Alternative titles; symbols
HGNC Approved Gene Symbol: FEN1
Cytogenetic location: 11q12.2 Genomic coordinates (GRCh38): 11:61,792,911-61,797,238 (from NCBI)
Harrington and Lieber (1994) purified and cloned the gene for a DNA structure-specific endonuclease, FEN1, from mouse cells. In a second publication, Harrington and Lieber (1994) showed that functional domains within FEN1 and RAD2 (133530) define a family of structure-specific endonucleases. The murine protein recognizes 5-prime DNA flap structures that have been proposed in DNA replication, repair, and recombination. Hiraoka et al. (1995) reported the sequence of the human FEN1 gene. They showed that the translated sequence is identical to the peptide sequence obtained from maturation factor-1 (MF1), which is 1 of the 10 essential proteins for cell-free DNA replication. The human protein has the same structure-specific DNA endonuclease activity as the murine protein.
Gordenin et al. (1997) examined the mechanism of expansion of triplet repeat sequences. They pointed to the work of Kolodner and colleagues (Tishkoff et al., 1997) concerning RAD27 endonuclease, which, as well as its mammalian homolog FEN1, is responsible for removing a 5-prime flap that is generated by displacement synthesis when DNA polymerase encounters the 5-prime end of a downstream Okazaki fragment. Gordenin et al. (1997) stated that 'an emerging view holds that the integrity of DNA is determined by a critical interplay between DNA metabolic enzymes and specific DNA sequences, which we term At-Risk Motifs (ARMs).' According to their hypothesis, FEN1-resistant flap sequences provide a class of ARMs in that they are poor substrates for a specific enzymatic process that normally protects the genome against mutations.
FEN1 removes 5-prime overhanging flaps in DNA repair and processes the 5-prime ends of Okazaki fragments in lagging strand DNA synthesis. Hosfield et al. (1998) noted that the crystal structure of Pyrococcus furiosus FEN1, active-site metal ions, and mutational information indicated interactions for the single- and double-stranded portions of the flap DNA substrate and identified an unusual DNA-binding motif. The active-site structure of the enzyme suggested that DNA binding induces FEN1 to clamp onto the cleavage junction to form the productive complex. The conserved FEN1 carboxyl terminus binds proliferating cell nuclear antigen (PCNA) and positions FEN1 to act primarily as an exonuclease in DNA replication, in contrast to its endonuclease activity in DNA repair. Hosfield et al. (1998) predicted that FEN1 mutations altering PCNA binding should reduce activity during replication, likely causing DNA repeat expansions as seen in some cancers and genetic diseases.
The mechanism by which trinucleotide expansion occurs in human genes is not understood. It has been hypothesized that DNA secondary structure may actively participate by preventing FEN1 cleavage of displaced Okazaki fragments. Spiro et al. (1999) showed that secondary structure can, indeed, play a role in expansion through a FEN1-dependent mechanism. They found that secondary structure inhibits flap processing at CAG, CGG, or CTG repeats in a length-dependent manner by concealing the 5-prime end of the flap that is necessary for both binding and cleavage by FEN1. Thus, secondary structure can defeat the protective function of FEN1, leading to site-specific expansions. However, Spiro et al. (1999) found that when FEN1 is absent from the cell, alternative pathways to simple inhibition of flap processing contribute to expansion.
The flap endonuclease, FEN1, is an evolutionarily conserved component of DNA replication from archaebacteria to humans. Based on in vitro results, it processes Okazaki fragments during replication and is involved in base excision repair. FEN1 removes the last primer ribonucleotide on the lagging strand and it cleaves a 5-prime flap that may result from strand displacement during replication or during base excision repair. Its biologic importance has been revealed largely through studies in the yeast Saccharomyces cerevisiae, wherein deletion of the homologous gene Rad27 results in genome instability and mutagen sensitivity. While the in vivo function of Rad27 has been well characterized through genetic and biochemical approaches, little is understood about the in vivo functions of human FEN1. Greene et al. (1999) explored the function of human FEN1 in yeast. They found that the human FEN1 protein complements a yeast Rad27 null mutant for a variety of defects including mutagen sensitivity, genetic instability, and the synthetic lethal interactions such as a Rad27/Rad51 mutant. Furthermore, a mutant form of FEN1 lacking nuclease function exhibited dominant-negative effects on cell growth and genome instability similar to those seen with the homologous yeast Rad27 mutation. This genetic impact was stronger when the human and yeast PCNA-binding domains were exchanged. These findings indicated that the human FEN1 and yeast Rad27 proteins act on the same substrate in vivo. They defined a sensitive yeast system for the identification and characterization of mutations in FEN1.
Hasan et al. (2001) found that p300 (602700) formed a complex with FEN1 and acetylated FEN1 in vitro. Furthermore, FEN1 acetylation was observed in vivo and was enhanced upon ultraviolet treatment of human cells. Acetylation of the FEN1 C terminus by p300 significantly reduced DNA binding and nuclease activity of FEN1. PCNA was able to stimulate both acetylated and unacetylated FEN1 activity to the same extent. These results identified acetylation as a novel regulatory modification of FEN1 and suggested that p300 is not only a component of the chromatin remodeling machinery but might also play a critical role in regulating DNA metabolic events.
Huggins et al. (2002) prepared model nucleosome substrates containing FEN1-cleavable DNA flaps. They found that human FEN1 bound and cleaved such substrates with efficiencies similar to that displayed with naked DNA. Moreover, both FEN1 and human DNA ligase I (126391) could operate successively on DNA within the same nucleosome. These results suggested that some base excision repair steps may not require nucleosome remodeling in vivo and that FEN1 activity during Okazaki fragment processing can occur on nucleosomal substrates.
Werner syndrome (WRN; 277700), a genetic disorder characterized by genomic instability, elevated recombination, and replication defects, is caused by mutation in the RECQL2 gene (604611), which encodes a RecQ helicase. Sharma et al. (2004) examined the ability of RECQL2 to rescue cellular phenotypes of a yeast dna2 mutant defective in a helicase-endonuclease that participates with FEN1 in Okazaki fragment processing. Complementation studies indicated that a conserved noncatalytic C-terminal domain of human RECQL2 rescued dna2-1 mutant phenotypes of growth, cell cycle arrest, and sensitivity to the replication inhibitor hydroxyurea or DNA-damaging agent methylmethane sulfonate. Physical interactions between RECQL2 and yeast FEN1 were demonstrated by coimmunoprecipitation, affinity pull-down experiments, and by ELISA assays with purified recombinant proteins. Biochemical analyses demonstrated that the C-terminal domain of RECQL2 or RECQL3 (604610) stimulated FEN1 cleavage of its proposed physiologic substrates during replication. Sharma et al. (2004) suggested that the RECQL2-FEN1 interaction is biologically important in DNA metabolism and supported a role of the conserved noncatalytic domain of a human RecQ helicase in DNA replication intermediate processing.
Using human genomic clones homologous to the mouse Fen1 gene, Hiraoka et al. (1995) found that fluorescence in situ hybridization yielded 2 hybridization signals on 11q12 and 1p22.2. The localization on human 11q12 was confirmed using radiation-reduced hybrids. The mouse Fen1 gene was assigned to chromosome 19 based on somatic cell hybrids.
By genomic sequence analysis, Adachi et al. (2002) determined that the 5-prime ends of the FEN1 gene and TMEM258 gene (617615) overlap on chromosome 11q12. The 5-prime ends of TMEM258 and FEN1 overlap.
Data from Saccharomyces cerevisiae suggested that FEN1 plays a role in expansion of repetitive DNA tracts. Otto et al. (2001) hypothesized that insufficiency of FEN1 or a mutant FEN1 might contribute to the occurrence of expansion events of long repetitive DNA tracts after polymerase slippage events during lagging strand synthesis in a condition such as Huntington disease (HD; 143100). They studied 15 HD parent/child pairs that demonstrated intergenerational increases in CAG length of greater than 10 repeats for possible mutations or polymorphisms within the FEN1 gene that could underlie the saltatory repeat expansions seen in these individuals. No alterations were observed compared to 50 controls, excluding FEN1 as a trans-acting factor underlying trinucleotide repeat expansion.
Zheng et al. (2007) screened 253 human specimens of 12 common cancers for FEN1 mutations by directly sequencing the coding region of the gene. The authors detected 5 mutations in 71 nonsmall cell lung carcinoma specimens. They also identified a missense mutation in melanoma and a silent mutation in esophageal cancer. The same mutations were not found in corresponding paired normal tissues, suggesting they were somatic mutations. Two additional mutations were identified from breast adenocarcinomas and another in a kidney hypernephroma. Nuclease activity profiling analysis revealed that several mutations were defective in 5-prime exonuclease (EXO) and gep-dependent endonuclease (GEN) activities, but retained flap-dependent endonuclease activity.
Because mutations in some genes involved in DNA replication and repair cause cancer predisposition, Kucherlapati et al. (2002) investigated the possibility that FEN1 may function in tumorigenesis of the gastrointestinal tract. Using gene knockout approaches, they introduced a null mutation into mouse Fen1. Mice homozygous for the Fen1 mutation were not obtained, suggesting that absence of Fen1 expression leads to embryonic lethality. Most Fen1 heterozygous animals appeared normal. However, when combined with a mutation in the adenomatous polyposis coli (APC; 611731) gene, double heterozygous animals had increased numbers of adenocarcinomas and decreased survival. The tumors from these mice showed microsatellite instability. Because one copy of the Fen1 gene remained intact in tumors, Fen1 haploinsufficiency appears to lead to rapid progression of cancer.
Using a gene targeting approach, Zheng et al. (2007) generated mice heterozygous and homozygous for a Fen1 point mutation, E160D, which abolished more than 90% of the 5-prime exonuclease (EXO) and gap-dependent endonuclease (GEN) activities of Fen1 but retained the flap-specific endonuclease activity. Selective elimination of nuclease activities led to frequent spontaneous mutations and accumulation of incompletely digested DNA fragments in apoptotic cells. Heterozygous and homozygous mice developed autoimmunity, chronic inflammation, and cancer, primarily benign lung adenoma, but malignant testis, ovary, and liver tumors were also seen. Zheng et al. (2007) concluded that the mutator phenotype resulted in the initiation of cancer, whereas the chronic inflammation promoted cancer progression.
Adachi, N., Karanjawala, Z. E., Matsuzaki, Y., Koyama, H., Lieber, M. R. Two overlapping divergent transcription units in the human genome: the FEN1/C11orf10 locus. OMICS 6: 273-279, 2002. [PubMed: 12427278] [Full Text: https://doi.org/10.1089/15362310260256927]
Gordenin, D. A., Kunkel, T. A., Resnick, M. A. Repeat expansion--all in a flap? Nature Genet. 16: 116-118, 1997. [PubMed: 9171819] [Full Text: https://doi.org/10.1038/ng0697-116]
Greene, A. L., Snipe, J. R., Gordenin, D. A., Resnick, M. A. Functional analysis of human FEN1 in Saccharomyces cerevisiae and its role in genome stability. Hum. Molec. Genet. 8: 2263-2273, 1999. [PubMed: 10545607] [Full Text: https://doi.org/10.1093/hmg/8.12.2263]
Harrington, J. J., Lieber, M. R. Functional domains within FEN-1 and RAD2 define a family of structure-specific endonucleases: implications for nucleotide excision repair. Genes Dev. 8: 1344-1355, 1994. [PubMed: 7926735] [Full Text: https://doi.org/10.1101/gad.8.11.1344]
Harrington, J. J., Lieber, M. R. The characterization of a mammalian DNA structure-specific endonuclease. EMBO J. 13: 1235-1246, 1994. [PubMed: 8131753] [Full Text: https://doi.org/10.1002/j.1460-2075.1994.tb06373.x]
Hasan, S., Stucki, M., Hassa, P. O., Imhof, R., Gehrig, P., Hunziker, P., Hubscher, U., Hottiger, M. O. Regulation of human flap endonuclease-1 activity by acetylation through the transcriptional coactivator p300. Molec. Cell 7: 1221-1231, 2001. [PubMed: 11430825] [Full Text: https://doi.org/10.1016/s1097-2765(01)00272-6]
Hiraoka, L. R., Harrington, J. J., Gerhard, D. S., Lieber, M. R., Hsieh, C.-L. Sequence of human FEN-1, a structure-specific endonuclease, and chromosomal localization of the gene (FEN1) in mouse and human. Genomics 25: 220-225, 1995. [PubMed: 7774922] [Full Text: https://doi.org/10.1016/0888-7543(95)80129-a]
Hosfield, D. J., Mol, C. D., Shen, B., Tainer, J. A. Structure of the DNA repair and replication endonuclease and exonuclease FEN-1: coupling DNA and PCNA binding to FEN-1 activity. Cell 95: 135-146, 1998. [PubMed: 9778254] [Full Text: https://doi.org/10.1016/s0092-8674(00)81789-4]
Huggins, C. F., Chafin, D. R., Aoyagi, S., Henricksen, L. A., Bambara, R. A., Hayes, J. J. Flap endonuclease 1 efficiently cleaves base excision repair and DNA replication intermediates assembled into nucleosomes. Molec. Cell 10: 1201-1211, 2002. [PubMed: 12453426] [Full Text: https://doi.org/10.1016/s1097-2765(02)00736-0]
Kucherlapati, M., Yang, K., Kuraguchi, M., Zhao, J., Lia, M., Heyer, J., Kane, M. F., Fan, K., Russell, R., Brown, A. M. C., Kneitz, B., Edelmann, W., Kolodner, R. D., Lipkin, M., Kucherlapati, R. Haploinsufficiency of Flap endonuclease (Fen1) leads to rapid tumor progression. Proc. Nat. Acad. Sci. 99: 9924-9929, 2002. [PubMed: 12119409] [Full Text: https://doi.org/10.1073/pnas.152321699]
Otto, C. J., Almqvist, E., Hayden, M. R., Andrew, S. E. The 'flap' endonuclease gene FEN1 is excluded as a candidate gene implicated in the CAG repeat expansion underlying Huntington disease. Clin. Genet. 59: 122-127, 2001. [PubMed: 11260214] [Full Text: https://doi.org/10.1034/j.1399-0004.2001.590210.x]
Sharma, S., Sommers, J. A., Brosh, R. M., Jr. In vivo function of the conserved non-catalytic domain of Werner syndrome helicase in DNA replication. Hum. Molec. Genet. 13: 2247-2261, 2004. [PubMed: 15282207] [Full Text: https://doi.org/10.1093/hmg/ddh234]
Spiro, C., Pelletier, R., Rolfsmeier, M. L., Dixon, M. J., Lahue, R. S., Gupta, G., Park, M. S., Chen, X., Mariappan, S. V. S., McMurray, C. T. Inhibition of FEN-1 processing by DNA secondary structure at trinucleotide repeats. Molec. Cell 4: 1079-1085, 1999. [PubMed: 10635332] [Full Text: https://doi.org/10.1016/s1097-2765(00)80236-1]
Tishkoff, D. X., Filosi, N., Gaida, G. M., Kolodner, R. D. A novel mutation avoidance mechanism dependent on S. cerevisiae RAD27 is distinct from DNA mismatch repair. Cell 88: 253-263, 1997. [PubMed: 9008166] [Full Text: https://doi.org/10.1016/s0092-8674(00)81846-2]
Zheng, L., Dai, H., Zhou, M., Li, M., Singh, P., Qiu, J., Tsark, W., Huang, Q., Kerstine, K., Zhang, X., Lin, D., Shen, B. Fen1 mutations result in autoimmunity, chronic inflammation and cancers. Nature Med. 13: 812-819, 2007. [PubMed: 17589521] [Full Text: https://doi.org/10.1038/nm1599]