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

Gene ID: 51106, updated on 5-Mar-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
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Genomic context

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Location:
6q25.3
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (155229871..155314484, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (156431886..156516508, complement)
105.20220307 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
  • 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. Loss of TFB1M results in mitochondrial dysfunction that leads to impaired insulin secretion and diabetes. Sharoyko VV, et al. Hum Mol Genet, 2014 Nov 1. PMID 24916378
  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 (63) 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 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
  
Process Evidence Code Pubs
involved_in rRNA methylation IBA
Inferred from Biological aspect of Ancestor
more info
  
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 

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_2023_10

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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