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BUD23 BUD23 rRNA methyltransferase and ribosome maturation factor [ Homo sapiens (human) ]

Gene ID: 114049, updated on 3-Apr-2024

Summary

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Official Symbol
BUD23provided by HGNC
Official Full Name
BUD23 rRNA methyltransferase and ribosome maturation factorprovided by HGNC
Primary source
HGNC:HGNC:16405
See related
Ensembl:ENSG00000071462 MIM:615733; AllianceGenome:HGNC:16405
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
WBMT; MERM1; PP3381; HUSSY-3; WBSCR22; HASJ4442
Summary
This gene encodes a protein containing a nuclear localization signal and an S-adenosyl-L-methionine binding motif typical of methyltransferases, suggesting that the encoded protein may act on DNA methylation. This gene is deleted in Williams syndrome, a multisystem developmental disorder caused by the deletion of contiguous genes at 7q11.23. Alternatively spliced transcript variants have been found. [provided by RefSeq, Feb 2011]
Expression
Ubiquitous expression in testis (RPKM 63.4), thyroid (RPKM 24.2) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
7q11.23
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (73683597..73698212)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (74884512..74899128)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (73097927..73112542)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18259 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73082323-73083318 Neighboring gene VPS37D subunit of ESCRT-I Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26127 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73098635-73099484 Neighboring gene DnaJ heat shock protein family (Hsp40) member C30 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73099485-73100334 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:73104307-73104476 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73113705-73114206 Neighboring gene uncharacterized LOC105375350 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18260 Neighboring gene syntaxin 1A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73121477-73122229 Neighboring gene microRNA 4284

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. WBSCR22 confers cell survival and predicts poor prognosis in glioma. Chi Y, et al. Brain Res Bull, 2020 Aug. PMID 32380188
  2. Metastasis-related methyltransferase 1 (Merm1) represses the methyltransferase activity of Dnmt3a and facilitates RNA polymerase I transcriptional elongation. Lyu G, et al. J Mol Cell Biol, 2019 Jan 1. PMID 30535232
  3. WBSCR22 confers oxaliplatin resistance in human colorectal cancer. Yan D, et al. Sci Rep, 2017 Nov 13. PMID 29133897, Free PMC Article
  4. WBSCR22/Merm1 is required for late nuclear pre-ribosomal RNA processing and mediates N7-methylation of G1639 in human 18S rRNA. Haag S, et al. RNA, 2015 Feb. PMID 25525153, Free PMC Article
  5. Knockdown of Merm1/Wbscr22 attenuates sensitivity of H460 non-small cell lung cancer cells to SN-38 and 5-FU without alteration to p53 expression levels. Yan D, et al. Mol Med Rep, 2015 Jan. PMID 25352209

See all (63) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. WBSCR22 and TRMT112 synergistically suppress cell proliferation, invasion and tumorigenesis in pancreatic cancer via transcriptional regulation of ISG15.
    Title: WBSCR22 and TRMT112 synergistically suppress cell proliferation, invasion and tumorigenesis in pancreatic cancer via transcriptional regulation of ISG15.
  2. WBSCR22 confers cell survival and predicts poor prognosis in glioma.
    Title: WBSCR22 confers cell survival and predicts poor prognosis in glioma.
  3. Cardiac mitochondrial function depends on BUD23 mediated ribosome programming.
    Title: Cardiac mitochondrial function depends on BUD23 mediated ribosome programming.
  4. Merm1 is capable of maintaining hypomethylated rRNA gene bodies and co-localizes with RNA polymerase I in the nucleolus. Merm1 interacts with Dnmt3a and represses its methyltransferase activity with the requirement of the binding motif for S-adenosyl-L-methionine.
    Title: Metastasis-related methyltransferase 1 (Merm1) represses the methyltransferase activity of Dnmt3a and facilitates RNA polymerase I transcriptional elongation.
  5. Study results demonstrated that WBSCR22 is involved in colorectal cancer (CRC) resistance to oxaliplatin, suggesting WBSCR22 may represent a novel oxaliplatin resistance biomarker as well as a potential target for CRC therapeutics.
    Title: WBSCR22 confers oxaliplatin resistance in human colorectal cancer.
  6. The localization of the TRMT112 protein is determined by WBSCR22, and the WBSCR22-TRMT112 complex is localized in the cell nucleus.
    Title: The Stability of Ribosome Biogenesis Factor WBSCR22 Is Regulated by Interaction with TRMT112 via Ubiquitin-Proteasome Pathway.
  7. DIMT1L and WBSCR22-TRMT112 are required for distinct pre-rRNA processing reactions leading to synthesis of 18S rRNA. Ribosome biogenesis requires the presence of the modification enzyme rather than its RNA-modifying catalytic activity.
    Title: The human 18S rRNA base methyltransferases DIMT1L and WBSCR22-TRMT112 but not rRNA modification are required for ribosome biogenesis.
  8. Knockdown of Merm1/Wbscr22 attenuates sensitivity of H460 non-small cell lung cancer cells to SN-38 and 5-FU without alteration to p53 expression levels.
    Title: Knockdown of Merm1/Wbscr22 attenuates sensitivity of H460 non-small cell lung cancer cells to SN-38 and 5-FU without alteration to p53 expression levels.
  9. The key role of WBSCR22 in 40S subunit biogenesis is independent of its function as an RNA methyltransferase.
    Title: WBSCR22/Merm1 is required for late nuclear pre-ribosomal RNA processing and mediates N7-methylation of G1639 in human 18S rRNA.
  10. WBSCR22 protein level is decreased in lymphoblastoid cell lines.
    Title: The human WBSCR22 protein is involved in the biogenesis of the 40S ribosomal subunits in mammalian cells.
Submit: New GeneRIF Correction See all GeneRIFs (12)

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

Clone Names

  • MGC2022, MGC5140, FLJ44236, MGC19709

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables methyltransferase activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein heterodimerization activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables rRNA (guanine) methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables rRNA (guanine) methyltransferase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of rRNA processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in rRNA (guanine-N7)-methylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in rRNA (guanine-N7)-methylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
probable 18S rRNA (guanine-N(7))-methyltransferase
Names
Williams-Beuren candidate region putative methyltransferase
Williams-Beuren syndrome chromosomal region 22 protein
Williams-Beuren syndrome chromosome region 22
bud site selection protein 23 homolog
metastasis-related methyltransferase 1
rRNA methyltransferase and ribosome maturation factor
ribosome biogenesis methyltransferase WBSCR22
NP_001189489.1
NP_059998.2
XP_006715910.1
XP_011514080.1
XP_011514081.1
XP_054213174.1
XP_054213175.1
XP_054213176.1

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.

mRNA and Protein(s)

  1. NM_001202560.3 → NP_001189489.1  probable 18S rRNA (guanine-N(7))-methyltransferase isoform 1

    See identical proteins and their annotated locations for NP_001189489.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AA099700, AA508840, AF412034, BQ927478
    Consensus CDS
    CCDS56490.1
    UniProtKB/TrEMBL
    Q75ME3
    Conserved Domains (1) summary
    PRK10258
    Location:34 → 130
    PRK10258; biotin biosynthesis protein BioC; Provisional

  2. NM_017528.5 → NP_059998.2  probable 18S rRNA (guanine-N(7))-methyltransferase isoform 2

    See identical proteins and their annotated locations for NP_059998.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 3' coding region but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AA508840, AF412034
    Consensus CDS
    CCDS5557.1
    UniProtKB/Swiss-Prot
    A8K501, C9K060, O43709, Q96P12, Q9BQ58, Q9HBP9
    UniProtKB/TrEMBL
    Q75ME3
    Related
    ENSP00000265758.3, ENST00000265758.7
    Conserved Domains (2) summary
    pfam12589
    Location:204 → 279
    WBS_methylT; Methyltransferase involved in Williams-Beuren syndrome
    pfam13649
    Location:58 → 156
    Methyltransf_25; Methyltransferase domain

RNA

  1. NR_037776.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 5' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AA508840, BM794274, BP280183, BQ961799

  2. NR_045512.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AA508840, BG108222, BP280183, BQ930813, DB276687

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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    73683597..73698212
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006715847.2 → XP_006715910.1  probable 18S rRNA (guanine-N(7))-methyltransferase isoform X1

    UniProtKB/TrEMBL
    Q75ME3
    Conserved Domains (3) summary
    pfam08241
    Location:81 → 184
    Methyltransf_11; Methyltransferase domain
    pfam12589
    Location:227 → 302
    WBS_methylT; Methyltransferase involved in Williams-Beuren syndrome
    cl17173
    Location:38 → 117
    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). ...

  2. XM_011515778.2 → XP_011514080.1  probable 18S rRNA (guanine-N(7))-methyltransferase isoform X2

    Conserved Domains (2) summary
    pfam08241
    Location:81 → 184
    Methyltransf_11; Methyltransferase domain
    cl17173
    Location:38 → 117
    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_011515779.3 → XP_011514081.1  probable 18S rRNA (guanine-N(7))-methyltransferase isoform X3

    Conserved Domains (1) summary
    pfam08241
    Location:58 → 161
    Methyltransf_11; Methyltransferase domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    74884512..74899128
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054357199.1 → XP_054213174.1  probable 18S rRNA (guanine-N(7))-methyltransferase isoform X1

  2. XM_054357200.1 → XP_054213175.1  probable 18S rRNA (guanine-N(7))-methyltransferase isoform X2

  3. XM_054357201.1 → XP_054213176.1  probable 18S rRNA (guanine-N(7))-methyltransferase isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O43709.2 GenPept UniProtKB/Swiss-Prot:O43709

Gene LinkOut

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