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    TFB1M transcription factor B1, mitochondrial [ Homo sapiens (human) ]

    Gene ID: 51106, updated on 3-Nov-2024

    Summary

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    Official Symbol
    TFB1Mprovided by HGNC
    Official Full Name
    transcription factor B1, mitochondrialprovided by HGNC
    Primary source
    HGNC:HGNC:17037
    See related
    Ensembl:ENSG00000029639 MIM:607033; AllianceGenome:HGNC:17037
    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
    CGI75; mtTFB; CGI-75; mtTFB1
    Summary
    The protein encoded by this gene is a dimethyltransferase that methylates the conserved stem loop of mitochondrial 12S rRNA. The encoded protein also is part of the basal mitochondrial transcription complex and is necessary for mitochondrial gene expression. The methylation and transcriptional activities of this protein are independent of one another. Variations in this gene may influence the severity of aminoglycoside-induced deafness (AID).[provided by RefSeq, Aug 2010]
    Expression
    Ubiquitous expression in testis (RPKM 2.2), adrenal (RPKM 1.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TFB1M in Genome Data Viewer
    Location:
    6q25.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (155229871..155314484, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (156431886..156516508, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (155551005..155635618, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak6235 silencer Neighboring gene Sharpr-MPRA regulatory region 2718 Neighboring gene microRNA 1273c Neighboring gene ReSE screen-validated silencer GRCh37_chr6:155259719-155259894 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:155272494-155272994 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155287362-155288008 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25298 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25299 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155316343-155316950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155316951-155317556 Neighboring gene lysophosphatidylcholine acyltransferase 3 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:155340532-155341032 Neighboring gene TIAM Rac1 associated GEF 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:155434365-155434864 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:155440095-155440876 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:155440877-155441659 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:155448114-155449313 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155450845-155451460 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91096 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25301 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25302 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25303 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:155499148-155499350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25304 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr6:155506493-155507300 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr6:155507301-155508106 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:155508589-155509092 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:155517063-155517562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:155539515-155540016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:155540017-155540516 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:155541579-155542078 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:155544888-155546087 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155568469-155569164 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155574917-155575491 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155575492-155576065 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25305 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155635711-155636701 Neighboring gene claudin 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25308 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25309 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:155748671-155749628 Neighboring gene NADPH oxidase 3 Neighboring gene uncharacterized LOC105378068 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:155844790-155845366

    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. Structural insights into dimethylation of 12S rRNA by TFB1M: indispensable role in translation of mitochondrial genes and mitochondrial function. Liu X, et al. Nucleic Acids Res, 2019 Aug 22. PMID 31251801, Free PMC Article
    2. Human mitochondrial transcription factor B1 as a modifier gene for hearing loss associated with the mitochondrial A1555G mutation. Bykhovskaya Y, et al. Mol Genet Metab, 2004 May. PMID 15110318
    3. A human mitochondrial transcription factor is related to RNA adenine methyltransferases and binds S-adenosylmethionine. McCulloch V, et al. Mol Cell Biol, 2002 Feb. PMID 11809803, Free PMC Article
    4. Relative abundance of the human mitochondrial transcription system and distinct roles for h-mtTFB1 and h-mtTFB2 in mitochondrial biogenesis and gene expression. Cotney J, et al. Nucleic Acids Res, 2007. PMID 17557812, Free PMC Article
    5. A common variant in TFB1M is associated with reduced insulin secretion and increased future risk of type 2 diabetes. Koeck T, et al. Cell Metab, 2011 Jan 5. PMID 21195351

    See all (71) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The suppression of transcription factor B1, mitochondrial protein (hsTFB1M) protein level or the overexpression of inactive hsTFB1M mutants resulted in decreased ATP production.
      Title: Structural insights into dimethylation of 12S rRNA by TFB1M: indispensable role in translation of mitochondrial genes and mitochondrial function.
    2. Loss of TFB1M results in mitochondrial dysfunction that leads to impaired insulin secretion and diabetes.
      Title: Loss of TFB1M results in mitochondrial dysfunction that leads to impaired insulin secretion and diabetes.
    3. Deficiency in TFB1M and impaired mitochondrial function contribute to the pathogenesis of type 2 diabetes.
      Title: A common variant in TFB1M is associated with reduced insulin secretion and increased future risk of type 2 diabetes.
    4. The mRNA levels of TFB1M and TFB2M are influenced by endurance training
      Title: Training response of mitochondrial transcription factors in human skeletal muscle.
    5. This study suggested that DNA variants in TFB1M did not contribute to the risk for parkinson disease.
      Title: Mutational screening of the mitochondrial transcription factors B1 and B2 (TFB1M and TFB2M) in Parkinson's disease.
    6. rRNA methyltransferase activity is necessary for induction of mitochondrial biogenesis by TFB1M, but not TFB2M.
      Title: Elucidation of separate, but collaborative functions of the rRNA methyltransferase-related human mitochondrial transcription factors B1 and B2 in mitochondrial biogenesis reveals new insight into maternally inherited deafness.
    7. determined the variation in the TFAM, TFB1M, and TFB2M genes in cardiac hypertrophy
      Title: Mitochondrial transcription factors TFA, TFB1 and TFB2: a search for DNA variants/haplotypes and the risk of cardiac hypertrophy.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    9. Human mitochondrial transcription factor B1 methylates ribosomal RNA at a conserved stem-loop
      Title: Human mitochondrial transcription factor B1 methylates ribosomal RNA at a conserved stem-loop.
    10. TFB1 interacts with the C-terminal activation region of h-mtTFA and stimulates transcription independently of its RNA methyltransferase activity
      Title: Human mitochondrial transcription factor B1 interacts with the C-terminal activation region of h-mtTFA and stimulates transcription independently of its RNA methyltransferase activity.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    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 DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding HDA PubMed 
    enables S-adenosyl-L-methionine binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables mitochondrial transcription factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables rRNA (adenine-N6,N6-)-dimethyltransferase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables rRNA (adenine-N6,N6-)-dimethyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables rRNA (adenine-N6,N6-)-dimethyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in rRNA methylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in rRNA methylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in rRNA modification TAS
    Traceable Author Statement
    more info
    		  
    involved_in transcription initiation at mitochondrial promoter IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in mitochondrial matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrial nucleoid IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion HTP PubMed 

    General protein information

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    Preferred Names
    dimethyladenosine transferase 1, mitochondrial
    Names
    S-adenosylmethionine-6-N', N'-adenosyl(rRNA) dimethyltransferase 1
    h-mtTFB1
    hTFB1M
    homolog of yeast mitochondrial transcription factor B
    mitochondrial 12S rRNA dimethylase 1
    mitochondrial dimethyladenosine transferase 1
    NP_001337430.1
    NP_001337431.1
    NP_057104.2
    XP_011534173.1
    XP_011534174.1
    XP_011534175.1
    XP_047274808.1
    XP_047274809.1
    XP_054211532.1
    XP_054211533.1
    XP_054211534.1
    XP_054211535.1
    XP_054211536.1

    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_027528.2 RefSeqGene

      Range
      5014..63364
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001350501.2 → NP_001337430.1  dimethyladenosine transferase 1, mitochondrial isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction in the 3' end compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AL139101
      UniProtKB/TrEMBL
      A8K0B9
      Conserved Domains (1) summary
      PRK00274
      Location:15 → 258
      ksgA; 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase RsmA

    2. NM_001350502.2 → NP_001337431.1  dimethyladenosine transferase 1, mitochondrial isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice junction in the 5' end compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AL139101
      Conserved Domains (1) summary
      cl17173
      Location:6 → 215
      AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

    3. NM_016020.4 → NP_057104.2  dimethyladenosine transferase 1, mitochondrial isoform 1

      See identical proteins and their annotated locations for NP_057104.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AL139101, BC017788
      Consensus CDS
      CCDS5248.1
      UniProtKB/Swiss-Prot
      Q05DR0, Q8WVM0, Q9Y384
      UniProtKB/TrEMBL
      A8K0B9, E5KTM5
      Related
      ENSP00000356134.4, ENST00000367166.5
      Conserved Domains (1) summary
      PRK00274
      Location:15 → 310
      ksgA; 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase RsmA

    RNA

    1. NR_146725.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 3' end compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL139101, AL355343, AL596202

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      155229871..155314484 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418852.1 → XP_047274808.1  dimethyladenosine transferase 1, mitochondrial isoform X1

    2. XM_011535871.3 → XP_011534173.1  dimethyladenosine transferase 1, mitochondrial isoform X1

      See identical proteins and their annotated locations for XP_011534173.1

      Conserved Domains (1) summary
      cl17173
      Location:15 → 223
      AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

    3. XM_011535872.3 → XP_011534174.1  dimethyladenosine transferase 1, mitochondrial isoform X1

      See identical proteins and their annotated locations for XP_011534174.1

      Conserved Domains (1) summary
      cl17173
      Location:15 → 223
      AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

    4. XM_011535873.3 → XP_011534175.1  dimethyladenosine transferase 1, mitochondrial isoform X2

      See identical proteins and their annotated locations for XP_011534175.1

      Conserved Domains (1) summary
      cl17173
      Location:6 → 215
      AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

    5. XM_047418853.1 → XP_047274809.1  dimethyladenosine transferase 1, mitochondrial isoform X3

    RNA

    1. XR_007059269.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      156431886..156516508 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355559.1 → XP_054211534.1  dimethyladenosine transferase 1, mitochondrial isoform X1

    2. XM_054355558.1 → XP_054211533.1  dimethyladenosine transferase 1, mitochondrial isoform X1

    3. XM_054355557.1 → XP_054211532.1  dimethyladenosine transferase 1, mitochondrial isoform X1

    4. XM_054355560.1 → XP_054211535.1  dimethyladenosine transferase 1, mitochondrial isoform X2

    5. XM_054355561.1 → XP_054211536.1  dimethyladenosine transferase 1, mitochondrial isoform X3

    RNA

    1. XR_008487338.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WVM0.1 GenPept UniProtKB/Swiss-Prot:Q8WVM0

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