{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T04:44:28Z","timestamp":1790052268688,"version":"4.0.1"},"reference-count":99,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2018,11,15]],"date-time":"2018-11-15T00:00:00Z","timestamp":1542240000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"DOI":"10.1371\/journal.ppat.1007321","type":"journal-article","created":{"date-parts":[[2018,11,15]],"date-time":"2018-11-15T19:53:52Z","timestamp":1542311632000},"page":"e1007321","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":35,"title":["Evaluation of mechanisms that may generate DNA lesions triggering antigenic variation in African trypanosomes"],"prefix":"10.1371","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4203-9299","authenticated-orcid":true,"given":"Marcelo Santos","family":"da Silva","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5995-9329","authenticated-orcid":true,"given":"Galadriel A.","family":"Hovel-Miner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6740-8882","authenticated-orcid":true,"given":"Emma M.","family":"Briggs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Carolina","family":"Elias","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5739-976X","authenticated-orcid":true,"given":"Richard","family":"McCulloch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2018,11,15]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0065-308X(01)49037-3","article-title":"Antigenic variation in trypanosomes: enhanced phenotypic variation in a eukaryotic parasite","volume":"49","author":"JD Barry","year":"2001","journal-title":"Adv Parasitol"},{"key":"ref2","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-017-00959-w","article-title":"Variant surface glycoprotein density defines an immune evasion threshold for African trypanosomes undergoing antigenic variation","volume":"8","author":"J Pinger","year":"2017","journal-title":"Nat Commun"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1111\/mmi.13838","article-title":"The role of genomic location and flanking 3\u2032UTR in the generation of functional levels of variant surface glycoprotein in Trypanosoma brucei","volume":"106","author":"S Ridewood","year":"2017","journal-title":"Mol Microbiol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1007\/s00294-016-0662-7","article-title":"Does DNA replication direct locus-specific recombination during host immune evasion by antigenic variation in the African trypanosome?","author":"R Devlin","year":"2017","journal-title":"Current Genetics"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/j.molbiopara.2014.05.001","article-title":"Antigenic variation in African trypanosomes","volume":"195","author":"D Horn","year":"2014","journal-title":"Mol Biochem Parasitol. Elsevier"},{"key":"ref6","article-title":"How Does the VSG Coat of Bloodstream Form African Trypanosomes Interact with External Proteins?","author":"A Schwede","year":"2015","journal-title":"PLoS Pathog"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1126\/science.1112642","article-title":"The Genome of the African Trypanosome Trypanosoma brucei","volume":"309","author":"M Berriman","year":"2005","journal-title":"Science (80-)"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.molbiopara.2014.06.004","article-title":"Capturing the variant surface glycoprotein repertoire (the VSGnome) of Trypanosoma brucei Lister 427","volume":"195","author":"GAM Cross","year":"2014","journal-title":"Mol Biochem Parasitol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1344","DOI":"10.1101\/gr.6421207","article-title":"Analysis of the VSG gene silent archive in Trypanosoma brucei reveals that mosaic gene expression is prominent in antigenic variation and is favored by archive substructure","volume":"17","author":"L Marcello","year":"2007","journal-title":"Genome Res"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"e3527","DOI":"10.1371\/journal.pone.0003527","article-title":"Telomeric Expression Sites Are Highly Conserved in Trypanosoma brucei","volume":"3","author":"C Hertz-Fowler","year":"2008","journal-title":"PLoS ONE"},{"key":"ref11","article-title":"Mosaic VSGs and the Scale of Trypanosoma brucei Antigenic Variation","volume":"9","author":"JPJ Hall","year":"2013","journal-title":"PLoS Pathog"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1470","DOI":"10.1126\/science.aaa4502","article-title":"The in vivo dynamics of antigenic variation in Trypanosoma brucei","volume":"347","author":"MR Mugnier","year":"2015","journal-title":"Science (80-)"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1016\/j.pt.2015.05.001","article-title":"Quantitative sequencing confirms VSG diversity as central to immune evasion by Trypanosoma brucei","author":"R McCulloch","year":"2015","journal-title":"Trends in Parasitology"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"5839","DOI":"10.1128\/MCB.19.9.5839","article-title":"Predominance of duplicative VSG gene conversion in antigenic variation in African trypanosomes","volume":"19","author":"NP Robinson","year":"1999","journal-title":"Mol Cell Biol"},{"key":"ref15","article-title":"Telomere Length Affects the Frequency and Mechanism of Antigenic Variation in Trypanosoma brucei","volume":"8","author":"GA Hovel-Miner","year":"2012","journal-title":"PLoS Pathog"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"3416","DOI":"10.1073\/pnas.1117313109","article-title":"Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species","volume":"109","author":"AP Jackson","year":"2012","journal-title":"Proc Natl Acad Sci"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"2875","DOI":"10.1101\/gad.13.21.2875","article-title":"A role for RAD51 and homologous recombination in Trypanosoma brucei antigenic variation","volume":"13","author":"R McCulloch","year":"1999","journal-title":"Genes Dev"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1038\/nature07982","article-title":"A yeast-endonuclease-generated DNA break induces antigenic switching in Trypanosoma brucei","volume":"459","author":"CE Boothroyd","year":"2009","journal-title":"Nature"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"e1003260","DOI":"10.1371\/journal.ppat.1003260","article-title":"DNA break site at fragile subtelomeres determines probability and mechanism of antigenic variation in African trypanosomes","volume":"9","author":"L Glover","year":"2013","journal-title":"PLoS Pathog"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"700","DOI":"10.1016\/j.mib.2010.08.009","article-title":"Molecular mechanisms underlying the control of antigenic variation in African trypanosomes","author":"D Horn","year":"2010","journal-title":"Current Opinion in Microbiology"},{"key":"ref21","article-title":"DNA Recombination Strategies During Antigenic Variation in the African Trypanosome","volume":"3","author":"LJ Morrison","year":"2015","journal-title":"Microbiol Spectr"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1016\/S0169-4758(97)01039-9","article-title":"The relative significance of mechanisms of antigenic variation in African trypanosomes","author":"JD Barry","year":"1997","journal-title":"Parasitology Today"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1534\/genetics.111.134577","article-title":"Mating-type genes and MAT switching in Saccharomyces cerevisiae","volume":"191","author":"JE Haber","year":"2012","journal-title":"Genetics"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/0092-8674(83)90219-2","article-title":"A site-specific endonuclease essential for mating-type switching in Saccharomyces cerevisiae","volume":"35","author":"R Kostriken","year":"1983","journal-title":"Cell"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"2380","DOI":"10.1002\/jcp.25367","article-title":"Programmable Site-Specific Nucleases for Targeted Genome Engineering in Higher Eukaryotes","volume":"231","author":"G Govindan","year":"2016","journal-title":"J Cell Physiol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"26185","DOI":"10.1074\/jbc.M203205200","article-title":"Inactivation of Mre11 does not affect VSG gene duplication mediated by homologous recombination in Trypanosoma brucei","volume":"277","author":"NP Robinson","year":"2002","journal-title":"J Biol Chem"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1016\/S0092-8674(01)00536-0","article-title":"Mus81-Eme1 are essential components of a Holliday junction resolvase","volume":"107","author":"MN Boddy","year":"2001","journal-title":"Cell"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"4826","DOI":"10.1091\/mbc.e03-05-0276","article-title":"Mus81 endonuclease localizes to nucleoli and to regions of DNA damage in human S-phase cells","volume":"14","author":"H Gao","year":"2003","journal-title":"Mol Biol Cell"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"3833","DOI":"10.1093\/nar\/gkt1333","article-title":"Substrate specificity of the MUS81-EME2 structure selective endonuclease","volume":"42","author":"A Pepe","year":"2014","journal-title":"Nucleic Acids Res. Oxford University Press"},{"key":"ref30","article-title":"The DNA repair endonuclease Mus81 facilitates fast DNA replication in the absence of exogenous damage","volume":"6","author":"H Fu","year":"2015","journal-title":"Nat Commun"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"756","DOI":"10.1111\/mmi.12589","article-title":"Nucleotide excision repair in <italic>T rypanosoma brucei<\/italic>: specialization of transcription-coupled repair due to multigenic transcription","volume":"92","author":"CR Machado","year":"2014","journal-title":"Mol Microbiol"},{"key":"ref32","first-page":"1","article-title":"TOPO3\u03b1 influences antigenic variation by monitoring expression-site-associated VSG switching in Trypanosoma brucei","volume":"6","author":"HS Kim","year":"2010","journal-title":"PLoS Pathog"},{"key":"ref33","article-title":"Identification of trypanosoma brucei RMI1\/BLAP75 homologue and its roles in antigenic variation","volume":"6","author":"HS Kim","year":"2011","journal-title":"PLoS ONE"},{"key":"ref34","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.12765","article-title":"Mapping replication dynamics in <italic>Trypanosoma brucei<\/italic> reveals a link with telomere transcription and antigenic variation","volume":"5","author":"R Devlin","year":"2016","journal-title":"Elife"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"12600","DOI":"10.1093\/nar\/gku900","article-title":"Locus-specific control of DNA resection and suppression of subtelomeric VSGrecombination by HAT3 in the African trypanosome","volume":"42","author":"L Glover","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"2759","DOI":"10.1093\/nar\/12.6.2759","article-title":"The 5\u2032-limit of transposition and upstream barren region of a trypanosome VSG gene: Tandem 76 base-pair repeats flanking (TAA)90","volume":"12","author":"DA Campbell","year":"1984","journal-title":"Nucleic Acids Res"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/S0022-2836(83)80034-5","article-title":"The transposition unit of variant surface glycoprotein gene 118 of Trypanosoma brucei","volume":"167","author":"AYC Liu","year":"1983","journal-title":"J Mol Biol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"3161","DOI":"10.1093\/nar\/13.9.3161","article-title":"(TAA)nwithin sequences flanking several intrachromosomal variant surface glycoprotein genes in Trypanosoma brucei","volume":"13","author":"R Aline","year":"1985","journal-title":"Nucleic Acids Res"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1128\/MCB.17.2.833","article-title":"Gene conversions mediating antigenic variation in Trypanosoma brucei can occur in variant surface glycoprotein expression sites lacking 70-base-pair repeat sequences","volume":"17","author":"R McCulloch","year":"1997","journal-title":"Mol Cell Biol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"16784","DOI":"10.1074\/jbc.271.28.16784","article-title":"TTA\u00b7TAA triplet repeats in plasmids form a non-H bonded structure","volume":"271","author":"K Ohshima","year":"1996","journal-title":"J Biol Chem"},{"key":"ref41","article-title":"Transcription of AAT\u00b7ATT Triplet Repeats in Escherichia coli Is Silenced by H-NS and IS1E Transposition","volume":"5","author":"X Pan","year":"2010","journal-title":"PLoS ONE"},{"key":"ref42","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1005994","article-title":"A Conserved DNA Repeat Promotes Selection of a Diverse Repertoire of Trypanosoma brucei Surface Antigens from the Genomic Archive","volume":"12","author":"G Hovel-Miner","year":"2016","journal-title":"PLoS Genet"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"8319","DOI":"10.1073\/pnas.111008398","article-title":"Instability of repetitive DNA sequences: The role of replication in multiple mechanisms","volume":"98","author":"M Bzymek","year":"2001","journal-title":"Proc Natl Acad Sci"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1016\/S1097-2765(00)80236-1","article-title":"Inhibition of FEN-1 processing by DNA secondary structure at trinucleotide repeats","volume":"4","author":"C Spiro","year":"1999","journal-title":"Mol Cell"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1038\/nrg1689","article-title":"Repeat instability: Mechanisms of dynamic mutations","author":"CE Pearson","year":"2005","journal-title":"Nature Reviews Genetics"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1038\/ncb2897","article-title":"Causes and consequences of replication stress","volume":"16","author":"MK Zeman","year":"2014","journal-title":"Nat Cell Biol. NIH Public Access"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1038\/303592a0","article-title":"Growth of chromosome ends in multiplying trypanosomes","volume":"303","author":"A Bernards","year":"1983","journal-title":"Nature"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/j.exppara.2007.07.016","article-title":"Telomere length in Trypanosoma brucei","volume":"118","author":"O Dreesen","year":"2008","journal-title":"Exp Parasitol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1016\/j.pt.2007.06.005","article-title":"Telomere biology of trypanosomatids: beginning to answer some questions","volume":"23","author":"CBB Lira","year":"2007","journal-title":"Trends Parasitol"},{"key":"ref50","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-017-16182-y","article-title":"Telomerase activity is required for the telomere G-overhang structure in Trypanosoma brucei","volume":"7","author":"R Sandhu","year":"2017","journal-title":"Sci Rep"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"875","DOI":"10.1038\/nsmb.3106","article-title":"Molecular mechanisms of activity and derepression of alternative lengthening of telomeres","author":"HA Pickett","year":"2015","journal-title":"Nature Structural and Molecular Biology"},{"key":"ref52","first-page":"2615","article-title":"Alternative lengthening of telomeres can be maintained by preferential elongation of lagging strands","volume":"45","author":"J Min","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1038\/sj.onc.1205079","article-title":"Telomere maintenance without telomerase","author":"V Lundblad","year":"2002","journal-title":"Oncogene"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"870","DOI":"10.1038\/cr.2014.60","article-title":"Trypanosoma brucei TIF2 suppresses VSG switching by maintaining subtelomere integrity","volume":"24","author":"SE Jehi","year":"2014","journal-title":"Cell Res"},{"key":"ref55","article-title":"Trypanosoma brucei TIF2 and TRF suppress VSG switching using overlapping and independent mechanisms","volume":"11","author":"SE Jehi","year":"2016","journal-title":"PLoS ONE"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"5785","DOI":"10.1093\/nar\/gkx184","article-title":"Trypanosoma brucei RAP1 maintains telomere and subtelomere integrity by suppressing TERRA and telomeric RNA: DNA hybrids","volume":"45","author":"V Nanavaty","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"4911","DOI":"10.1128\/MCB.00212-06","article-title":"Telomerase-Independent Stabilization of Short Telomeres in Trypanosoma brucei","volume":"26","author":"O Dreesen","year":"2006","journal-title":"Mol Cell Biol"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1038\/nrmicro1577","article-title":"Telomere structure and function in trypanosomes: A proposal","volume":"5","author":"O Dreesen","year":"2007","journal-title":"Nat Rev Microbiol"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1128\/EC.00059-06","article-title":"Consequences of telomere shortening at an active VSG expression site in telomerase-deficient Trypanosoma brucei","volume":"5","author":"O Dreesen","year":"2006","journal-title":"Eukaryot Cell"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1128\/EC.00207-14","article-title":"DNA double-strand breaks and telomeres play important roles in trypanosoma brucei antigenic variation","volume":"14","author":"B Li","year":"2015","journal-title":"Eukaryot Cell. American Society for Microbiology"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1128\/MCB.00816-07","article-title":"Transcription-Associated Recombination Is Dependent on Replication in Mammalian Cells","volume":"28","author":"P Gottipati","year":"2008","journal-title":"Mol Cell Biol"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1093\/genetics\/162.2.603","article-title":"Transcription and double-strand breaks induce similar mitotic recombination events in Saccharomyces cerevisiae","volume":"162","author":"S Gonz\u00e1lez-Barrera","year":"2002","journal-title":"Genetics"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.molbiopara.2007.01.013","article-title":"RNA polymerase I transcription stimulates homologous recombination in Trypanosoma brucei","volume":"153","author":"S Alsford","year":"2007","journal-title":"Mol Biochem Parasitol"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1128\/EC.2.3.542-551.2003","article-title":"RNA polymerase I transcribes procyclin genes and variant surface glycoprotein gene expression sites in Trypanosoma brucei","volume":"2","author":"A G\u00fcnzl","year":"2003","journal-title":"Eukaryot Cell"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1093\/genetics\/143.2.713","article-title":"Destabilization of simple repetitive DNA sequences by transcription in yeast","volume":"143","author":"M Wierdl","year":"1996","journal-title":"Genetics"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1016\/j.molcel.2014.12.011","article-title":"Caught in the Act: R-Loops Are Cleaved by Structure-Specific Endonucleases to Generate DSBs","author":"YL Lin","year":"2014","journal-title":"Molecular Cell"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1016\/j.molcel.2014.10.020","article-title":"Transcription-Coupled Nucleotide Excision Repair Factors Promote R-Loop-Induced Genome Instability","volume":"56","author":"J Sollier","year":"2014","journal-title":"Mol Cell"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1002\/mc.20488","article-title":"Transcription destabilizes triplet repeats","volume":"48","author":"Y Lin","year":"2009","journal-title":"Mol Carcinog"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"1299","DOI":"10.1515\/hsz-2012-0218","article-title":"Triplet repeats in transcripts: Structural insights into RNA toxicity","author":"P Galka-Marciniak","year":"2012","journal-title":"Biological Chemistry"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1016\/j.molcel.2003.08.010","article-title":"Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination","volume":"12","author":"P Huertas","year":"2003","journal-title":"Mol Cell"},{"key":"ref71","article-title":"RibonucleaseH1-targeted R-loops in surface antigen gene expression sites can direct trypanosome immune evasion","author":"E Briggs","journal-title":"PLoS Genet"},{"key":"ref72","article-title":"Genome-wide mapping reveals conserved and diverged R-loop activities in the unusual genetic landscape of the African trypanosome genome","author":"E Briggs","journal-title":"Nucleic Acids Res"},{"key":"ref73","article-title":"Transcription activity contributes to the activation of non-constitutive origins to maintain the robustness of S phase duration in African trypanosomes","author":"MS da Silva","year":"2018","journal-title":"BioRxiv"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"4067","DOI":"10.1093\/nar\/gkv271","article-title":"Differences in genome-wide repeat sequence instability conferred by proofreading and mismatch repair defects","volume":"43","author":"SA Lujan","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"45182","DOI":"10.1074\/jbc.M308123200","article-title":"Mismatch Repair Regulates Homologous Recombination, but Has Little Influence on Antigenic Variation, in Trypanosoma brucei","volume":"278","author":"JS Bell","year":"2003","journal-title":"J Biol Chem"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"986","DOI":"10.1016\/j.dnarep.2012.09.007","article-title":"Increased uracil insertion in DNA is cytotoxic and increases the frequency of mutation, double strand break formation and VSG switching in Trypanosoma brucei","volume":"11","author":"VM Castillo-Acosta","year":"2012","journal-title":"DNA Repair (Amst)"},{"key":"ref77","article-title":"VEX1 controls the allelic exclusion required for antigenic variation in trypanosomes","author":"L Glover","year":"2016","journal-title":"Proc Natl Acad Sci"},{"key":"ref78","first-page":"593","article-title":"How to create coats for all seasons: elucidating antigenic variation in African trypanosomes","volume":"1","author":"C-P Ooi","year":"2017","journal-title":"Emerg Top Life Sci. Portland Press Journals portal"},{"key":"ref79","article-title":"Base J and H3.V Regulate Transcriptional Termination in Trypanosoma brucei","author":"D Schulz","year":"2016","journal-title":"PLoS Genet"},{"key":"ref80","article-title":"Histone H3 Variant Regulates RNA Polymerase II Transcription Termination and Dual Strand Transcription of siRNA Loci in Trypanosoma brucei","author":"D Reynolds","year":"2016","journal-title":"PLoS Genet"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/nrm.2016.88","article-title":"Transcription\u2013replication conflicts: how they occur and how they are resolved","volume":"17","author":"T Garc\u00eda-Muse","year":"2016","journal-title":"Nat Rev Mol Cell Biol"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"888","DOI":"10.1128\/MCB.25.3.888-895.2005","article-title":"Mechanisms of transcription-replication collisions in bacteria","volume":"25","author":"E V Mirkin","year":"2005","journal-title":"Mol Cell Biol. American Society for Microbiology (ASM)"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"1280","DOI":"10.1038\/embor.2011.196","article-title":"Fast transcription rates of RNA polymerase II in human cells","volume":"12","author":"P Maiuri","year":"2011","journal-title":"EMBO Rep"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1002\/bies.201300057","article-title":"What do you mean by transcription rate?","volume":"35","author":"JE P\u00e9rez-Ort\u00edn","year":"2013","journal-title":"BioEssays"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1038\/nature07527","article-title":"The replisome uses mRNA as a primer after colliding with RNA polymerase","volume":"456","author":"RT Pomerantz","year":"2008","journal-title":"Nature"},{"key":"ref86","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1000810","article-title":"Co-orientation of replication and transcription preserves genome integrity","volume":"6","author":"A Srivatsan","year":"2010","journal-title":"PLoS Genet"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"1267","DOI":"10.1038\/sj.emboj.7600602","article-title":"Impairment of replication fork progression mediates RNA polII transcription-associated recombination","volume":"24","author":"F Prado","year":"2005","journal-title":"EMBO J"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1016\/j.celrep.2012.06.007","article-title":"Genome-wide Analysis Reveals Extensive Functional Interaction between DNA Replication Initiation and Transcription in the Genome of Trypanosoma brucei","volume":"2","author":"C Tiengwe","year":"2012","journal-title":"Cell Rep"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1083\/jcb.200607174","article-title":"Nuclear repositioning of the VSG promoter during developmental silencing in Trypanosoma brucei","volume":"176","author":"D Landeira","year":"2007","journal-title":"J Cell Biol"},{"key":"ref90","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a010132","article-title":"DNA replication timing","volume":"5","author":"N Rhind","year":"2013","journal-title":"Cold Spring Harb Perspect Biol"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"3330","DOI":"10.1016\/j.jmb.2014.05.027","article-title":"Chromatin structure and replication origins: Determinants of chromosome replication and nuclear organization","author":"OK Smith","year":"2014","journal-title":"Journal of Molecular Biology"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1016\/j.ceb.2016.03.022","article-title":"Replication timing and transcriptional control: Beyond cause and effect\u2014part III","author":"JC Rivera-Mulia","year":"2016","journal-title":"Current Opinion in Cell Biology"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"8638","DOI":"10.1021\/cr400017y","article-title":"Transcription-associated genome instability","author":"H Gaillard","year":"2013","journal-title":"Chemical Reviews"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1146\/annurev-pathol-012414-040424","article-title":"DNA Replication Stress as a Hallmark of Cancer","volume":"10","author":"M Macheret","year":"2015","journal-title":"Annu Rev Pathol Mech Dis"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1146\/annurev-biochem-060815-014908","article-title":"Transcription as a Threat to Genome Integrity","volume":"85","author":"H Gaillard","year":"2016","journal-title":"Annu Rev Biochem"},{"key":"ref96","article-title":"The within-host dynamics of African trypanosome infections","author":"KR Matthews","year":"2015","journal-title":"Philosophical Transactions of the Royal Society B: Biological Sciences"},{"key":"ref97","article-title":"Nuclear DNA Replication in Trypanosomatids: There Are No Easy Methods for Solving Difficult Problems","author":"MS da Silva","year":"2017","journal-title":"Trends Parasitol"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1126\/science.1112631","article-title":"The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease","volume":"309","author":"NM El-Sayed","year":"2005","journal-title":"Science"},{"key":"ref99","article-title":"Interactions between BRCA2 and RAD51 for promoting homologous recombination in Leishmania infantum","author":"MM Genois","year":"2012","journal-title":"Nucleic Acids Res"}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.ppat.1007321","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,6]],"date-time":"2022-09-06T03:20:34Z","timestamp":1662434434000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1007321"}},"subtitle":[],"editor":[{"given":"Marc-Jan","family":"Gubbels","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,11,15]]},"references-count":99,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2018,11,15]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1007321","relation":{},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,11,15]]}}}