Alternative titles; symbols
HGNC Approved Gene Symbol: PCNA
SNOMEDCT: 1228871002;
Cytogenetic location: 20p12.3 Genomic coordinates (GRCh38): 20:5,114,953-5,126,622 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 20p12.3 | ?Ataxia-telangiectasia-like disorder 2 | 615919 | Autosomal recessive | 3 |
The PCNA gene encodes an essential DNA replication accessory protein. It plays a central role at the replication fork, recruiting and retaining many of the enzymes required for DNA replication and repair (summary by Baple et al., 2014).
Travali et al. (1989) isolated a cDNA clone of the entire human PCNA gene and flanking sequences.
PCNA was originally identified by immunofluorescence as a nuclear protein whose appearance correlated with the proliferative state of the cell. A cell cycle-dependent protein described by Bravo (1986) and called cyclin was shown to be identical to PCNA. The PCNA protein has been highly conserved during evolution; the deduced amino acid sequences of rat and human differ by only 4 of 261 amino acids. The human anti-PCNA autoantibodies react not only with the nuclei of proliferating cells of all experimental animals so far examined but also with the nuclei of plant cells. Suzuka et al. (1989) demonstrated the presence of the PCNA/cyclin-related genes in higher plants.
PCNA is required for replication of SV40 DNA in vitro and has been identified as the auxiliary protein (cofactor) for DNA polymerase delta (174761). Unlike DNA polymerases alpha (312040), beta (174760), and gamma (174763), DNA polymerase delta has exonuclease activity. Since the exonuclease activity is in the 3-prime-to-5-prime direction, DNA polymerase delta has a proofreading activity and is expected to play a significant role in the maintenance of the fidelity of mammalian DNA replication (Suzuka et al., 1989).
It had been speculated that genetic engineering could improve the long-term function of vascular grafts that are prone to atherosclerosis and occlusion. Mann et al. (1995) showed that an 'intraoperative gene therapy approach' using antisense oligodeoxynucleotides to block medial smooth muscle cell proliferation can prevent the accelerated atherosclerosis that is responsible for autologous vein graft failure. Selective prevention of the expression of genes for 2 cell cycle regulatory proteins, PCNA and cell division cycle kinase-2 (CDK2; 116953), was achieved in the smooth muscle cells of rabbit jugular veins grafted into the carotid arteries. This alteration of gene expression successfully redirected vein graft biology away from neointimal hyperplasia and toward medial hypertrophy, yielding conduits that more closely resembled normal arteries. Furthermore, the genetically engineered grafts proved resistant to diet-induced atherosclerosis.
Hasan et al. (2001) demonstrated that p300 (602700) may have a role in DNA repair synthesis through its interaction with PCNA. Hasan et al. (2001) demonstrated that in vitro and in vivo p300 forms a complex with PCNA that does not depend on the S phase of the cell cycle. A large fraction of both p300 and PCNA colocalized to speckled structures in the nucleus. Furthermore, the endogenous p300-PCNA complex stimulates DNA synthesis in vitro. Chromatin immunoprecipitation experiments indicated that p300 is associated with freshly synthesized DNA after ultraviolet irradiation. Hasan et al. (2001) suggested the p300 may participate in chromatin remodeling at DNA lesion sites to facilitate PCNA function in DNA repair synthesis.
The RAD6 pathway (312180, 179095) is central to postreplicative DNA repair in eukaryotic cells. Two principal elements of this pathway are the ubiquitin-conjugating enzymes RAD6 and the MMS2 (603001)-UBC13 (603679) heterodimer, which are recruited to chromatin by the RING finger proteins RAD18 (605256) and RAD5 (608048), respectively. Hoege et al. (2002) showed that UBC9 (601661), a SUMO (see 601912)-conjugating enzyme, is also affiliated with this pathway and that PCNA, a DNA polymerase sliding clamp involved in DNA synthesis and repair, is a substrate. PCNA is monoubiquitinated through RAD6 and RAD18, modified by lys63-linked multiubiquitination, which additionally requires MMS2, UBC13, and RAD5, and is conjugated to SUMO by UBC9. All 3 modifications affect the same lysine residue of PCNA, lys164, suggesting that they label PCNA for alternative functions. Hoege et al. (2002) demonstrated that these modifications differentially affect resistance to DNA damage, and that damage-induced PCNA ubiquitination is elementary for DNA repair and occurs at the same conserved residue in yeast and humans.
SUMO uses a ubiquitin conjugation system to counteract the effects of ubiquitination. Ubiquitin and SUMO compete for modification of PCNA, an essential processivity factor for DNA replication and repair. Whereas multiubiquitination is mediated by components of the RAD6 pathway and promotes error-free repair, SUMO modification is associated with replication. Stelter and Ulrich (2003) demonstrated that RAD6-mediated monoubiquitination of PCNA activates translesion DNA synthesis by the damage-tolerant polymerases eta (603968) and zeta (602776) in yeast. Moreover, polymerase zeta is differentially affected by monoubiquitin and SUMO modification of PCNA. Whereas ubiquitination is required for damage-induced mutagenesis, both SUMO and monoubiquitin contribute to spontaneous mutagenesis in the absence of DNA damage. Stelter and Ulrich (2003) concluded that their data assigned a function to SUMO during S phase and demonstrated how ubiquitin and SUMO, by regulating the accuracy of replication and repair, contribute to overall genomic stability.
Poot et al. (2004) identified 4 potential PCNA-binding motifs in Williams syndrome transcription factor (WSTF, or BAZ1B; 605681). By immunoprecipitation and in vitro protein pull-down experiments with HeLa cell nuclear extracts, they confirmed a direct interaction between PCNA and WSTF that did not require DNA. The complex containing PCNA was distinct from the WSTF-including nucleosome assembly complex (WINAC). Poot et al. (2004) found that PCNA targeted WSTF to DNA replication foci, and WSTF, in turn, recruited SNF2H (SMARCA5; 603375) to replication sites. RNA interference-mediated depletion of WSTF or SNF2H caused compaction of newly replicated chromatin and increased the amount of heterochromatin markers.
In yeast, chromatid cohesion is essential for viability and is triggered by the conserved protein Eco1. Moldovan et al. (2006) found that yeast Eco1 and its human homolog, ESCO2 (609353), interacted directly with PCNA via a conserved PIP box variant in their N termini. Yeast Eco1 mutants deficient in Eco1-Pcna interaction were defective in chromatid cohesion and inviable. Moldovan et al. (2006) concluded that PCNA is crucially involved in the establishment of cohesion in S phase.
Maga et al. (2007) analyzed the effects of human PCNA and replication protein A (RPA; 179835) on 6 different human DNA polymerases belonging to the B, Y, and X classes during in vitro bypass of different lesions. The mutagenic lesion 8-oxo-guanine has high miscoding potential. A major and specific effect was found for 8-oxo-G bypass with DNA pol-lambda (606343) and -eta (603968). PCNA and RPA allowed correct incorporation of dCTP opposite an 8-oxo-G template 1,200-fold more efficiently than the incorrect dATP by DNA pol-lambda, and 68-fold by DNA pol-eta, respectively. Experiments with DNA pol-gamma (174763)-null cell extracts suggested an important role for DNA pol-lambda. On the other hand, DNA pol-iota (605252) together with DNA pol-alpha (312040), -delta (174761), and -beta (174760), showed a much lower correct bypass efficiency. Maga et al. (2007) concluded that their findings showed the existence of an accurate mechanism to reduce the deleterious consequences of oxidative damage and, in addition, pointed to an important role for PCNA and RPA in determining a functional hierarchy among different DNA pols in lesion bypass.
Vannier et al. (2013) established that RTEL1 (608833) associates with the replisome through binding to PCNA. Mouse cells disrupted for the Rtel1-Pcna interaction (mutant in PIP; 176720) exhibited accelerated senescence, replication fork instability, reduced replication fork extension rates, and increased origin usage. Although T-loop disassembly at telomeres was unaffected in the mutant cells, telomere replication was compromised, leading to fragile sites at telomeres. Rtel1-Pip mutant mice were viable, but loss of the Rtel1-Pcna interaction accelerated the onset of tumorigenesis in p53 (191170)-deficient mice. Vannier et al. (2013) proposed that RTEL1 plays a critical role in both telomere and genomewide replication, which is crucial for genetic stability and tumor avoidance.
Dilley et al. (2016) defined break-induced telomere synthesis and showed that it utilizes a specialized replisome, which underlies alternate lengthening of telomeres (ALT) maintenance. DNA double-strand breaks enact nascent telomere synthesis by long-tract unidirectional replication. PCNA loading by replication factor C (RFC; see 102579) acts as the initial sensor of telomere damage to establish predominance of DNA polymerase delta through its POLD3 (611415) subunit. Break-induced telomere synthesis requires the RFC-PCNA-Pol-delta axis, but is independent of other canonical replisome components, ATM (607585) and ATR (601215), or the homologous recombination protein Rad51 (179617).
Cannavo et al. (2020) showed that human MutS-gamma, a complex of MSH4 (602105) and MSH5 (603382) that supports crossing over, bound branched recombination intermediates and associated with MutL-gamma, a complex of MLH1 (120436) and MLH3 (604395), stabilizing the ensemble at joint molecule structures and adjacent double-stranded DNA. MutS-gamma directly stimulated DNA cleavage by the MutL-gamma endonuclease. MutL-gamma activity was further stimulated by exonuclease-1 (EXO1; 606063), but only when MutS-gamma was present. RFC and PCNA were additional components of the nuclease ensemble, thereby triggering crossing over. S. cerevisiae strains in which MutL-gamma could not interact with Pcna presented defects in forming crossovers. The MutL-gamma-MutS-gamma-EXO1-RFC-PCNA nuclease ensemble preferentially cleaved DNA with Holliday junctions, but it showed no canonical resolvase activity. Instead, the data suggested that the nuclease ensemble processed meiotic recombination intermediates by nicking double-stranded DNA adjacent to the junction points. The authors proposed that, since DNA nicking by MutL-gamma depends on its cofactors, the asymmetric distribution of MutS-gamma and RFC-PCNA on meiotic recombination intermediates may drive biased DNA cleavage. They suggested that this mode of MutL-gamma nuclease activation may explain crossover-specific processing of Holliday junctions or their precursors in meiotic chromosomes.
Independently, Kulkarni et al. (2020) showed that PCNA was important for crossover-biased resolution. In vitro assays with human enzymes showed that PCNA and RFC were sufficient to activate the MutL-gamma endonuclease. MutL-gamma was further stimulated by the codependent activity of the pro-crossover factors EXO1 and MutS-gamma, the latter of which binds Holliday junctions. The authors found that MutL-gamma also bound various branched DNAs, including Holliday junctions, but it did not show canonical resolvase activity, suggesting that the endonuclease incises adjacent to junction branch points to achieve resolution. In vivo, Rfc facilitated MutL-gamma-dependent crossing over in budding yeast. Moreover, Pcna localized to prospective crossover sites along synapsed chromosomes. Kulkarni et al. (2020) concluded that their data highlight similarities between crossover resolution and the initiation steps of DNA mismatch repair and evoke a novel model for crossover-specific resolution of double Holliday junctions during meiosis.
Crystal Structure
Bowman et al. (2004) reported the crystal structure of the 5-protein clamp loader complex (RFC) of the yeast S. cerevisiae, bound to the sliding clamp (PCNA). Tight interfacial coordination of the ATP analog ATP-gamma-S by RFC resulted in a spiral arrangement of the ATPase domains of the clamp loader above the PCNA ring. Placement of a model for primed DNA within the central hole of PCNA revealed a striking correspondence between the RFC spiral and the grooves of the DNA double helix. Bowman et al. (2004) concluded that this model, in which the clamp loader complex locks into primed DNA in a screwcap-like arrangement, provides a simple explanation for the process by which the engagement of primer-template junctions by the RFC:PCNA complex results in ATP hydrolysis and release of the sliding clamp on DNA.
Travali et al. (1989) showed that the human PCNA gene is present in single copy and has 6 exons. It spans 4,961 bp, from the cap site to the poly(A) signal. An unusual feature was the presence of extensive sequence similarities among introns and between introns and exons.
Ku et al. (1989) mapped the PCNA gene to chromosome 20 by Southern analysis of somatic cell hybrid DNA. Two pseudogenes were identified, one mapping to Xpter-q13 and a second mapping to 6pter-p12. By in situ hybridization, Webb et al. (1990) assigned the locus to 20p13. They also found 2 strong secondary peaks of grains over 11p15.1 and Xp11.4. From studies by in situ hybridization, Rao et al. (1991) concluded that the PCNA gene is located at or close to 20p12.
PSEUDOGENES
Taniguchi et al. (1996) characterized 2 'new' PCNA pseudogenes that are tandemly localized on 4q24. One is a pseudogene and the other is a truncated pseudogene.
In 4 individuals from an extended Ohio Amish pedigree with ataxia-telangiectasia-like disorder-2 (ATLD2; 615919), Baple et al. (2014) identified a homozygous missense mutation in the PCNA gene (S228I; 176740.0001). The mutation was found by homozygosity mapping followed by candidate gene sequencing. In vitro studies as well as studies of patient cells showed that the mutation caused a defect in nucleotide excision repair. Affected individuals had a neurodegenerative phenotype characterized by developmental delay, ataxia, and sensorineural hearing loss. Other features included short stature, cutaneous and ocular telangiectasia, and photosensitivity.
In 4 individuals from an extended Ohio Amish pedigree with ataxia-telangiectasia-like disorder-2 (ATLD2; 615919), Baple et al. (2014) identified a homozygous c.683G-T transversion in exon 6 of the PCNA gene, resulting in a ser228-to-ile (S228I) substitution at a highly conserved residue. The mutation, which was found by homozygosity mapping followed by candidate gene sequencing, segregated with the disorder in the family, and was not found in 360 control chromosomes. Two heterozygous carriers were found among 310 Ohio Amish control chromosomes, and 1 carrier was found in the 1000 Genomes Project and Exome Variant Server databases. Studies in patient cells showed that the mutation did not interfere with the major replicative function of PCNA and that bulk DNA replication was not perturbed. However, patient cells showed marked abnormalities in response to UV irradiation compared to controls, including decreased survival, decreased unscheduled DNA synthesis, and decreased RNA synthesis recovery. The findings were consistent with a defect in nucleotide excision repair (NER), particularly transcription-coupled NER. Further experiments demonstrated a significant reduction in the interaction of mutant PCNA with the binding partners FEN1 (600393), LIG1 (126391), and XPG (ERCC5; 133530) compared to wildtype. Baple et al. (2014) concluded that the S228I mutant is a hypomorphic allele.
Baple, E. L., Chambers, H., Cross, H. E., Fawcett, H., Nakazawa, Y., Chioza, B. A., Harlalka, G. V., Mansour, S., Sreekantan-Nair, A., Patton, M. A., Muggenthaler, M., Rich, P., and 10 others. Hypomorphic PCNA mutation underlies a human DNA repair disorder. J. Clin. Invest. 124: 3137-3146, 2014. [PubMed: 24911150] [Full Text: https://doi.org/10.1172/JCI74593]
Bowman, G. D., O'Donnell, M., Kuriyan, J. Structural analysis of a eukaryotic sliding DNA clamp-clamp loader complex. Nature 429: 724-730, 2004. [PubMed: 15201901] [Full Text: https://doi.org/10.1038/nature02585]
Bravo, R. Synthesis of the nuclear protein cyclin (PCNA) and its relationship with DNA replication. Exp. Cell Res. 163: 287-293, 1986. [PubMed: 2869964] [Full Text: https://doi.org/10.1016/0014-4827(86)90059-5]
Cannavo, E., Sanchez, A., Anand, R., Ranjha, L., Hugener, J., Adam, C., Acharya, A., Weyland, N., Aran-Guiu, X., Charbonnier, J.-B., Hoffmann, E. R., Borde, V., Matos, J., Cejka, P. Regulation of the MLH1-MLH3 endonuclease in meiosis. Nature 586: 618-622, 2020. Note: Erratum: Nature 590: E29, 2021. Electronic Article. [PubMed: 32814904] [Full Text: https://doi.org/10.1038/s41586-020-2592-2]
Dilley, R. L., Verma, P., Cho, N. W., Winters, H. D., Wondisford, A. R., Greenberg, R. A. Break-induced telomere synthesis underlies alternative telomere maintenance. Nature 539: 54-58, 2016. [PubMed: 27760120] [Full Text: https://doi.org/10.1038/nature20099]
Hasan, S., Hassa, P. O., Imhof, R., Hottiger, M. O. Transcription coactivator p300 binds PCNA and may have a role in DNA repair synthesis. Nature 410: 387-391, 2001. [PubMed: 11268218] [Full Text: https://doi.org/10.1038/35066610]
Hoege, C., Pfander, B., Moldovan, G.-L., Pyrowolakis, G., Jentsch, S. RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature 419: 135-141, 2002. [PubMed: 12226657] [Full Text: https://doi.org/10.1038/nature00991]
Ku, D.-H., Travali, S., Calabretta, B., Huebner, K., Baserga, R. Human gene for proliferating cell nuclear antigen has pseudogenes and localizes to chromosome 20. Somat. Cell Molec. Genet. 15: 297-307, 1989. [PubMed: 2569765] [Full Text: https://doi.org/10.1007/BF01534969]
Kulkarni, D. S., Owens, S. N., Honda, M., Ito, M., Yang, Y., Corrigan, M. W., Chen, L., Quan, A. L., Hunter, N. PCNA activates the MutL-gamma endonuclease to promote meiotic crossing over. Nature 586: 623-627, 2020. Note: Erratum: Nature 590: E30, 2021. Electronic Article. [PubMed: 32814343] [Full Text: https://doi.org/10.1038/s41586-020-2645-6]
Maga, G., Villani, G., Crespan, E., Wimmer, U., Ferrari, E., Bertocci, B., Hubscher, U. 8-oxo-guanine bypass by human DNA polymerases in the presence of auxiliary proteins. Nature 447: 606-608, 2007. [PubMed: 17507928] [Full Text: https://doi.org/10.1038/nature05843]
Mann, M. J., Gibbons, G. H., Kernoff, R. S., Diet, F. P., Tsao, P. S., Cooke, J. P., Kaneda, Y., Dzau, V. J. Genetic engineering of vein grafts resistant to atherosclerosis. Proc. Nat. Acad. Sci. 92: 4502-4506, 1995. [PubMed: 7753833] [Full Text: https://doi.org/10.1073/pnas.92.10.4502]
Moldovan, G.-L., Pfander, B., Jentsch, S. PCNA controls establishment of sister chromatid cohesion during S phase. Molec. Cell 23: 723-732, 2006. [PubMed: 16934511] [Full Text: https://doi.org/10.1016/j.molcel.2006.07.007]
Poot, R. A., Bozhenok, L., van den Berg, D. L. C., Steffensen, S., Ferreira, F., Grimaldi, M., Gilbert, N., Ferreira, J., Varga-Weisz, P. D. The Williams syndrome transcription factor interacts with PCNA to target chromatin remodelling by ISWI to replication foci. Nature Cell Biol. 6: 1236-1244, 2004. [PubMed: 15543136] [Full Text: https://doi.org/10.1038/ncb1196]
Rao, V. V. N. G., Schnittger, S., Hansmann, I. Chromosomal localization of the human proliferating cell nuclear antigen (PCNA) gene to or close to 20p12 by in situ hybridization. Cytogenet. Cell Genet. 56: 169-170, 1991. [PubMed: 1675981] [Full Text: https://doi.org/10.1159/000133079]
Stelter, P., Ulrich, H. D. Control of spontaneous and damage-induced mutagenesis by SUMO and ubiquitin conjugation. Nature 425: 188-191, 2003. [PubMed: 12968183] [Full Text: https://doi.org/10.1038/nature01965]
Suzuka, I., Daidoji, H., Matsuoka, M., Kadowaki, K., Takasaki, Y., Nakane, P. K., Moriuchi, T. Gene for proliferating-cell nuclear antigen (DNA polymerase delta auxiliary protein) is present in both mammalian and higher plant genomes. Proc. Nat. Acad. Sci. 86: 3189-3193, 1989. [PubMed: 2566167] [Full Text: https://doi.org/10.1073/pnas.86.9.3189]
Taniguchi, Y., Katsumata, Y., Koido, S., Suemizu, H., Yoshimura, S., Moriuchi, T., Okumura, K., Kagotani, K., Taguchi, H., Imanishi, T., Gojobori, T., Inoko, H. Cloning, sequencing, and chromosomal localization of two tandemly arranged human pseudogenes for the proliferating cell nuclear antigen (PCNA). Mammalian Genome 7: 906-908, 1996. [PubMed: 8995762] [Full Text: https://doi.org/10.1007/s003359900266]
Travali, S., Ku, D.-H., Rizzo, M. G., Ottavio, L., Baserga, R., Calabretta, B. Structure of the human gene for the proliferating cell nuclear antigen. J. Biol. Chem. 264: 7466-7472, 1989. [PubMed: 2565339]
Vannier, J.-B., Sandhu, S., Petalcorin, M. I. R., Wu, X., Nabi, Z., Ding, H., Boulton, S. J. RTEL1 is a replisome-associated helicase that promotes telomere and genome-wide replication. Science 342: 239-242, 2013. [PubMed: 24115439] [Full Text: https://doi.org/10.1126/science.1241779]
Webb, G., Parsons, P., Chenevix-Trench, G. Localization of the gene for human proliferating nuclear antigen/cyclin by in situ hybridization. Hum. Genet. 86: 84-86, 1990. [PubMed: 1979311] [Full Text: https://doi.org/10.1007/BF00205180]