{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T13:58:16Z","timestamp":1740146296180,"version":"3.37.3"},"reference-count":42,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2018,3,9]],"date-time":"2018-03-09T00:00:00Z","timestamp":1520553600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ministry of Education, Science and Technology (KR)","award":["2009-0093821"],"award-info":[{"award-number":["2009-0093821"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0193823","type":"journal-article","created":{"date-parts":[[2018,3,9]],"date-time":"2018-03-09T18:32:22Z","timestamp":1520620342000},"page":"e0193823","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":4,"title":["Yeast-based assays for characterization of the functional effects of single nucleotide polymorphisms in human DNA repair genes"],"prefix":"10.1371","volume":"13","author":[{"given":"Changshin","family":"Kim","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinmo","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Su-Hyun","family":"Jeong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hayoung","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Geun-hee","family":"Park","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hwa Beom","family":"Shin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"MyungJa","family":"Ro","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kyoung-Yeon","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"YoungJoon","family":"Park","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Keun Pil","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7784-512X","authenticated-orcid":true,"given":"KyuBum","family":"Kwack","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2018,3,9]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"7915","DOI":"10.1073\/pnas.90.17.7915","article-title":"Oxidants, antioxidants, and the degenerative diseases of aging","volume":"90","author":"BN Ames","year":"1993","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"808934","DOI":"10.1155\/2012\/808934","article-title":"Transcriptional Regulation of the p53 Tumor Suppressor Gene in S-Phase of the Cell-Cycle and the Cellular Response to DNA Damage","volume":"2012","author":"D Reisman","year":"2012","journal-title":"Biochem Res Int"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1016\/0092-8674(95)90385-2","article-title":"The retinoblastoma protein and cell cycle control","volume":"81","author":"RA Weinberg","year":"1995","journal-title":"Cell"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1080\/095530098141429","article-title":"Conservation of eukaryotic DNA repair mechanisms","volume":"74","author":"EM Taylor","year":"1998","journal-title":"Int J Radiat Biol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"e203","DOI":"10.1371\/journal.pbio.0040203","article-title":"DNA repair: dynamic defenders against cancer and aging","volume":"4","author":"JO Fuss","year":"2006","journal-title":"PLoS Biol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1016\/j.molcel.2010.02.009","article-title":"Three DNA polymerases, recruited by different mechanisms, carry out NER repair synthesis in human cells","volume":"37","author":"T Ogi","year":"2010","journal-title":"Mol Cell"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.dnarep.2015.03.007","article-title":"Cell cycle regulation of human DNA repair and chromatin remodeling genes","volume":"30","author":"R Mjelle","year":"2015","journal-title":"DNA Repair (Amst)"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1126\/science.7624801","article-title":"Excision of deoxyribose phosphate residues by DNA polymerase beta during DNA repair","volume":"269","author":"Y Matsumoto","year":"1995","journal-title":"Science"},{"key":"ref9","first-page":"2189","article-title":"Expression of human MutS homolog 2 (hMSH2) protein in resting and proliferating cells","volume":"13","author":"G Marra","year":"1996","journal-title":"Oncogene"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"329","DOI":"10.15698\/mic2016.08.517","article-title":"Functions and regulation of the MRX complex at DNA double-strand breaks","volume":"3","author":"E Gobbini","year":"2016","journal-title":"Microbial Cell"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1038\/nrm3047","article-title":"The MRE11 complex: starting from the ends","volume":"12","author":"TH Stracker","year":"2011","journal-title":"Nat Rev Mol Cell Biol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"3682","DOI":"10.1016\/j.febslet.2010.07.029","article-title":"The MRN complex in double-strand break repair and telomere maintenance","volume":"584","author":"BJ Lamarche","year":"2010","journal-title":"FEBS Lett"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"931","DOI":"10.4161\/cc.6.8.4180","article-title":"ATM activation and DNA damage response","volume":"6","author":"MF Lavin","year":"2007","journal-title":"Cell Cycle"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1146\/annurev.biochem.052308.093131","article-title":"The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway","volume":"79","author":"MR Lieber","year":"2010","journal-title":"Annu Rev Biochem"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"15981","DOI":"10.1016\/S0021-9258(17)33960-1","article-title":"Absence of a Ku-like DNA end binding activity in the xrs double-strand DNA repair-deficient mutant","volume":"269","author":"RC Getts","year":"1994","journal-title":"J Biol Chem"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1016\/j.tig.2008.08.007","article-title":"MMEJ repair of double-strand breaks (director&apos;s cut): deleted sequences and alternative endings","volume":"24","author":"M McVey","year":"2008","journal-title":"Trends Genet"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1093\/protein\/7.8.961","article-title":"Torsion angle differences as a means of pinpointing local polypeptide chain trajectory changes for identical proteins in different conformational states","volume":"7","author":"AP Korn","year":"1994","journal-title":"Protein Eng"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1016\/j.biochi.2003.09.010","article-title":"DNA repair-deficient diseases, xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy","volume":"85","author":"A Lehmann","year":"2003","journal-title":"Biochimie"},{"key":"ref19","first-page":"320","article-title":"A mutation in the XPB\/ERCC3 DNA repair transcription gene, associated with trichothiodystrophy","volume":"60","author":"G Weeda","year":"1997","journal-title":"Am J Hum Genet"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"e56952","DOI":"10.1371\/journal.pone.0056952","article-title":"Comprehensive SNP scan of DNA repair and DNA damage response genes reveal multiple susceptibility loci conferring risk to tobacco associated leukoplakia and oral cancer","volume":"8","author":"P Mondal","year":"2013","journal-title":"PLoS One"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"2333","DOI":"10.1093\/hmg\/ddm190","article-title":"Genetic variation in the DNA repair genes is predictive of outcome in lung cancer","volume":"16","author":"A Matakidou","year":"2007","journal-title":"Hum Mol Genet"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1273","DOI":"10.1016\/j.neuroscience.2006.09.004","article-title":"Computational prediction of the effects of non-synonymous single nucleotide polymorphisms in human DNA repair genes","volume":"145","author":"S Nakken","year":"2007","journal-title":"Neuroscience"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1038\/79866","article-title":"How many diseases does it take to map a gene with SNPs?","volume":"26","author":"KM Weiss","year":"2000","journal-title":"Nat Genet"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1038\/35052543","article-title":"Association study designs for complex diseases","volume":"2","author":"LR Cardon","year":"2001","journal-title":"Nat Rev Genet"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1038\/ng1071","article-title":"Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease","volume":"33","author":"KE Lohmueller","year":"2003","journal-title":"Nat Genet"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"W695","DOI":"10.1093\/nar\/gkq313","article-title":"A new bioinformatics analysis tools framework at EMBL-EBI","volume":"38","author":"M Goujon","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1038\/nprot.2009.86","article-title":"Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm","volume":"4","author":"P Kumar","year":"2009","journal-title":"Nat Protoc"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/nmeth0410-248","article-title":"A method and server for predicting damaging missense mutations","volume":"7","author":"IA Adzhubei","year":"2010","journal-title":"Nat Methods"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/35087607","article-title":"Regulation of DNA replication fork progression through damaged DNA by the Mec1\/Rad53 checkpoint","volume":"412","author":"JA Tercero","year":"2001","journal-title":"Nature"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"5852","DOI":"10.1093\/nar\/gkl741","article-title":"Limiting amounts of budding yeast Rad53 S-phase checkpoint activity results in increased resistance to DNA alkylation damage","volume":"34","author":"V Cordon-Preciado","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref31","first-page":"e1006248","article-title":"Identification and Functional Testing of ERCC2 Mutations in a Multi-national Cohort of Patients with Familial Breast- and Ovarian Cancer","volume":"12","author":"A Rump","year":"2016","journal-title":"Identification and Functional Testing of ERCC2 Mutations in a Multi-national Cohort of Patients with Familial Breast- and Ovarian Cancer"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1016\/S0968-0004(00)01563-2","article-title":"FAT: a novel domain in PIK-related kinases","volume":"25","author":"R Bosotti","year":"2000","journal-title":"Trends Biochem Sci"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1364","DOI":"10.1016\/j.cub.2005.06.063","article-title":"Saccharomyces cerevisiae Rad9 acts as a Mec1 adaptor to allow Rad53 activation","volume":"15","author":"FD Sweeney","year":"2005","journal-title":"Curr Biol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1016\/S0968-0004(01)01957-0","article-title":"The hunchback and its neighbours: proline as an environmental modulator","volume":"26","author":"H Reiersen","year":"2001","journal-title":"Trends Biochem Sci"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1093\/genetics\/150.3.963","article-title":"Novel mutations in the RAD3 and SSL1 genes perturb genome stability by stimulating recombination between short repeats in Saccharomyces cerevisiae","volume":"150","author":"S Maines","year":"1998","journal-title":"Genetics"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"3926","DOI":"10.1073\/pnas.91.9.3926","article-title":"Yeast RAD3 protein binds directly to both SSL2 and SSL1 proteins: implications for the structure and function of transcription\/repair factor b","volume":"91","author":"L Bardwell","year":"1994","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1089\/cmb.2007.0138","article-title":"Protein conformational flexibility analysis with noisy data","volume":"15","author":"A Nigham","year":"2008","journal-title":"J Comput Biol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1748-7188-8-1","article-title":"The difficulty of protein structure alignment under the RMSD","volume":"8","author":"SC Li","year":"2013","journal-title":"Algorithms Mol Biol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1089\/cmb.2007.0079","article-title":"Efficient substructure RMSD query algorithms","volume":"14","author":"T Shibuya","year":"2007","journal-title":"J Comput Biol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"3211","DOI":"10.1128\/MCB.00091-07","article-title":"ELA1 and CUL3 are required along with ELC1 for RNA polymerase II polyubiquitylation and degradation in DNA-damaged yeast cells","volume":"27","author":"B Ribar","year":"2007","journal-title":"Mol Cell Biol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1038\/ncb1429","article-title":"Telomerase- and capping-independent yeast survivors with alternate telomere states","volume":"8","author":"M Larrivee","year":"2006","journal-title":"Nat Cell Biol"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1016\/S0092-8674(03)00075-8","article-title":"Survival of DNA damage in yeast directly depends on increased dNTP levels allowed by relaxed feedback inhibition of ribonucleotide reductase","volume":"112","author":"A Chabes","year":"2003","journal-title":"Cell"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0193823","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,8,15]],"date-time":"2022-08-15T19:40:30Z","timestamp":1660592430000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0193823"}},"subtitle":[],"editor":[{"given":"Jennifer C.","family":"Fung","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,3,9]]},"references-count":42,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2018,3,9]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0193823","relation":{},"ISSN":["1932-6203"],"issn-type":[{"type":"electronic","value":"1932-6203"}],"subject":[],"published":{"date-parts":[[2018,3,9]]}}}