Alternative titles; symbols
HGNC Approved Gene Symbol: DDB1
Cytogenetic location: 11q12.2 Genomic coordinates (GRCh38): 11:61,299,451-61,333,105 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 11q12.2 | White-Kernohan syndrome | 619426 | Autosomal dominant | 3 |
The DDB1 gene encodes damage-specific DNA-binding protein 1, which plays a vital role in the DNA damage response, specifically in the nucleotide excision repair pathway where it functions as part of the CUL4-DDB1 ubiquitin E3 ligase complex (CRL4). The CRL4 complex has been found to function in other cellular processes, including regulation of chromatin remodeling, DNA replication, and signal transduction (summary by White et al., 2021).
Chu and Chang (1988) found that cells from 2 consanguineous patients with xeroderma pigmentosum complementation group E (XPE; 278740) lacked a DNA damage-binding activity that recognizes UV-irradiated DNA. Keeney et al. (1993) purified the DDB protein to apparent homogeneity and characterized it from human placenta and from HeLa cells. It was apparently identical to an activity first described from human placenta. DDB activity was associated with a polypeptide of approximately 124 kD, which was found to be complexed with a 41-kD protein. This stable heterodimer could, in turn, form a higher order complex. To test whether the DNA-repair defect in the subset of XPE patients that lack DNA damage-binding activity is caused by a defect in DDB, Keeney et al. (1994) injected purified human DDB protein into XPE cells. The injected DDB protein stimulated DNA repair to normal levels in those strains that lacked the DDB activity but did not stimulate repair in cells from XPE patients that contained the activity. These results provided direct evidence that defective DDB activity causes the repair defect in a subset of XPE patients and establishes a role for this activity in nucleotide-excision repair in vivo.
The DNA damage-binding protein from HeLa cells is associated with polypeptides of relative mass 124,000 and 41,000 (DDB2; 600811) as determined by SDS-polyacrylamide gels. Dualan et al. (1995) isolated full-length human cDNAs encoding each polypeptide of DDB. The predicted peptide molecular masses based on open reading frames were 127,000 and 48,000. When expressed in an in vitro rabbit reticulocyte system, the p48 subunit migrated with a relative mass of 41 kD on SDS-polyacrylamide gels, similarly to the peptide purified from HeLa cells. There was no significant homology between the derived p48 peptide sequence in any proteins in databases, and the derived peptide sequence of p127 had homology only with the monkey DDB p127 (98% nucleotide identity and only 1 conserved amino acid substitution).
Wertz et al. (2004) reported that human DET1 (608727) promotes ubiquitination and degradation of the protooncogenic transcription factor c-Jun (165160) by assembling a multisubunit ubiquitin ligase containing DDB1, cullin 4A (CUL4A; 603137), regulator of cullins-1 (ROC1; 603814), and constitutively photomorphogenic-1 (COP1; 608067). Ablation of any subunit by RNA interference stabilized c-Jun and increased c-Jun-activated transcription. Wertz et al. (2004) concluded that their findings characterized a c-Jun ubiquitin ligase and define a specific function for DET1 in mammalian cells.
By analyzing proteins that immunoprecipitated with anti-CENPA (117139) antibodies from HeLa cell nuclear lysates, Obuse et al. (2004) showed that DDB1 associated with a centromeric complex, which also contained the major centromeric proteins CENPB (117140), CENPC (117141), CENPH (605607), CENPI (300065), and MIS12 (609178), and many others. DDB1 colocalized with CENPA at centromeres throughout the cell cycle in HeLa cells; it appeared in both the cytoplasm and nucleus in interphase and associated with chromosomes in metaphase.
By mass spectrometric analysis, Higa et al. (2006) identified over 20 WD40 repeat-containing (WDR) proteins that interacted with the CUL4-DDB1-ROC1 complex. Sequence alignment revealed that most of the interacting WDR proteins had a centrally positioned WDxR/K submotif. Knockdown studies suggested that the WDR proteins functioned as substrate-specific adaptors. For example, inactivation of L2DTL (DTL; 610617), but not other WDR proteins, prevented CUL4-DDB1-dependent proteolysis of CDT1 (605525) following gamma irradiation. Inactivation of WDR5 (609012) or EED (605984), but not other WDR proteins, altered the pattern of CUL4-DDB1-dependent histone H3 (see 602810) methylation.
Ito et al. (2010) demonstrated that the thalidomide-binding protein cereblon (CRBN; 609262) forms an E3 ubiquitin ligase complex with DDB1 and CUL4A that is important for limb outgrowth and expression of the fibroblast growth factor FGF8 (600483) in zebrafish and chicks. The authors found that thalidomide initiates its teratogenic effects by binding to CRBN and inhibiting the associated ubiquitin ligase activity. Ito et al. (2010) concluded that their study revealed a basis for thalidomide teratogenicity and may contribute to the development of thalidomide derivatives without teratogenic activity.
Yu et al. (2013) found that a cullin-ring finger ligase-4 (CRL4) complex is crucial in regulating the expression of genes necessary for follicle maintenance in female fertility. Yu et al. (2013) found that the oocyte-specific deletion of the CRL4 linker protein DDB1 or its substrate adaptor VPRBP (DCAF1; 617259) caused rapid oocyte loss, premature ovarian insufficiency, and silencing of fertility-maintaining genes. CRL4(VPRBP) activates the TET methylcytosine dioxygenases (see 607790), which are involved in female germ cell development and zygote genome reprogramming. Yu et al. (2013) thus concluded that CRL4(VPRBP) ubiquitin ligase is a guardian of female reproductive life in germ cells and a maternal reprogramming factor after fertilization.
Using wildtype and mutant S. pombe, Zeng et al. (2016) showed that Wdr70 (617233) interacted with Ddb1 in a Cul4-Ddb1 ubiquitin ligase complex to stimulate histone H2B (see 609904) monoubiquitination for repair of DNA double-strand breaks via homologous recombination. Both Wdr70 and Ddb1 directly associated proximal and distal to an induced double-strand break and mediated spreading of monoubiquitinated H2B by the Rnf20 (607699)-Rnf40 (607700)-Ubch6 (UBE2E1; 602916) complex. Wdr70 and monoubiquitinated H2B also recruited Exo1 (606063) nuclease to DNA double-strand breaks. Using short interfering RNA and CRISPR technology, Zeng et al. (2016) showed that human WDR70 and DDB1 participated in DNA damage-dependent monoubiquitination of H2B in HEK293T cells.
Decorsiere et al. (2016) demonstrated that the regulatory HBx protein, encoded by the hepatitis B virus, promotes hepatitis B viral replication by hijacking the cellular DDB1 (600045)-containing E3 ubiquitin ligase to target the 'structural maintenance of chromosomes' (Smc) complex Smc5/6 (609386/609387) for degradation. Blocking this event inhibits the stimulatory effect of HBx both on extrachromosomal reporter genes and on hepatitis B virus transcription. Conversely, silencing the Smc5/6 complex enhances extrachromosomal reporter gene transcription in the absence of HBx, restores replication of an HBx-deficient hepatitis B virus, and rescues wildtype hepatitis B virus in a DDB1-knockdown background. The Smc5/6 complex associates with extrachromosomal reporters and the hepatitis B virus genome, suggesting a direct mechanism of transcriptional inhibition. Decorsiere et al. (2016) concluded that their results uncovered a novel role for the Smc5/6 complex as a restriction factor selectively blocking extrachromosomal DNA transcription. By destroying this complex, HBx relieves the inhibition to allow productive hepatitis B virus gene expression.
Crystal Structure
To reveal how DDB1 incorporates into the CUL4A-ROC1 complex and mediates substrate recruitment, Angers et al. (2006) determined the 3.1-angstrom crystal structure of a DDB1-CUL4A-ROC1 complex bound to the V protein of simian virus 5 (SV5). DDB1 uses 1 beta-propeller domain for cullin scaffold binding and a variably attached separate double-beta-propeller fold for substrate presentation. Through tandem-affinity purification of human DDB1 and CUL4A complexes followed by mass spectrometry analysis, Angers et al. (2006) identified a novel family of WD40-repeat proteins, which directly bind to the double-propeller fold of DDB1 and serve as the substrate-recruiting module of the E3. Together, Angers et al. (2006) concluded that their structural and proteomic results reveal the structural mechanisms and molecular logic underlying the assembly and versatility of a new family of cullin-RING E3 complexes.
Fischer et al. (2014) presented crystal structures of the DDB1-CRBN (609262) complex bound to thalidomide, lenalidomide, and pomalidomide. The structures established that CRBN is a substrate receptor within the E3 ubiquitin ligase complex CRL4(CRBN) and enantioselectively binds immunomodulatory drugs. Using an unbiased screen, the authors identified the homeobox transcription factor MEIS2 (601740) as an endogenous substrate of CRL4(CRBN). Fischer et al. (2014) concluded that their studies suggested that immunomodulatory drugs block endogenous substrates like MEIS2 from binding to CRL4(CRBN) while the ligase complex is recruiting IKZF1 (603023) or IKZF3 (606221) for degradation. This dual activity implied that small molecules can modulate an E3 ubiquitin ligase.
Using fluorescence in situ hybridization (FISH), Dualan et al. (1995) mapped the DDB p127 locus (DDB1) to 11q12-q13, and the DDB p48 locus (DDB2) to 11p12-p11. Fernandes et al. (1998) used FISH and mouse/hamster somatic cell hybrid analysis to map the Ddb1 gene to mouse chromosome 19.
White-Kernohan Syndrome
In 8 unrelated patients with White-Kernohan syndrome (WHIKERS; 619426), White et al. (2021) identified 5 different de novo heterozygous mutations in the DDB1 gene (600045.0001-600045.0005). The mutations were found by exome sequencing, and the patients were ascertained through the Matchmaker Exchange Program. There was 1 in-frame deletion and 4 missense mutations; all occurred in the conserved MSS1 domain. Lymphoblasts derived from 2 patients (P2 and P4), who had missense mutations, showed normal DDB1 mRNA and protein levels. In vitro functional studies of these patient cells demonstrated altered DNA damage signaling responses and changes in histone methylation following UV-induced DNA damage compared to controls. The authors suggested either a dominant-negative or gain-of-function effect of the mutations, although a loss-of-function effect could not be excluded.
Associations Pending Confirmation
By examining 1,570 ethnically diverse African genomes from individuals with quantified pigmentation levels, Crawford et al. (2017) identified 33 SNPs, predicted to be causal for skin pigmentation, in an approximately 195-kb region of chromosome 11 that includes genes that play a role in ultraviolet response and melanoma risk. The region included the DDB1 and TMEM138 (614459) genes. The most significantly associated SNP in the DDB1/TMEM138 region was rs7948623 (p = 2.2 x 10(-11)), located 172 bp downstream of TMEM138. Constructs containing rs7948623 showed enhancer activity in a human melanoma cell line and interacted with the promoters of DDB1 and neighboring genes in a human breast adenocarcinoma cell line. The derived rs7948623T allele, associated with dark pigmentation, is most common in East African Nilo-Saharan populations and is at moderate to high frequency in South Asian and Australo-Melanesian populations. At SNP rs11230664, an intronic SNP within DDB1, the ancestral C allele, associated with dark pigmentation, is common in all sub-Saharan African populations, having the highest frequency in East African Nilo-Saharan, Hadza, and San populations (88 to 96%) and is at moderate to high frequency in South Asian and Australo-Melanesian populations (12 to 66%). The derived T allele, associated with light pigmentation, is nearly fixed in European, East Asian, and Native American populations. The times to the most recent common ancestor (TMRCAs) for the derived alleles rs7948623T and rs11230664T were estimated to be older than 600,000 and 250,000 years, respectively. RNA-seq data from 106 primary melanocyte cultures indicated that African ancestry is correlated with increased DDB1 gene expression (p = 2.6 x 10(-5)), and the ancestral rs7120594T allele, associated with dark pigmentation, was correlated with increased DDB1 expression. Variants associated with dark pigmentation in Africans were found to be identical by descent in South Asian and Australo-Melanesian populations.
Exclusion Studies
Stohr et al. (1998) investigated the possible involvement of DDB1 in the pathogenesis of Best vitelliform macular dystrophy (VMD; 153700) because that disorder maps to the same region on 11q and because the DDB1 gene is abundantly expressed in retina. The mutation screening of the DDB1 gene demonstrated no sequence alterations in patients with Best disease.
Cang et al. (2006) found that the deletion of the Ddb1 gene in mice caused early embryonic lethality. Conditional inactivation of Ddb1 in brain and lens led to neuronal and lens degeneration, brain hemorrhages, and neonatal death. These defects stemmed from a selective elimination of nearly all proliferating neuronal progenitor cells and lens epithelial cells by apoptosis. Cell death was preceded by aberrant accumulation of cell cycle regulators and increased genomic instability and could be partially rescued by deletion of p53 (TP53; 191170).
Cang et al. (2007) found that epidermis-specific deletion of Ddb1 in mice led to dramatic accumulation of c-Jun and p21Cip1 (CDKN1A; 116899), arrest of cell cycle at G2/M, selective apoptosis of proliferating cells, and as a result, nearly complete loss of the epidermis and hair follicles. Deletion of p53 partially rescued the epithelial progenitor cells from death and allowed for the accumulation of aneuploid cells in the epidermis.
In a 17-year-old girl (P1) with White-Kernohan syndrome (WHIKERS; 619426), White et al. (2021) identified a de novo heterozygous 9-bp deletion (c.551_559del, NM_001923.3) in the DDB1 gene, resulting in an in-frame deletion of 3 amino acids (Asp184_Gln186del) in the MMS1 domain. The mutation, which was found by exome sequencing, was not present in the gnomAD database (v.2.1.1). Analysis of patient cells showed normal levels of the DDB1 protein. Additional functional studies were not performed.
In a 9 year-old-girl (P2) with White-Kernohan syndrome (WHIKERS; 619426), White et al. (2021) identified a de novo heterozygous c.562C-T transition (c.562C-T, NM_001923.4) in the DDB1 gene, resulting in an arg188-to-trp (R188W) substitution at a conserved residue in the MMS1 domain. The mutation, which was found by exome sequencing, was not present in the gnomAD database (v.2.1.1). Patient cells showed normal DDB1 mRNA and protein levels. In vitro functional studies of patient lymphoblasts showed abnormal DNA damage signatures and histone methylation following UV-induced DNA damage, suggesting disruption of DDB1-regulated pathways.
In a 10-year-old boy (P3) with White-Kernohan syndrome (WHIKERS; 619426), White et al. (2021) identified a de novo heterozygous c.563G-A transition (c.563G-A, NM_001923.4) in the DDB1 gene, resulting in an arg188-to-gln (R188Q) substitution at a conserved residue in the MMS1 domain. The mutation, which was found by exome sequencing, was not present in the gnomAD database (v.2.1.1). Functional studies of the variant and studies of patient cells were not performed.
In 4 unrelated patients (P4-P7) with White-Kernohan syndrome (WHIKERS; 619426), White et al. (2021) identified a de novo heterozygous c.637G-A transition (c.637G-A, NM_001923.4) in the DDB1 gene, resulting in a glu213-to-lys (E213K) substitution at a conserved residue in the MMS1 domain. The mutation, which was found by exome sequencing, was not present in the gnomAD database (v.2.1.1). Patient cells showed normal DDB1 mRNA and protein levels. In vitro functional studies of patient lymphoblasts showed abnormal DNA damage signatures and histone methylation following UV-induced DNA damage, suggesting disruption of DDB1-regulated pathways.
In a 1-year-old girl (P8) with White-Kernohan syndrome (WHIKERS; 619426), White et al. (2021) identified a de novo heterozygous c.1285T-G transversion (c.1285T-G, NM_001923.4) in the DDB1 gene, resulting in a phe429-to-val (F429V) substitution at a conserved residue in the MMS1 domain. The mutation, which was found by exome sequencing, was not present in the gnomAD database (v.2.1.1). Functional studies of the variant and studies of patient cells were not performed.
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