighboring gene pentatricopeptide repeat domain 3 Neighboring gene Sharpr-MPRA regulatory region 1812 Neighboring gene MPRA-validated peak3777 silencer Neighboring gene small nucleolar RNA, C/D box 94 Neighboring gene inner membrane mitochondrial protein Neighboring gene microRNA 4779

    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. Upregulated long non-coding RNA LOC90784 promotes cell proliferation and invasion and is associated with poor clinical features in HCC. Xu JH, et al. Biochem Biophys Res Commun, 2017 Aug 26. PMID 28651931
    2. Severe neurodegenerative disease in brothers with homozygous mutation in POLR1A. Kara B, et al. Eur J Hum Genet, 2017 Feb. PMID 28051070, Free PMC Article
    3. Identification of an E3 ligase that targets the catalytic subunit of RNA Polymerase I upon transcription stress. Pitts S, et al. J Biol Chem, 2022 Dec. PMID 36372232, Free PMC Article
    4. BLM helicase facilitates RNA polymerase I-mediated ribosomal RNA transcription. Grierson PM, et al. Hum Mol Genet, 2012 Mar 1. PMID 22106380, Free PMC Article
    5. Human Nopp140, which interacts with RNA polymerase I: implications for rRNA gene transcription and nucleolar structural organization. Chen HK, et al. Mol Cell Biol, 1999 Dec. PMID 10567578, Free PMC Article

    See all (105) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Expression of RNA polymerase I catalytic core is influenced by RPA12.
      Title: Expression of RNA polymerase I catalytic core is influenced by RPA12.
    2. POLR1A variants underlie phenotypic heterogeneity in craniofacial, neural, and cardiac anomalies.
      Title: POLR1A variants underlie phenotypic heterogeneity in craniofacial, neural, and cardiac anomalies.
    3. Data show that BRCA1 interacts directly with the basal RNA polymerase I (Pol-I) transcription factors as well as interacting with RNA Pol-I itself.
      Title: The identification of a novel role for BRCA1 in regulating RNA polymerase I transcription.
    4. Homozygous c.2801C>T (p.(Ser934Leu)) in POLR1A was identified in two brothers with unusual neurological disease that manifested with ataxia, psychomotor retardation, cerebellar and cerebral atrophy, and leukodystrophy.
      Title: Severe neurodegenerative disease in brothers with homozygous mutation in POLR1A.
    5. Consistent with this observation, we discovered that polr1a mutant zebrafish exhibited cranioskeletal anomalies mimicking the human phenotype. polr1a loss of function led to perturbed ribosome biogenesis and p53-dependent cell death
      Title: Acrofacial Dysostosis, Cincinnati Type, a Mandibulofacial Dysostosis Syndrome with Limb Anomalies, Is Caused by POLR1A Dysfunction.
    6. SIRT7 knockdown leads to reduced levels of RNA Pol I protein, but not messenger RNA
      Title: Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription.
    7. findings demonstrate that Bloom's syndrome helicase (BLM)interacts with RPA194; studies suggest that nucleolar BLM modulates rDNA structures in association with RNA polymerase I to facilitate RNA polymerase I-mediated rRNA transcription
      Title: BLM helicase facilitates RNA polymerase I-mediated ribosomal RNA transcription.
    8. Interference of POLR1A inhibited the synthesis of rRNA and hindered cell cycle progression in cells with inactivated p53, as a consequence of downregulation of the transcription factor E2F-1.
      Title: Selective inhibition of rRNA transcription downregulates E2F-1: a new p53-independent mechanism linking cell growth to cell proliferation.
    9. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    10. analyzed the kinetics of assembly and elongation of the RNA polymerase I complex on endogenous ribosomal genes in the nuclei of living cells with the use of in vivo microscopy [RPA43]
      Title: A kinetic framework for a mammalian RNA polymerase in vivo.
    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

    Associated conditions

    Description Tests
    Acrofacial dysostosis Cincinnati type
    MedGen: C4225317 OMIM: 616462 GeneReviews: Not available
    		Compare labs
    Leukodystrophy, hypomyelinating, 27
    MedGen: CN376030 OMIM: 620675 GeneReviews: Not available
    		not available

    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

    Clone Names

    • FLJ10750, FLJ21915, MGC87965, DKFZp586M0122

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    contributes_to DNA-directed 5'-3' RNA polymerase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-directed 5'-3' RNA polymerase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA/RNA hybrid binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA polymerase I activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables magnesium ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of protein localization to nucleolus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in transcription by RNA polymerase I IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of RNA polymerase I complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of RNA polymerase I complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chromosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    DNA-directed RNA polymerase I subunit RPA1
    Names
    DNA-directed RNA polymerase I largest subunit
    DNA-directed RNA polymerase I subunit A
    DNA-directed RNA polymerase I subunit A1
    RNA polymerase I 194 kDa subunit
    polymerase (RNA) I polypeptide A, 194kDa
    polymerase (RNA) I subunit A
    NP_056240.2

    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_050742.2 RefSeqGene

      Range
      5270..90940
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_015425.6 → NP_056240.2  DNA-directed RNA polymerase I subunit RPA1

      See identical proteins and their annotated locations for NP_056240.2

      Status: REVIEWED

      Source sequence(s)
      AC012511, AK302458, AK307490, BC073824, BP363163
      Consensus CDS
      CCDS42706.1
      UniProtKB/Swiss-Prot
      B7Z7T0, D6W5M0, O95602, Q0VG05, Q9UEH0, Q9UFT9
      UniProtKB/TrEMBL
      B7ZKR9
      Related
      ENSP00000263857.6, ENST00000263857.11
      Conserved Domains (4) summary
      cd02735
      Location:1199 → 1716
      RNAP_I_Rpa1_C; Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain
      PRK08566
      Location:4 → 1025
      PRK08566; DNA-directed RNA polymerase subunit A'; Validated
      cd01435
      Location:16 → 1004
      RNAP_I_RPA1_N; Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain
      pfam04998
      Location:958 → 1671
      RNA_pol_Rpb1_5; RNA polymerase Rpb1, domain 5

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      86020216..86105886 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      86022315..86107956 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O95602.2 GenPept UniProtKB/Swiss-Prot:O95602

    Gene LinkOut

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

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