{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,9]],"date-time":"2026-06-09T06:48:19Z","timestamp":1780987699526,"version":"3.54.1"},"reference-count":66,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2010,7,22]],"date-time":"2010-07-22T00:00:00Z","timestamp":1279756800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000861","type":"journal-article","created":{"date-parts":[[2010,7,22]],"date-time":"2010-07-22T20:18:22Z","timestamp":1279829902000},"page":"e1000861","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":239,"title":["G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated with Distinct Genomic Features in Saccharomyces cerevisiae"],"prefix":"10.1371","volume":"6","author":[{"given":"John A.","family":"Capra","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katrin","family":"Paeschke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mona","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Virginia A.","family":"Zakian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2010,7,22]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1038\/334364a0","article-title":"Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis.","volume":"334","author":"D Sen","year":"1988","journal-title":"Nature"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1038\/342825a0","article-title":"Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops.","volume":"342","author":"WI Sundquist","year":"1989","journal-title":"Nature"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"5402","DOI":"10.1093\/nar\/gkl655","article-title":"Quadruplex DNA: sequence, topology and structure.","volume":"34","author":"S Burge","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"i374","DOI":"10.1093\/bioinformatics\/btp210","article-title":"Predicting and understanding the stability of G-quadruplexes.","volume":"25","author":"O Stegle","year":"2009","journal-title":"Bioinformatics"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1038\/nsmb1171","article-title":"Dynamic roles for G4 DNA in the biology of eukaryotic cells.","volume":"13","author":"N Maizels","year":"2006","journal-title":"Nat Struct Mol Biol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1038\/nsmb.1422","article-title":"Telomerase recruitment by the telomere end binding protein-beta facilitates G-quadruplex DNA unfolding in ciliates.","volume":"15","author":"K Paeschke","year":"2008","journal-title":"Nat Struct Mol Biol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1038\/nsmb982","article-title":"Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo.","volume":"12","author":"K Paeschke","year":"2005","journal-title":"Nat Struct Mol Biol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"8572","DOI":"10.1073\/pnas.141229498","article-title":"In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei.","volume":"98","author":"C Schaffitzel","year":"2001","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1016\/j.tcb.2009.05.002","article-title":"G-quadruplex structures: in vivo evidence and function.","volume":"19","author":"HJ Lipps","year":"2009","journal-title":"Trends Cell Biol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1093\/nar\/gkm986","article-title":"Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae.","volume":"36","author":"SG Hershman","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"2908","DOI":"10.1093\/nar\/gki609","article-title":"Prevalence of quadruplexes in the human genome.","volume":"33","author":"JL Huppert","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"2901","DOI":"10.1093\/nar\/gki553","article-title":"Highly prevalent putative quadruplex sequence motifs in human DNA.","volume":"33","author":"AK Todd","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1101\/gr.4508806","article-title":"Genome-wide prediction of G4 DNA as regulatory motifs: role in Escherichia coli global regulation.","volume":"16","author":"P Rawal","year":"2006","journal-title":"Genome Res"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"3887","DOI":"10.1093\/nar\/gkl529","article-title":"Gene function correlates with potential for G4 DNA formation in the human genome.","volume":"34","author":"J Eddy","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1093\/nar\/gkl1057","article-title":"G-quadruplexes in promoters throughout the human genome.","volume":"35","author":"JL Huppert","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref16","article-title":"The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts.","author":"S Nakken","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"2536","DOI":"10.1093\/nar\/gkl286","article-title":"G-quadruplex formation within the promoter of the KRAS proto-oncogene and its effect on transcription.","volume":"34","author":"S Cogoi","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1093\/nar\/gkm1138","article-title":"Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes.","volume":"36","author":"J Eddy","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"4194","DOI":"10.1093\/nar\/gkn1076","article-title":"Evidence of genome-wide G4 DNA-mediated gene expression in human cancer cells.","volume":"37","author":"A Verma","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"e4399","DOI":"10.1371\/journal.pone.0004399","article-title":"Genome-wide analyses of recombination prone regions predict role of DNA structural motif in recombination.","volume":"4","author":"P Mani","year":"2009","journal-title":"PLoS One"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1126\/science.1084337","article-title":"Finding functional features in Saccharomyces genomes by phylogenetic footprinting.","volume":"301","author":"P Cliften","year":"2003","journal-title":"Science"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1038\/nature01644","article-title":"Sequencing and comparison of yeast species to identify genes and regulatory elements.","volume":"423","author":"M Kellis","year":"2003","journal-title":"Nature"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1038\/43025","article-title":"Genetic and physical maps of Saccharomyces cerevisiae.","volume":"387","author":"JM Cherry","year":"1997","journal-title":"Nature"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1140","DOI":"10.1016\/j.biochi.2008.01.014","article-title":"Hunting G-quadruplexes.","volume":"90","author":"JL Huppert","year":"2008","journal-title":"Biochimie"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"D381","DOI":"10.1093\/nar\/gkm781","article-title":"QuadBase: genome-wide database of G4 DNA\u2013occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes.","volume":"36","author":"VK Yadav","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"11094","DOI":"10.1021\/ja0608040","article-title":"Quadruplex-based molecular beacons as tunable DNA probes.","volume":"128","author":"A Bourdoncle","year":"2006","journal-title":"J Am Chem Soc"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1101\/gr.3715005","article-title":"Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.","volume":"15","author":"A Siepel","year":"2005","journal-title":"Genome Res"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1089\/1066527041410472","article-title":"Combining phylogenetic and hidden Markov models in biosequence analysis.","volume":"11","author":"A Siepel","year":"2004","journal-title":"J Comput Biol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing.","volume":"57","author":"Y Benjamini","year":"1995","journal-title":"J Roy Statist Soc Ser B"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"2013","DOI":"10.1214\/aos\/1074290335","article-title":"The positive false discovery rate: A Bayesian interpretation and the q-value.","volume":"31","author":"JD Storey","year":"2003","journal-title":"Annals of Statistics"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"2700","DOI":"10.1093\/nar\/gkn078","article-title":"The relationship of potential G-quadruplex sequences in cis-upstream regions of the human genome to SP1-binding elements.","volume":"36","author":"AK Todd","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1038\/nature02800","article-title":"Transcriptional regulatory code of a eukaryotic genome.","volume":"431","author":"CT Harbison","year":"2004","journal-title":"Nature"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1038\/35050000","article-title":"A role for Saccharomyces cerevisiae histone H2A in DNA repair.","volume":"408","author":"JA Downs","year":"2000","journal-title":"Nature"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"3231","DOI":"10.1111\/j.1742-4658.2005.04741.x","article-title":"Histone H2A phosphorylation in DNA double-strand break repair.","volume":"272","author":"ER Foster","year":"2005","journal-title":"FEBS J"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1042\/BST0340523","article-title":"Initiation of meiotic recombination by formation of DNA double-strand breaks: mechanism and regulation.","volume":"34","author":"S Keeney","year":"2006","journal-title":"Biochem Soc Trans"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"e324","DOI":"10.1371\/journal.pbio.0050324","article-title":"Mapping meiotic single-strand DNA reveals a new landscape of DNA double-strand breaks in Saccharomyces cerevisiae.","volume":"5","author":"C Buhler","year":"2007","journal-title":"PLoS Biol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1002\/1439-7633(20010202)2:2<124::AID-CBIC124>3.0.CO;2-L","article-title":"Fluorescence resonance energy transfer as a probe for G-quartet formation by a telomeric repeat.","volume":"2","author":"JL Mergny","year":"2001","journal-title":"Chembiochem"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1016\/S0076-6879(05)09005-1","article-title":"Analysis of the DNA unwinding activity of RecQ family helicases.","volume":"409","author":"CZ Bachrati","year":"2006","journal-title":"Methods Enzymol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1126\/science.1105322","article-title":"Comparison of fine-scale recombination rates in humans and chimpanzees.","volume":"308","author":"W Winckler","year":"2005","journal-title":"Science"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1016\/S0092-8674(00)80683-2","article-title":"The Saccharomyces Pif1p DNA helicase and the highly related Rrm3p have opposite effects on replication fork progression in ribosomal DNA.","volume":"100","author":"AS Ivessa","year":"2000","journal-title":"Cell"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1038\/nature04638","article-title":"Semi-conservative DNA replication through telomeres requires Taz1.","volume":"440","author":"KM Miller","year":"2006","journal-title":"Nature"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1016\/j.cell.2009.06.021","article-title":"Mammalian telomeres resemble fragile sites and require TRF1 for efficient replication.","volume":"138","author":"A Sfeir","year":"2009","journal-title":"Cell"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"900","DOI":"10.1016\/j.cub.2008.05.013","article-title":"Mutagenic capacity of endogenous G4 DNA underlies genome instability in FANCJ-defective C. elegans.","volume":"18","author":"E Kruisselbrink","year":"2008","journal-title":"Curr Biol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"36132","DOI":"10.1074\/jbc.M808152200","article-title":"FANCJ is a structure-specific DNA helicase associated with the maintenance of genomic G\/C tracts.","volume":"283","author":"TB London","year":"2008","journal-title":"J Biol Chem"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"4116","DOI":"10.1128\/MCB.02210-07","article-title":"FANCJ helicase defective in Fanconia anemia and breast cancer unwinds G-quadruplex DNA to defend genomic stability.","volume":"28","author":"Y Wu","year":"2008","journal-title":"Mol Cell Biol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1016\/j.dnarep.2010.01.005","article-title":"FANCJ: solving problems in DNA replication.","volume":"9","author":"K Hiom","journal-title":"DNA Repair (Amst)"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"1209","DOI":"10.1007\/s00018-008-8580-6","article-title":"Welcome the family of FANCJ-like helicases to the block of genome stability maintenance proteins.","volume":"66","author":"Y Wu","year":"2009","journal-title":"Cell Mol Life Sci"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"4692","DOI":"10.1093\/nar\/gki777","article-title":"Saccharomyces cerevisiae Mre11 is a high-affinity G4 DNA-binding protein and a G-rich DNA-specific endonuclease: implications for replication of telomeric DNA.","volume":"33","author":"G Ghosal","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"3954","DOI":"10.1093\/nar\/gkf530","article-title":"G4 DNA unwinding by BLM and Sgs1p: substrate specificity and substrate-specific inhibition.","volume":"30","author":"MD Huber","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"2378","DOI":"10.1093\/nar\/gkh559","article-title":"Meiosis-specific yeast Hop1 protein promotes synapsis of double-stranded DNA helices via the formation of guanine quartets.","volume":"32","author":"S Anuradha","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"1361","DOI":"10.1128\/MCB.20.4.1361-1369.2000","article-title":"Yeast meiosis-specific protein Hop1 binds to G4 DNA and promotes its formation.","volume":"20","author":"K Muniyappa","year":"2000","journal-title":"Mol Cell Biol"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1128\/MCB.22.4.1106-1115.2002","article-title":"Identification of residues in yeast Spo11p critical for meiotic DNA double-strand break formation.","volume":"22","author":"RL Diaz","year":"2002","journal-title":"Mol Cell Biol"},{"key":"ref53","article-title":"Biogenesis of Yeast Mitochondria.","author":"L Pon","year":"1991"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"e1000475","DOI":"10.1371\/journal.pgen.1000475","article-title":"The yeast Pif1 helicase prevents genomic instability caused by G-quadruplex-forming CEB1 sequences in vivo.","volume":"5","author":"C Ribeyre","year":"2009","journal-title":"PLoS Genet"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"17766","DOI":"10.1074\/jbc.M709749200","article-title":"The Human RecQ helicases, BLM and RECQ1, display distinct DNA substrate specificities.","volume":"283","author":"V Popuri","year":"2008","journal-title":"J Biol Chem"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/0092-8674(94)90179-1","article-title":"The saccharomyces PIF1 DNA helicase inhibits telomere elongation and de novo telomere formation.","volume":"76","author":"VP Schulz","year":"1994","journal-title":"Cell"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"5345","DOI":"10.1073\/pnas.80.17.5345","article-title":"pif mutation blocks recombination between mitochondrial rho+ and rho- genomes having tandemly arrayed repeat units in Saccharomyces cerevisiae.","volume":"80","author":"F Foury","year":"1983","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1038\/nature00935","article-title":"Functional profiling of the Saccharomyces cerevisiae genome.","volume":"418","author":"G Giaever","year":"2002","journal-title":"Nature"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"D40","DOI":"10.1093\/nar\/gkl758","article-title":"OriDB: a DNA replication origin database.","volume":"35","author":"CA Nieduszynski","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1016\/S0092-8674(00)81641-4","article-title":"Dissecting the regulatory circuitry of a eukaryotic genome.","volume":"95","author":"FC Holstege","year":"1998","journal-title":"Cell"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"1344","DOI":"10.1126\/science.1158441","article-title":"The transcriptional landscape of the yeast genome defined by RNA sequencing.","volume":"320","author":"U Nagalakshmi","year":"2008","journal-title":"Science"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1038\/ng569","article-title":"Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association.","volume":"28","author":"JD Lieb","year":"2001","journal-title":"Nat Genet"},{"key":"ref63","article-title":"Telomere structure.","author":"D Rhodes","year":"2006"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"2077","DOI":"10.1126\/science.8091229","article-title":"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII.","volume":"265","author":"M Johnston","year":"1994","journal-title":"Science"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102. Article published online before print in May 2002","article-title":"The human genome browser at UCSC.","volume":"12","author":"WJ Kent","year":"2002","journal-title":"Genome Res"},{"key":"ref66","article-title":"R: A Language and Environment for Statistical Computing"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000861","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,23]],"date-time":"2025-02-23T07:30:02Z","timestamp":1740295802000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000861"}},"subtitle":[],"editor":[{"given":"Gary D.","family":"Stormo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2010,7,22]]},"references-count":66,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2010,7,22]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000861","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,7,22]]}}}