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

Summary

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: mouse all
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Genomic context

Location:: 7q11.23

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (73683597..73698212)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (74884512..74899128)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (73097927..73112542)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
WBSCR22 confers cell survival and predicts poor prognosis in glioma.
Title: WBSCR22 confers cell survival and predicts poor prognosis in glioma.
Cardiac mitochondrial function depends on BUD23 mediated ribosome programming.
Title: Cardiac mitochondrial function depends on BUD23 mediated ribosome programming.
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.
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.
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.
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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-154307 (e-PCR)
- UniSTS:178067

SHGC-56098 (e-PCR)
- UniSTS:82085

RH103672 (e-PCR)
- UniSTS:97997

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	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: 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; probable 18S rRNA (guanine-N(7))-methyltransferase; rRNA methyltransferase and ribosome maturation factor; ribosome biogenesis methyltransferase WBSCR22

NP_001189489.1

EC 2.1.1.309

NP_059998.2

EC 2.1.1.309

XP_006715910.1

EC 2.1.1.309

XP_011514080.1

EC 2.1.1.309

XP_011514081.1

EC 2.1.1.309

XP_054213174.1

EC 2.1.1.309

XP_054213175.1

EC 2.1.1.309

XP_054213176.1

EC 2.1.1.309

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)

NM_001202560.3 → NP_001189489.1 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
NM_017528.5 → NP_059998.2 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

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
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_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

73683597..73698212

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006715847.2 → XP_006715910.1 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). ...
XM_011515778.2 → XP_011514080.1 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). ...
XM_011515779.3 → XP_011514081.1 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

NC_060931.1 Alternate T2T-CHM13v2.0

Range

74884512..74899128

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054357199.1 → XP_054213174.1 18S rRNA (guanine-N(7))-methyltransferase isoform X1
XM_054357200.1 → XP_054213175.1 18S rRNA (guanine-N(7))-methyltransferase isoform X2
XM_054357201.1 → XP_054213176.1 18S rRNA (guanine-N(7))-methyltransferase isoform X3