Dkc1 dyskeratosis congenita 1, dyskerin [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Dkc1provided by MGI
Official Full Name: dyskeratosis congenita 1, dyskerinprovided by MGI
Primary source: MGI:MGI:1861727
See related: Ensembl:ENSMUSG00000031403 AllianceGenome:MGI:1861727
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Summary: Predicted to enable box H/ACA snoRNA binding activity; pseudouridine synthase activity; and telomerase RNA binding activity. Predicted to contribute to telomerase activity. Acts upstream of or within ncRNA metabolic process and positive regulation of DNA biosynthetic process. Located in Cajal body and nucleolus. Is expressed in several structures, including brain; epithelium; genitourinary system; skin; and surface ectoderm. Used to study dyskeratosis congenita. Human ortholog(s) of this gene implicated in X-linked dyskeratosis congenita; aplastic anemia; and dyskeratosis congenita. Orthologous to human DKC1 (dyskerin pseudouridine synthase 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in liver E14 (RPKM 19.1), CNS E11.5 (RPKM 18.3) and 22 other tissues See more
Orthologs: human all
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Genomic context

Location:: X A7.3; X 38.15 cM

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	X	NC_000086.8 (74139460..74153382)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	X	NC_000086.7 (75095854..75109776)

Chromosome X - NC_000086.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Mechanism of Dcp2/RNCR3/Dkc1/Snora62 axis regulating neuronal apoptosis in chronic cerebral ischemia.
Title: Mechanism of Dcp2/RNCR3/Dkc1/Snora62 axis regulating neuronal apoptosis in chronic cerebral ischemia.
miRNA326-5p Targets DKC1 Gene to Regulate Apoptosis-Related Proteins and Intervene in the Development of Neuroblastoma.
Title: miRNA326-5p Targets DKC1 Gene to Regulate Apoptosis-Related Proteins and Intervene in the Development of Neuroblastoma.
Mouse embryonic fibroblasts cells with no pseudouridylation activity in H/ACA snoRNPs due to lack of Dkc1, can produce mature ribosomes, however, the ribosomes are very unstable and cell growth and division is very slow.
Title: Slow growth and unstable ribosomal RNA lacking pseudouridine in mouse embryonic fibroblast cells expressing catalytically inactive dyskerin.
mTR stability and telomerase activity produced by the Dkc1 A353V mutation in dyskeratosis congenita are rescued by a peptide from the dyskerin TruB domain.
Title: Defects in mTR stability and telomerase activity produced by the Dkc1 A353V mutation in dyskeratosis congenita are rescued by a peptide from the dyskerin TruB domain.
A mouse small nucleolar snoRNA microarray was used to monitor changes in abundance of snoRNAs after ablation of dyskerin, an H/ACA snoRNA protein component, from mouse liver, which causes a decrease in ribosome production.
Title: SnoRNA microarray analysis reveals changes in H/ACA and C/D RNA levels caused by dyskerin ablation in mouse liver.
hepatocytes can survive without dyskerin but the role of dyskerin in RNA modification is essential for cellular proliferation.
Title: Dyskerin ablation in mouse liver inhibits rRNA processing and cell division.
dyskerin mutations cause slow growth independently of telomere shortening and this slow growth is the result of the induction of DNA damage. Thus, dyskerin interacts with telomerase and affects telomere maintenance independently of telomere length.
Title: A pathogenic dyskerin mutation impairs proliferation and activates a DNA damage response independent of telomere length in mice.
Data show that point mutations in dyskerin may affect both the telomerase and pseudouridylation pathways and the extent to which these functions are altered can vary for different mutations.
Title: Mouse dyskerin mutations affect accumulation of telomerase RNA and small nucleolar RNA, telomerase activity, and ribosomal RNA processing.
specific defect in IRES (internal ribosome entry site)-dependent translation in Dkc1 mutant mice; defect results in impaired translation of mRNAs containing IRES elements, including those encoding p27Kip1), Bcl-xL and XIAP
Title: Impaired control of IRES-mediated translation in X-linked dyskeratosis congenita.
results establish a role of dyskerin for deregulated rRNA modification in tumor formation and disease pathogenesis in dyskeratosis congenita
Title: Dyskeratosis congenita and cancer in mice deficient in ribosomal RNA modification.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3)
Targeted (9) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables box H/ACA snoRNA binding	ISO Inferred from Sequence Orthology more info
enables isomerase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables pseudouridine synthase activity	IBA Inferred from Biological aspect of Ancestor more info
enables pseudouridine synthase activity	ISO Inferred from Sequence Orthology more info
enables telomerase RNA binding	ISO Inferred from Sequence Orthology more info
contributes_to telomerase activity	ISO Inferred from Sequence Orthology more info
enables telomerase activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in RNA modification	IEA Inferred from Electronic Annotation more info
involved_in RNA processing	IEA Inferred from Electronic Annotation more info
involved_in box H/ACA sno(s)RNA 3'-end processing	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within box H/ACA sno(s)RNA metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in enzyme-directed rRNA pseudouridine synthesis	ISO Inferred from Sequence Orthology more info
involved_in mRNA pseudouridine synthesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of establishment of protein localization to telomere	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of telomerase RNA localization to Cajal body	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of telomerase activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of telomerase activity	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of telomere maintenance via telomerase	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in pseudouridine synthesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within rRNA processing	IEA Inferred from Electronic Annotation more info
involved_in rRNA pseudouridine synthesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within rRNA pseudouridine synthesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of telomerase RNA localization to Cajal body	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ribosome biogenesis	IEA Inferred from Electronic Annotation more info
involved_in scaRNA localization to Cajal body	ISO Inferred from Sequence Orthology more info
involved_in snRNA pseudouridine synthesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in snoRNA guided rRNA pseudouridine synthesis	ISO Inferred from Sequence Orthology more info
involved_in telomerase RNA stabilization	ISO Inferred from Sequence Orthology more info
involved_in telomere maintenance via telomerase	ISO Inferred from Sequence Orthology more info
involved_in telomere maintenance via telomerase	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in Cajal body	IDA Inferred from Direct Assay more info	PubMed
located_in Cajal body	ISO Inferred from Sequence Orthology more info
part_of box H/ACA snoRNP complex	IBA Inferred from Biological aspect of Ancestor more info
part_of box H/ACA snoRNP complex	ISO Inferred from Sequence Orthology more info
part_of box H/ACA telomerase RNP complex	ISO Inferred from Sequence Orthology more info
located_in fibrillar center	ISO Inferred from Sequence Orthology more info
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of ribonucleoprotein complex	IEA Inferred from Electronic Annotation more info
part_of telomerase holoenzyme complex	ISO Inferred from Sequence Orthology more info
part_of telomerase holoenzyme complex	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: H/ACA ribonucleoprotein complex subunit DKC1

Names: dyskeratosis congenita 1, dyskerin homolog; dyskerin; h/ACA ribonucleoprotein complex subunit 4; nopp140-associated protein of 57 kDa; nucleolar protein NAP57; nucleolar protein family A member 4; snoRNP protein DKC1

NP_001025478.1

EC 5.4.99.-

NP_001346340.1

EC 5.4.99.-

NP_001346341.1

EC 5.4.99.-

NP_001346342.1

EC 5.4.99.-

XP_030107198.1

EC 5.4.99.-

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_001030307.2 → NP_001025478.1 H/ACA ribonucleoprotein complex subunit DKC1 isoform 3

See identical proteins and their annotated locations for NP_001025478.1

Status: VALIDATED

Source sequence(s)

AK136418, AL808110, BY126448

Consensus CDS

CCDS41029.1

UniProtKB/Swiss-Prot

Q3UWE5, Q9ESX5

UniProtKB/TrEMBL

Q3TI79

Related

ENSMUSP00000033776.9, ENSMUST00000033776.15

Conserved Domains (4) summary

cd02572
Location:88 → 270

PseudoU_synth_hDyskerin; Pseudouridine synthase, human dyskerin like

TIGR00425
Location:56 → 381

CBF5; rRNA pseudouridine synthase, putative

pfam01472
Location:297 → 370

PUA; PUA domain

pfam08068
Location:49 → 106

DKCLD; DKCLD (NUC011) domain
NM_001359411.1 → NP_001346340.1 H/ACA ribonucleoprotein complex subunit DKC1 isoform 1

Status: VALIDATED

Source sequence(s)

AL808110

UniProtKB/TrEMBL

Q3TI79

Conserved Domains (1) summary

cl27547
Location:81 → 406

TruB_N; TruB family pseudouridylate synthase (N terminal domain)
NM_001359412.1 → NP_001346341.1 H/ACA ribonucleoprotein complex subunit DKC1 isoform 2

Status: VALIDATED

Source sequence(s)

AL808110

UniProtKB/TrEMBL

Q3TI79

Conserved Domains (1) summary

cl27547
Location:72 → 397

TruB_N; TruB family pseudouridylate synthase (N terminal domain)
NM_001359413.1 → NP_001346342.1 H/ACA ribonucleoprotein complex subunit DKC1 isoform 4

Status: VALIDATED

Source sequence(s)

AL808110

Conserved Domains (1) summary

cl27547
Location:1 → 178

TruB_N; TruB family pseudouridylate synthase (N terminal domain)

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000086.8 Reference GRCm39 C57BL/6J

Range

74139460..74153382

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030251338.1 → XP_030107198.1 H/ACA ribonucleoprotein complex subunit DKC1 isoform X1

UniProtKB/TrEMBL

Q3TM67

Conserved Domains (1) summary

TIGR00425
Location:56 → 381

CBF5; rRNA pseudouridine synthase, putative