Alternative titles; symbols
HGNC Approved Gene Symbol: DNA2
Cytogenetic location: 10q21.3 Genomic coordinates (GRCh38): 10:68,414,064-68,472,521 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 10q21.3 | ?Seckel syndrome 8 | 615807 | Autosomal recessive | 3 |
| Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 6 | 615156 | Autosomal dominant | 3 |
DNA2 is a conserved helicase/nuclease involved in the maintenance of mitochondrial and nuclear DNA stability (Duxin et al., 2009). DNA2 is critical for long-patch base-excision repair, the predominant pathway for repairing small DNA lesions induced by oxidation, alkylation, and spontaneous hydrolysis. It likely plays a role in the repair of oxidative lesions in mitochondrial DNA (summary by Ronchi et al., 2013).
By sequencing random cDNAs from a myeloid cell line KG-1 cDNA library, Nagase et al. (1995) obtained a DNA2 cDNA that they called KIAA0083. The deduced 1,076-amino acid protein has a putative ATP/GTP-binding site motif A and a predicted transmembrane domain. Northern blot analysis detected low expression in KG-1 and HeLa cells and in thymus, but not in any other human tissue examined. Eki et al. (1996) noted that the C-terminal half of KIAA0083 shares 41% identity with yeast Dna2 helicase over a 458-amino acid overlap. Yeast Dna2 helicase is a DNA-dependent ATPase that unwinds duplex DNA to generate single-stranded DNA, which then acts as a template for DNA polymerization during DNA replication.
By sequence analysis, Zheng et al. (2008) found that the 1,146-amino acid human DNA2 protein has nuclease and ATPase domains in its N-terminal half and a helicase domain in its C-terminal half. However, it lacks the RPA (see 179835)-binding domain and nuclear localization signals found in yeast Dna2. Immunofluorescence microscopy showed that DNA2 colocalized with a mitochondrial marker in HeLa cells. Cell fractionation and Western blot analysis confirmed the presence of DNA2 in mitochondrial extract. DNA2 was resistant to protease treatment, suggesting that it resides in the inner membrane or matrix of mitochondria.
Using confocal immunofluorescence analysis and subcellular fractionation of several human cell lines, Duxin et al. (2009) found that DNA2 localized to both nuclei and mitochondria. Within mitochondria, at least a subfraction of DNA2 localized to DNA-containing nucleoids of the inner membrane and/or matrix.
Ronchi et al. (2013) found relatively high expression of DNA2 in human brain, cerebellum, kidney, and heart tissue, with lower expression in skeletal muscle.
Using a panel of human-rodent hybrid cell lines, Nagase et al. (1995) mapped the DNA2 gene to chromosome 10. Eki et al. (1996) used human-rodent PCR panels and fluorescence in situ hybridization to map the human DNA2 gene to chromosome 10q21.3-q22.1.
Zheng et al. (2008) showed that DNA2 interacted with mitochondrial DNA polymerase-gamma (see 174763) and significantly stimulated its polymerase activity. DNA2 and flap endonuclease-1 (FEN1; 600393) synergistically processed intermediate 5-prime flap structures occurring in DNA replication and long-patch base excision repair (LP-BER) in mitochondria. Depletion of DNA2 from mitochondrial extracts reduced its efficiency in RNA primer removal and LP-BER.
Duxin et al. (2009) found that knockdown of DNA2 in several human cell lines reduced the capacity of mitochondrial DNA to replicate and repair H2O2-induced oxidative DNA lesions. In U2OS human osteosarcoma cells, DNA2 depletion reduced cell growth, caused accumulation of cells in the G2/M phase of the cell cycle, and led to the appearance of aneuploid cells and internuclear chromatin bridges, which are indicative of genomic instability. Some point mutations in the mitochondrial nucleoid helicase Twinkle (C10ORF2; 606075) induced accumulation of DNA2 in nucleoids. Duxin et al. (2009) concluded that DNA2 is essential for the stability of mitochondrial and nuclear DNA.
Progressive External Ophthalmoplegia with Mitochondrial DNA Deletions 6
In 2 sibs and 2 unrelated women with autosomal dominant progressive external ophthalmoplegia with mitochondrial DNA deletions-6 (PEOA6; 615156), Ronchi et al. (2013) identified 3 different heterozygous mutations in the DNA2 gene (601810.0001-601810.0003). The first mutation was identified by exome sequencing of the sibs, and the additional patients were ascertained from a larger cohort of 44 patients with mtDNA deletions. In vitro functional expression assays showed that all mutant proteins had impaired nuclease, helicase, and ATPase activities. The phenotype was characterized by muscle weakness, mainly affecting the lower limbs, external ophthalmoplegia, exercise intolerance, and mitochondrial DNA (mtDNA) deletions on muscle biopsy. Symptoms appeared in childhood or adulthood and showed slow progression.
Seckel Syndrome 8
In an uncle and niece with Seckel syndrome-8 (SCKL8; 615807), both born of consanguineous marriages, Shaheen et al. (2014) identified homozygosity for a 1-bp deletion in the DNA2 gene (601810.0004).
In 2 sibs with autosomal dominant progressive external ophthalmoplegia with DNA deletions-6 (PEOA6; 615156), Ronchi et al. (2013) identified a heterozygous 851G-A transition in exon 5 of the DNA2 gene, resulting in an arg284-to-his (R284H) substitution at a highly conserved residue in the nuclease domain. The side chain of arg284 is in direct DNA contact, suggesting that the mutation may impact substrate binding. The mutation was identified by exome sequencing and confirmed by Sanger sequencing. It was not found in several large control databases and was not present in an unaffected brother. In vitro functional expression assays showed that the R284H mutant protein had a complete loss of nuclease activity and severely impaired helicase activity. Coexpression with wildtype DNA resulted in about half of normal activity, consistent with a loss of function.
In a patient with adult-onset PEOA6 (615156), Ronchi et al. (2013) identified a heterozygous 937A-G transition in exon 5 of the DNA2 gene, resulting in a lys313-to-glu (K313E) substitution at a highly conserved residue in the nuclease domain. The side chain of lys313 is in direct contact with DNA, suggesting that the mutation may impact substrate binding. In vitro functional expression assays showed that the K313E mutant protein had significantly reduced nuclease and helicase activity. Coexpression with wildtype DNA resulted in about half of normal activity, consistent with a loss of function.
In a patient with adult-onset PEOA6 (615156), Ronchi et al. (2013) identified a heterozygous 2167G-A transition in exon 12 of the DNA2 gene, resulting in a val723-to-ile (V723I) substitution at a highly conserved residue between the ATPase and helicase domain. In vitro functional expression assays showed that the V723I mutant protein had decreased nuclease activity (30% of wildtype) and enhanced helicase activity. Coexpression with wildtype DNA resulted in about half of normal activity, consistent with a loss of function.
In an 18-year-old uncle and 9-year-old niece, both born of consanguineous marriages, with short stature and strikingly similar facial features consistent with Seckel syndrome (SCKL8; 615807), Shaheen et al. (2014) identified homozygosity for a 1-bp deletion (c.3372+6delC) in intron 20 of the DNA2 gene, predicted to cause truncation of 1 transcript and abnormal splicing of another 2 transcripts. RT-PCR confirmed the abnormal splicing, revealing 5 aberrant transcripts that all shared the same abnormal donor site but that each had a different acceptor site; all 5 predicted a frameshift and/or truncation. Western blot analysis showed an approximately 50% reduction in protein level compared to controls. Patient fibroblasts exhibited key features of senescence, being remarkably larger and flatter than control fibroblasts; senescence assay showed blue beta-galactosidase staining in addition to the characteristic 'fried egg' appearance. In addition, comet tails were significantly longer in patient cells than controls, suggestive of marked DNA damage sensitivity; the phenotype was rescued by exogenous expression of DNA2. Shaheen et al. (2014) noted that both parental pairs in the extended family had had numerous miscarriages, suggesting that severe reduction in DNA2 may be incompatible with life.
Duxin, J. P., Dao, B., Martinsson, P., Rajala, N., Guittat, L., Campbell, J. L., Spelbrink, J. N., Stewart, S. A. Human Dna2 is a nuclear and mitochondrial DNA maintenance protein. Molec. Cell. Biol. 29: 4274-4282, 2009. [PubMed: 19487465] [Full Text: https://doi.org/10.1128/MCB.01834-08]
Eki, T, Okumura, K., Shiratori, A., Abe, M., Nogami, M., Taguchi, H., Shibata, T., Murakami, Y., Hanaoka, F. Assignment of the closest human homologue (DNA2L; KIAA0083) of the yeast Dna2 helicase gene to chromosome band 10q21.3-q22.1 Genomics 37: 408-410, 1996. [PubMed: 8938459] [Full Text: https://doi.org/10.1006/geno.1996.0581]
Nagase, T, Miyajima, N, Tanaka, A., Sazuka, T., Seki, N., Sato, S., Tabata, S., Ishikawa, K., Kawarabayashi, Y., Kotani, H., Nomura, N. Prediction of the coding sequences of unidentified human genes. III. The coding sequences of 40 new genes (KIAA0081-KIAA0120) deduced by analysis of cDNA clones from human cell line KG-1. DNA Res. 2: 37-43, 1995. [PubMed: 7788527] [Full Text: https://doi.org/10.1093/dnares/2.1.37]
Ronchi, D., Di Fonzo, A., Lin, W., Bordoni, A., Liu, C., Fassone, E., Pagliarani, S., Rizzuti, M., Zheng, L., Filosto, M., Ferro, M. T., Ranieri, M., and 10 others. Mutations in DNA2 link progressive myopathy to mitochondrial DNA instability. Am. J. Hum. Genet. 92: 293-300, 2013. [PubMed: 23352259] [Full Text: https://doi.org/10.1016/j.ajhg.2012.12.014]
Shaheen, R., Faqeih, E., Ansari, S., Abdel-Salam, G., Al-Hassnan, Z. N., Al-Shidi, T., Alomar, R., Sogaty, S., Alkuraya, F. S. Genomic analysis of primordial dwarfism reveals novel disease genes. Genome Res. 24: 291-299, 2014. [PubMed: 24389050] [Full Text: https://doi.org/10.1101/gr.160572.113]
Zheng, L., Zhou, M., Guo, Z., Lu, H., Qian, L., Dai, H., Qiu, J., Yakubovskaya, E., Bogenhagen, D. F., Demple, B., Shen, B. Human DNA2 is a mitochondrial nuclease/helicase for efficient processing of DNA replication and repair intermediates. Molec. Cell 32: 325-336, 2008. [PubMed: 18995831] [Full Text: https://doi.org/10.1016/j.molcel.2008.09.024]