{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T14:25:57Z","timestamp":1790778357368,"version":"4.1.0"},"reference-count":75,"publisher":"Elsevier BV","issue":"19","license":[{"start":{"date-parts":[[2022,10,1]],"date-time":"2022-10-01T00:00:00Z","timestamp":1664582400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2022,10,1]],"date-time":"2022-10-01T00:00:00Z","timestamp":1664582400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2023,10,7]],"date-time":"2023-10-07T00:00:00Z","timestamp":1696636800000},"content-version":"vor","delay-in-days":371,"URL":"http:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"}],"funder":[{"DOI":"10.13039\/100000863","name":"Ellison Medical Foundation","doi-asserted-by":"publisher","award":["AG-SS-2633-11"],"award-info":[{"award-number":["AG-SS-2633-11"]}],"id":[{"id":"10.13039\/100000863","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001445","name":"Alex's Lemonade Stand Foundation for Childhood Cancer","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001445","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["5R35GM130322"],"award-info":[{"award-number":["5R35GM130322"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100002108","name":"Friedreich's Ataxia Research Alliance","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100002108","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000005","name":"U.S. Department of Defense","doi-asserted-by":"publisher","award":["W81XWH-16-1-599"],"award-info":[{"award-number":["W81XWH-16-1-599"]}],"id":[{"id":"10.13039\/100000005","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000005","name":"U.S. Department of Defense","doi-asserted-by":"publisher","award":["W81XWH-19-1-0652"],"award-info":[{"award-number":["W81XWH-19-1-0652"]}],"id":[{"id":"10.13039\/100000005","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012524","name":"American Lebanese Syrian Associated Charities","doi-asserted-by":"publisher","award":["NS081366"],"award-info":[{"award-number":["NS081366"]}],"id":[{"id":"10.13039\/100012524","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012524","name":"American Lebanese Syrian Associated Charities","doi-asserted-by":"publisher","award":["NS121038"],"award-info":[{"award-number":["NS121038"]}],"id":[{"id":"10.13039\/100012524","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000065","name":"National Institute of Neurological Disorders and Stroke","doi-asserted-by":"publisher","award":["NS108376"],"award-info":[{"award-number":["NS108376"]}],"id":[{"id":"10.13039\/100000065","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Molecular Cell"],"published-print":{"date-parts":[[2022,10]]},"DOI":"10.1016\/j.molcel.2022.08.007","type":"journal-article","created":{"date-parts":[[2022,9,7]],"date-time":"2022-09-07T10:36:20Z","timestamp":1662546980000},"page":"3538-3552.e5","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":71,"title":["S1-END-seq reveals DNA secondary structures in human cells"],"prefix":"10.1016","volume":"82","author":[{"given":"Gabriel","family":"Matos-Rodrigues","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Niek","family":"van Wietmarschen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veenu","family":"Tripathi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natasha C.","family":"Koussa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raphael","family":"Pavani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William J.","family":"Nathan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elsa","family":"Callen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frida","family":"Belinky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashraf","family":"Mohammed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marek","family":"Napierala","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen","family":"Usdin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aseem Z.","family":"Ansari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergei M.","family":"Mirkin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andr\u00e9","family":"Nussenzweig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.molcel.2022.08.007_bib1","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1042\/bj3160461","article-title":"Triplex DNA in the nucleus: direct binding of triplex-specific antibodies and their effect on transcription, replication and cell growth","volume":"316","author":"Agazie","year":"1996","journal-title":"Biochem. J."},{"key":"10.1016\/j.molcel.2022.08.007_bib2","doi-asserted-by":"crossref","first-page":"7019","DOI":"10.1016\/S0021-9258(17)37476-8","article-title":"Characterization of a new monoclonal antibody to triplex DNA and immunofluorescent staining of mammalian chromosomes","volume":"269","author":"Agazie","year":"1994","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.molcel.2022.08.007_bib3","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1038\/s41586-020-1943-3","article-title":"The repertoire of mutational signatures in human cancer","volume":"578","author":"Alexandrov","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.molcel.2022.08.007_bib4","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1016\/j.ajhg.2009.01.024","article-title":"Replication stress induces genome-wide copy number changes in human cells that resemble polymorphic and pathogenic variants","volume":"84","author":"Arlt","year":"2009","journal-title":"Am. J. Hum. Genet."},{"key":"10.1016\/j.molcel.2022.08.007_bib5","doi-asserted-by":"crossref","first-page":"8620","DOI":"10.1021\/cr400078y","article-title":"DNA sequences that interfere with transcription: implications for genome function and stability","volume":"113","author":"Belotserkovskii","year":"2013","journal-title":"Chem. Rev."},{"key":"10.1016\/j.molcel.2022.08.007_bib6","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1083\/jcb.106.3.761","article-title":"Normal keratinization in a spontaneously immortalized aneuploid human keratinocyte cell line","volume":"106","author":"Boukamp","year":"1988","journal-title":"J.\u00a0Cell Biol."},{"key":"10.1016\/j.molcel.2022.08.007_bib7","doi-asserted-by":"crossref","first-page":"11497","DOI":"10.1073\/pnas.0604939103","article-title":"DNA sequence-specific polyamides alleviate transcription inhibition associated with long GAA.TTC repeats in Friedreich\u2019s ataxia","volume":"103","author":"Burnett","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.molcel.2022.08.007_bib8","doi-asserted-by":"crossref","first-page":"1423","DOI":"10.1126\/science.271.5254.1423","article-title":"Friedreich\u2019s ataxia: autosomal recessive disease caused by an intronic GAA triplet repeat expansion","volume":"271","author":"Campuzano","year":"1996","journal-title":"Science"},{"key":"10.1016\/j.molcel.2022.08.007_bib9","doi-asserted-by":"crossref","first-page":"898","DOI":"10.1016\/j.molcel.2016.06.034","article-title":"DNA breaks and end resection measured genome-wide by end sequencing","volume":"63","author":"Canela","year":"2016","journal-title":"Mol. Cell"},{"key":"10.1016\/j.molcel.2022.08.007_bib10","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1038\/s41586-019-1102-x","article-title":"WRN helicase is a synthetic lethal target in microsatellite unstable cancers","volume":"568","author":"Chan","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.molcel.2022.08.007_bib11","doi-asserted-by":"crossref","first-page":"5991","DOI":"10.1093\/nar\/20.22.5991","article-title":"Transcriptionally driven cruciform formation in\u00a0vivo","volume":"20","author":"Dayn","year":"1992","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.molcel.2022.08.007_bib12","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1146\/annurev.bi.49.070180.003211","article-title":"Replication of eukaryotic chromosomes: a close-up of the replication fork","volume":"49","author":"DePamphilis","year":"1980","journal-title":"Annu. Rev. Biochem."},{"key":"10.1016\/j.molcel.2022.08.007_bib13","doi-asserted-by":"crossref","first-page":"109722","DOI":"10.1016\/j.celrep.2021.109722","article-title":"DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity","volume":"36","author":"Du","year":"2021","journal-title":"Cell Rep."},{"key":"10.1016\/j.molcel.2022.08.007_bib14","doi-asserted-by":"crossref","first-page":"8463","DOI":"10.1128\/JVI.72.11.8463-8471.1998","article-title":"A third-generation lentivirus vector with a conditional packaging system","volume":"72","author":"Dull","year":"1998","journal-title":"J.\u00a0Virol."},{"key":"10.1016\/j.molcel.2022.08.007_bib15","doi-asserted-by":"crossref","first-page":"2182","DOI":"10.1093\/nar\/gkm1152","article-title":"Saccharomyces cerevisiae Mus81-Mms4 is a catalytic, DNA structure-selective endonuclease","volume":"36","author":"Ehmsen","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.molcel.2022.08.007_bib16","doi-asserted-by":"crossref","first-page":"1617","DOI":"10.1126\/science.aan6414","article-title":"Synthetic transcription elongation factors license transcription across repressive chromatin","volume":"358","author":"Erwin","year":"2017","journal-title":"Science"},{"key":"10.1016\/j.molcel.2022.08.007_bib17","doi-asserted-by":"crossref","first-page":"e51","DOI":"10.1002\/cpcb.51","article-title":"Transcription factor-mediated differentiation of human iPSCs into neurons","volume":"79","author":"Fernandopulle","year":"2018","journal-title":"Curr. Protoc. Cell Biol."},{"key":"10.1016\/j.molcel.2022.08.007_bib18","first-page":"554","article-title":"The relationship between trinucleotide (GAA) repeat length and clinical features in Friedreich ataxia","volume":"59","author":"Filla","year":"1996","journal-title":"Am. J. Hum. Genet."},{"key":"10.1016\/j.molcel.2022.08.007_bib19","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1038\/nsmb.2520","article-title":"Friedreich\u2019s ataxia-associated GAA repeats induce replication-fork reversal and unusual molecular junctions","volume":"20","author":"Follonier","year":"2013","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.molcel.2022.08.007_bib20","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1146\/annurev.bi.64.070195.000433","article-title":"Triplex DNA structures","volume":"64","author":"Frank-Kamenetskii","year":"1995","journal-title":"Annu. Rev. Biochem."},{"key":"10.1016\/j.molcel.2022.08.007_bib21","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1016\/S1097-2765(03)00342-3","article-title":"The endogenous Mus81-Eme1 complex resolves Holliday junctions by a nick and counternick mechanism","volume":"12","author":"Gaillard","year":"2003","journal-title":"Mol. Cell"},{"key":"10.1016\/j.molcel.2022.08.007_bib22","doi-asserted-by":"crossref","first-page":"1264","DOI":"10.1101\/gr.231688.117","article-title":"Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis","volume":"28","author":"Georgakopoulos-Soares","year":"2018","journal-title":"Genome Res."},{"key":"10.1016\/j.molcel.2022.08.007_bib23","doi-asserted-by":"crossref","first-page":"1218","DOI":"10.1016\/j.celrep.2016.06.075","article-title":"Stalled DNA replication forks at the endogenous GAA repeats drive repeat expansion in Friedreich's ataxia cells","volume":"16","author":"Gerhardt","year":"2016","journal-title":"Cell Rep."},{"key":"10.1016\/j.molcel.2022.08.007_bib24","doi-asserted-by":"crossref","first-page":"2815","DOI":"10.1093\/nar\/28.14.2815","article-title":"The GAA\u2217TTC triplet repeat expanded in Friedreich's ataxia impedes transcription elongation by T7 RNA polymerase in a length and supercoil dependent manner","volume":"28","author":"Grabczyk","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.molcel.2022.08.007_bib25","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1093\/nar\/gkaa1269","article-title":"Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome","volume":"49","author":"Guiblet","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.molcel.2022.08.007_bib26","doi-asserted-by":"crossref","first-page":"4343","DOI":"10.1093\/nar\/13.12.4343","article-title":"Transition of a cloned d(AT)n-d(AT)n tract to a cruciform in\u00a0vivo","volume":"13","author":"Haniford","year":"1985","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.molcel.2022.08.007_bib27","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1038\/s41586-020-1969-6","article-title":"Pan-cancer analysis of whole genomes","volume":"578","author":"ICGC\/TCGA Pan-Cancer Analysis of Whole Genomes Consortium","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.molcel.2022.08.007_bib28","doi-asserted-by":"crossref","first-page":"D493","DOI":"10.1093\/nar\/gkh103","article-title":"The UCSC Table\u00a0Browser data retrieval tool","volume":"32","author":"Karolchik","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.molcel.2022.08.007_bib29","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1002\/gcc.22721","article-title":"The role of fork stalling and DNA structures in causing chromosome fragility","volume":"58","author":"Kaushal","year":"2019","journal-title":"Genes Chromosomes Cancer"},{"key":"10.1016\/j.molcel.2022.08.007_bib30","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at UCSC","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"10.1016\/j.molcel.2022.08.007_bib31","doi-asserted-by":"crossref","first-page":"1628","DOI":"10.1073\/pnas.1913416117","article-title":"Large-scale contractions of Friedreich's ataxia GAA repeats in yeast occur during DNA replication due to their triplex-forming ability","volume":"117","author":"Khristich","year":"2020","journal-title":"Proc Natl Acad Sci USA"},{"key":"10.1016\/j.molcel.2022.08.007_bib32","first-page":"3050","article-title":"Binding properties of replication protein A from human and yeast cells","volume":"12","author":"Kim","year":"1992","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.molcel.2022.08.007_bib33","doi-asserted-by":"crossref","first-page":"2896","DOI":"10.1038\/emboj.2008.205","article-title":"Chromosome fragility at GAA tracts in yeast depends on repeat orientation and requires mismatch repair","volume":"27","author":"Kim","year":"2008","journal-title":"EMBO J."},{"key":"10.1016\/j.molcel.2022.08.007_bib34","doi-asserted-by":"crossref","first-page":"1766","DOI":"10.1101\/gad.7.9.1766","article-title":"Transcription-dependent recombination induced by triple-helix formation","volume":"7","author":"Kohwi","year":"1993","journal-title":"Genes Dev."},{"key":"10.1016\/j.molcel.2022.08.007_bib35","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1158\/2159-8290.CD-17-1461","article-title":"Mechanisms of oncogene-induced replication stress: jigsaw falling into place","volume":"8","author":"Kotsantis","year":"2018","journal-title":"Cancer Discov."},{"key":"10.1016\/j.molcel.2022.08.007_bib36","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1016\/j.cels.2017.01.013","article-title":"Permanganate\/S1 nuclease footprinting reveals non-B DNA structures with regulatory potential across a mammalian genome","volume":"4","author":"Kouzine","year":"2017","journal-title":"Cell Syst."},{"key":"10.1016\/j.molcel.2022.08.007_bib37","doi-asserted-by":"crossref","first-page":"2286","DOI":"10.1128\/MCB.24.6.2286-2295.2004","article-title":"Replication stalling at Friedreich's ataxia (GAA)n repeats in\u00a0vivo","volume":"24","author":"Krasilnikova","year":"2004","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.molcel.2022.08.007_bib38","doi-asserted-by":"crossref","first-page":"1136","DOI":"10.1016\/j.dnarep.2006.05.035","article-title":"Palindrome-mediated chromosomal translocations in humans","volume":"5","author":"Kurahashi","year":"2006","journal-title":"DNA Repair (Amst)"},{"key":"10.1016\/j.molcel.2022.08.007_bib39","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"10.1016\/j.molcel.2022.08.007_bib40","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.molcel.2022.08.007_bib41","doi-asserted-by":"crossref","first-page":"33412","DOI":"10.1074\/jbc.M112.402503","article-title":"Replication fork stalling and checkpoint activation by a PKD1 locus mirror repeat polypurine-polypyrimidine (Pu-Py) tract","volume":"287","author":"Liu","year":"2012","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.molcel.2022.08.007_bib42","doi-asserted-by":"crossref","first-page":"7024","DOI":"10.1073\/pnas.84.20.7024","article-title":"Supercoiling of the DNA template during transcription","volume":"84","author":"Liu","year":"1987","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.molcel.2022.08.007_bib43","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1038\/nrm2854","article-title":"Repeat instability as the basis for human diseases and as a potential target for therapy","volume":"11","author":"L\u00f3pez Castel","year":"2010","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.molcel.2022.08.007_bib45","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2203967119","article-title":"Triple-helix potential of the mouse genome","volume":"119","author":"Maekawa","year":"2022","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.molcel.2022.08.007_bib46","doi-asserted-by":"crossref","first-page":"e1003468","DOI":"10.1371\/journal.pgen.1003468","article-title":"The G4 genome","volume":"9","author":"Maizels","year":"2013","journal-title":"PLoS Genet."},{"key":"10.1016\/j.molcel.2022.08.007_bib47","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1038\/nrg2828","article-title":"Mechanisms of trinucleotide repeat instability during human development","volume":"11","author":"McMurray","year":"2010","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.molcel.2022.08.007_bib48","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1128\/MMBR.00030-06","article-title":"Replication fork stalling at natural impediments","volume":"71","author":"Mirkin","year":"2007","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"10.1016\/j.molcel.2022.08.007_bib49","series-title":"DNA Topology: Fundamentals. Encylopedia of Life Sciences","author":"Mirkin","year":"2001"},{"key":"10.1016\/j.molcel.2022.08.007_bib50","doi-asserted-by":"crossref","first-page":"932","DOI":"10.1038\/nature05977","article-title":"Expandable DNA repeats and human disease","volume":"447","author":"Mirkin","year":"2007","journal-title":"Nature"},{"key":"10.1016\/j.molcel.2022.08.007_bib51","doi-asserted-by":"crossref","first-page":"1064","DOI":"10.2741\/2744","article-title":"Discovery of alternative DNA structures: a heroic decade (1979\u20131989)","volume":"13","author":"Mirkin","year":"2008","journal-title":"Front. Biosci."},{"key":"10.1016\/j.molcel.2022.08.007_bib52","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1146\/annurev.bb.23.060194.002545","article-title":"H-DNA and related structures","volume":"23","author":"Mirkin","year":"1994","journal-title":"Annu. Rev. Biophys. Biomol. Struct."},{"key":"10.1016\/j.molcel.2022.08.007_bib53","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/330495a0","article-title":"DNA H form requires a homopurine-homopyrimidine mirror repeat","volume":"330","author":"Mirkin","year":"1987","journal-title":"Nature"},{"key":"10.1016\/j.molcel.2022.08.007_bib54","doi-asserted-by":"crossref","first-page":"9641","DOI":"10.1093\/nar\/15.23.9641","article-title":"The mechanism of cruciform formation in supercoiled DNA: initial opening of central basepairs in salt-dependent extrusion","volume":"15","author":"Murchie","year":"1987","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.molcel.2022.08.007_bib55","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1016\/0076-6879(92)11010-G","article-title":"Supercoiled DNA and cruciform structures","volume":"211","author":"Murchie","year":"1992","journal-title":"Methods Enzymol."},{"key":"10.1016\/j.molcel.2022.08.007_bib56","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1146\/annurev.bi.49.070180.002225","article-title":"Discontinuous DNA replication","volume":"49","author":"Ogawa","year":"1980","journal-title":"Annu. Rev. Biochem."},{"key":"10.1016\/j.molcel.2022.08.007_bib57","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1038\/nbt.4235","article-title":"A universal SNP and small-indel variant caller using deep neural networks","volume":"36","author":"Poplin","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.molcel.2022.08.007_bib58","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.molcel.2022.08.007_bib59","doi-asserted-by":"crossref","first-page":"W160","DOI":"10.1093\/nar\/gkw257","article-title":"deepTools2: a next generation web server for deep-sequencing data analysis","volume":"44","author":"Ram\u00edrez","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.molcel.2022.08.007_bib60","doi-asserted-by":"crossref","first-page":"8419","DOI":"10.1093\/nar\/gkab609","article-title":"DNA G-quadruplex structures: more than simple roadblocks to transcription?","volume":"49","author":"Robinson","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.molcel.2022.08.007_bib61","doi-asserted-by":"crossref","first-page":"27178","DOI":"10.1074\/jbc.M101852200","article-title":"GGA\u2217TCC-interrupted triplets in long GAA\u2217TTC repeats inhibit the formation of triplex and sticky DNA structures, alleviate transcription inhibition, and reduce genetic instabilities","volume":"276","author":"Sakamoto","year":"2001","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.molcel.2022.08.007_bib62","doi-asserted-by":"crossref","first-page":"4975","DOI":"10.1002\/j.1460-2075.1993.tb06191.x","article-title":"Suicidal nucleotide sequences for DNA polymerization","volume":"12","author":"Samadashwily","year":"1993","journal-title":"EMBO J."},{"key":"10.1016\/j.molcel.2022.08.007_bib63","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1038\/nmeth.3047","article-title":"Improved vectors and genome-wide libraries for CRISPR screening","volume":"11","author":"Sanjana","year":"2014","journal-title":"Nat. Methods"},{"key":"10.1016\/j.molcel.2022.08.007_bib64","doi-asserted-by":"crossref","first-page":"4788","DOI":"10.2741\/2427","article-title":"Slipped strand DNA structures","volume":"12","author":"Sinden","year":"2007","journal-title":"Front. Biosci."},{"key":"10.1016\/j.molcel.2022.08.007_bib65","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1016\/j.molcel.2017.05.001","article-title":"Replication catastrophe: when a checkpoint fails because of exhaustion","volume":"66","author":"Toledo","year":"2017","journal-title":"Mol. Cell"},{"key":"10.1016\/j.molcel.2022.08.007_bib66","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1016\/j.cell.2013.10.043","article-title":"ATR prohibits replication catastrophe by preventing global exhaustion of RPA","volume":"155","author":"Toledo","year":"2013","journal-title":"Cell"},{"key":"10.1016\/j.molcel.2022.08.007_bib67","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1038\/s41586-020-2769-8","article-title":"Repeat expansions confer WRN dependence in microsatellite-unstable cancers","volume":"586","author":"van Wietmarschen","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.molcel.2022.08.007_bib68","doi-asserted-by":"crossref","first-page":"1221","DOI":"10.1016\/j.stemcr.2017.08.019","article-title":"Scalable production of iPSC-derived human neurons to identify tau-lowering compounds by high-content screening","volume":"9","author":"Wang","year":"2017","journal-title":"Stem Cell Rep."},{"key":"10.1016\/j.molcel.2022.08.007_bib69","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/j.dnarep.2014.03.017","article-title":"Impact of alternative DNA structures on DNA damage, DNA repair, and genetic instability","volume":"19","author":"Wang","year":"2014","journal-title":"DNA Repair (Amst)"},{"key":"10.1016\/j.molcel.2022.08.007_bib70","doi-asserted-by":"crossref","first-page":"2939","DOI":"10.1096\/fasebj.2.14.3053307","article-title":"The chemistry and biology of unusual DNA structures adopted by oligopurine.oligopyrimidine sequences","volume":"2","author":"Wells","year":"1988","journal-title":"FASEB J."},{"key":"10.1016\/j.molcel.2022.08.007_bib71","doi-asserted-by":"crossref","first-page":"12752","DOI":"10.1016\/S0021-9258(18)45270-2","article-title":"Purification and properties of a nuclease from Saccharomyces cerevisiae that cleaves DNA at cruciform junctions","volume":"262","author":"West","year":"1987","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.molcel.2022.08.007_bib72","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1007\/978-1-0716-0644-5_2","article-title":"END-seq: an unbiased, high-resolution, and genome-wide approach to map DNA double-strand breaks and resection in human cells","volume":"2153","author":"Wong","year":"2021","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.molcel.2022.08.007_bib73","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1038\/s41586-021-03468-5","article-title":"Neuronal enhancers are hotspots for DNA single-strand break repair","volume":"593","author":"Wu","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.molcel.2022.08.007_bib74","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1016\/j.molcel.2007.06.012","article-title":"An AT-rich sequence in human common fragile site FRA16D causes fork stalling and chromosome breakage in S.\u00a0cerevisiae","volume":"27","author":"Zhang","year":"2007","journal-title":"Mol. Cell"},{"key":"10.1016\/j.molcel.2022.08.007_bib75","doi-asserted-by":"crossref","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-Seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biol."},{"key":"10.1016\/j.molcel.2022.08.007_bib76","doi-asserted-by":"crossref","first-page":"1200","DOI":"10.1016\/j.celrep.2018.01.014","article-title":"Distinct mechanisms of nuclease-directed DNA-structure-induced genetic instability in cancer genomes","volume":"22","author":"Zhao","year":"2018","journal-title":"Cell Rep."}],"container-title":["Molecular Cell"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1097276522007602?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1097276522007602?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T00:47:29Z","timestamp":1761094049000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1097276522007602"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,10]]},"references-count":75,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2022,10]]}},"alternative-id":["S1097276522007602"],"URL":"https:\/\/doi.org\/10.1016\/j.molcel.2022.08.007","relation":{},"ISSN":["1097-2765"],"issn-type":[{"value":"1097-2765","type":"print"}],"subject":[],"published":{"date-parts":[[2022,10]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"S1-END-seq reveals DNA secondary structures in human cells","name":"articletitle","label":"Article Title"},{"value":"Molecular Cell","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.molcel.2022.08.007","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2022 Elsevier Inc.","name":"copyright","label":"Copyright"}]}}