DDB1

damage specific DNA binding protein 1

The protein encoded by this gene is the large subunit (p127) of the heterodimeric DNA damage-binding (DDB) complex while another protein (p48) forms the small subunit. This protein complex functions in nucleotide-excision repair and binds to DNA following UV damage. Defective activity of this complex causes the repair defect in patients with xeroderma pigmentosum complementation group E (XPE) - an autosomal recessive disorder characterized by photosensitivity and early onset of carcinomas. However, it remains for mutation analysis to demonstrate whether the defect in XPE patients is in this gene or the gene encoding the small subunit. In addition, Best vitelliform mascular dystrophy is mapped to the same region as this gene on 11q, but no sequence alternations of this gene are demonstrated in Best disease patients. The protein encoded by this gene also functions as an adaptor molecule for the cullin 4 (CUL4) ubiquitin E3 ligase complex by facilitating the binding of substrates to this complex and the ubiquitination of proteins. [provided by RefSeq, May 2012]

Member of: DE-5

Biological processes 83 terms

Cul4-RING E3 ubiquitin ligase complex (GO:0080008)Cul4-RING E3 ubiquitin ligase complex (GO:0080008)Cul4-RING E3 ubiquitin ligase complex (GO:0080008)Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)DNA binding (GO:0003677)DNA damage response (GO:0006974)DNA damage response (GO:0006974)DNA damage response (GO:0006974)DNA repair (GO:0006281)DNA repair (GO:0006281)UV-damage excision repair (GO:0070914)WD40-repeat domain binding (GO:0071987)biological process involved in interaction with symbiont (GO:0051702)cell population proliferation (GO:0008283)cellular response to UV (GO:0034644)cellular response to UV (GO:0034644)cellular response to UV (GO:0034644)chromosome, telomeric region (GO:0000781)cullin family protein binding (GO:0097602)cullin family protein binding (GO:0097602)cytoplasm (GO:0005737)cytoplasm (GO:0005737)damaged DNA binding (GO:0003684)damaged DNA binding (GO:0003684)epigenetic programming in the zygotic pronuclei (GO:0044725)epigenetic regulation of gene expression (GO:0040029)extracellular exosome (GO:0070062)extracellular region (GO:0005576)negative regulation of adipose tissue development (GO:1904178)nucleic acid binding (GO:0003676)nucleolus (GO:0005730)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleotide-excision repair (GO:0006289)nucleotide-excision repair (GO:0006289)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation by virus of viral protein levels in host cell (GO:0046726)positive regulation of gluconeogenesis (GO:0045722)positive regulation of gluconeogenesis (GO:0045722)positive regulation of protein catabolic process (GO:0045732)positive regulation of protein catabolic process (GO:0045732)positive regulation of viral genome replication (GO:0045070)proteasomal protein catabolic process (GO:0010498)proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)protein binding (GO:0005515)protein ubiquitination (GO:0016567)protein ubiquitination (GO:0016567)protein ubiquitination (GO:0016567)protein-containing complex (GO:0032991)protein-containing complex (GO:0032991)protein-containing complex binding (GO:0044877)protein-macromolecule adaptor activity (GO:0030674)regulation of DNA-templated DNA replication initiation (GO:0030174)regulation of apoptotic process (GO:0042981)regulation of autophagy (GO:0010506)regulation of cell cycle phase transition (GO:1901987)regulation of cell population proliferation (GO:0042127)regulation of cellular response to stress (GO:0080135)regulation of circadian rhythm (GO:0042752)regulation of embryonic development (GO:0045995)regulation of miRNA-mediated gene silencing (GO:0060964)regulation of mitotic cell cycle phase transition (GO:1901990)regulation of mitotic cytokinesis (GO:1902412)regulation of natural killer cell activation (GO:0032814)regulation of stem cell population maintenance (GO:2000036)replication fork processing (GO:0031297)site of double-strand break (GO:0035861)spermatogenesis (GO:0007283)spindle assembly involved in female meiosis (GO:0007056)ubiquitin ligase complex scaffold activity (GO:0160072)ubiquitin ligase complex scaffold activity (GO:0160072)ubiquitin-dependent protein catabolic process (GO:0006511)ubiquitin-dependent protein catabolic process (GO:0006511)ubiquitin-dependent protein catabolic process (GO:0006511)viral release from host cell (GO:0019076)

Expression (TPM)

TFs regulating DDB1 0 TFs

Transcription factors with Perturb-seq knockdown data for DDB1. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = DDB1 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to DDB1

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of DDB1, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Element	Dist. to TSS	Link type	TFs
chr11:61,158,562–61,159,021	174.4 kb	Distal (>10kb) Multiome	223
chr11:61,160,742–61,162,049	171.7 kb	Distal (>10kb) Multiome	851
chr11:61,281,385–61,282,193	51.5 kb	Distal (>10kb) Multiome	231
chr11:61,294,197–61,295,784	38.0 kb	Distal (>10kb) Multiome	761
chr11:61,332,596–61,333,687	57 bp	At TSS Multiome	897
chr11:61,336,082–61,336,509	3.0 kb	Proximal (<10kb)	454
chr11:61,361,602–61,362,481	28.9 kb	Distal (>10kb) Multiome	905
chr11:61,392,209–61,392,929	59.3 kb	Distal (>10kb) Multiome	800
chr11:61,429,326–61,430,423	96.7 kb	Distal (>10kb) Multiome	975
chr11:61,508,087–61,510,095	175.4 kb	Distal (>10kb) Multiome	740
chr11:61,567,110–61,568,033	234.4 kb	Distal (>10kb) Multiome	1078
chr11:61,580,454–61,581,871	248.1 kb	Distal (>10kb) Multiome	760
chr11:61,587,343–61,588,726	255.1 kb	Distal (>10kb) Multiome	271

Genome Browser

Genomic view of the DDB1 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.