{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T15:14:20Z","timestamp":1780499660478,"version":"3.54.1"},"reference-count":235,"publisher":"Elsevier BV","issue":"15","license":[{"start":{"date-parts":[[2020,7,1]],"date-time":"2020-07-01T00:00:00Z","timestamp":1593561600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2020,7,1]],"date-time":"2020-07-01T00:00:00Z","timestamp":1593561600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2021,7,14]],"date-time":"2021-07-14T00:00:00Z","timestamp":1626220800000},"content-version":"am","delay-in-days":378,"URL":"http:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["AI066095"],"award-info":[{"award-number":["AI066095"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01"],"award-info":[{"award-number":["R01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008982","name":"National Science Foundation","doi-asserted-by":"publisher","award":["MCB 1615896"],"award-info":[{"award-number":["MCB 1615896"]}],"id":[{"id":"10.13039\/501100008982","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008134","name":"California State University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008134","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100003187","name":"National Sleep Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100003187","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["AI127562"],"award-info":[{"award-number":["AI127562"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Molecular Biology"],"published-print":{"date-parts":[[2020,7]]},"DOI":"10.1016\/j.jmb.2019.10.025","type":"journal-article","created":{"date-parts":[[2019,11,2]],"date-time":"2019-11-02T17:04:33Z","timestamp":1572714273000},"page":"4167-4185","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":26,"title":["Telomere and Subtelomere R-loops and Antigenic Variation in Trypanosomes"],"prefix":"10.1016","volume":"432","author":[{"given":"Arpita","family":"Saha","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vishal P.","family":"Nanavaty","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5804-9876","authenticated-orcid":false,"given":"Bibo","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jmb.2019.10.025_bib1","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.ceb.2015.04.008","article-title":"The Yin and Yang of R-loop biology","volume":"34","author":"Costantino","year":"2015","journal-title":"Curr. Opin. Cell Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib2","doi-asserted-by":"crossref","first-page":"1389","DOI":"10.1111\/febs.14363","article-title":"Genomic origin and nuclear localization of TERRA telomeric repeat-containing RNA: from Darkness to Dawn","volume":"285","author":"Diman","year":"2018","journal-title":"FEBS J."},{"key":"10.1016\/j.jmb.2019.10.025_bib3","doi-asserted-by":"crossref","DOI":"10.1016\/j.dnarep.2019.102660","article-title":"What causes an RNA-DNA hybrid to compromise genome integrity","author":"Rond\u00f3n","year":"2019","journal-title":"DNA Repair (Amst)"},{"key":"10.1016\/j.jmb.2019.10.025_bib4","doi-asserted-by":"crossref","first-page":"2552","DOI":"10.1111\/febs.14464","article-title":"DNA:RNA hybrids at telomeres \u2013 when it is better to be out of the (R) loop","volume":"285","author":"Toubiana","year":"2018","journal-title":"FEBS J."},{"key":"10.1016\/j.jmb.2019.10.025_bib5","first-page":"1","article-title":"Antigenic variation in trypanosomes: enhanced phenotypic variation in a eukaryotic parasite","volume":"49","author":"Barry","year":"2001","journal-title":"Adv. Parasitol."},{"key":"10.1016\/j.jmb.2019.10.025_bib6","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":"Nanavaty","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib7","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1007729","article-title":"Ribonuclease H1-targeted R-loops in surface antigen gene expression sites can direct trypanosome immune evasion","volume":"14","author":"Briggs","year":"2018","journal-title":"PLoS Genet."},{"key":"10.1016\/j.jmb.2019.10.025_bib8","doi-asserted-by":"crossref","first-page":"9180","DOI":"10.1093\/nar\/gkz644","article-title":"Trypanosoma brucei ribonuclease H2A is an essential R-loop processing enzyme whose loss causes DNA damage during transcription initiation and antigenic variation","volume":"47","author":"Briggs","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib9","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1016\/j.molcel.2019.01.024","article-title":"R-loops as cellular regulators and genomic threats","volume":"73","author":"Crossley","year":"2019","journal-title":"Mol. Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib10","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/nrg3961","article-title":"R\u00a0loops: new modulators of genome dynamics and function","volume":"16","author":"Santos-Pereira","year":"2015","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.jmb.2019.10.025_bib11","doi-asserted-by":"crossref","first-page":"2294","DOI":"10.1073\/pnas.73.7.2294","article-title":"Hybridization of RNA to double-stranded DNA: formation of R-loops","volume":"73","author":"Thomas","year":"1976","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jmb.2019.10.025_bib12","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1016\/j.cell.2004.10.016","article-title":"Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center","volume":"119","author":"Westover","year":"2004","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib13","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1038\/ni919","article-title":"R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells","volume":"4","author":"Yu","year":"2003","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.jmb.2019.10.025_bib14","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. U. S. A."},{"key":"10.1016\/j.jmb.2019.10.025_bib15","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":"Huertas","year":"2003","journal-title":"Mol. Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib16","doi-asserted-by":"crossref","first-page":"3106","DOI":"10.1038\/emboj.2011.206","article-title":"Genome-wide function of THO\/TREX in active genes prevents R-loop-dependent replication obstacles","volume":"30","author":"G\u00f3mez-Gonz\u00e1lez","year":"2011","journal-title":"EMBO J."},{"key":"10.1016\/j.jmb.2019.10.025_bib17","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1002386","article-title":"Genome instability and transcription elongation impairment in human cells depleted of THO\/TREX","volume":"7","author":"Dom\u00ednguez-S\u00e1nchez","year":"2011","journal-title":"PLoS Genet."},{"key":"10.1016\/j.jmb.2019.10.025_bib18","doi-asserted-by":"crossref","first-page":"978","DOI":"10.1016\/j.molcel.2011.10.017","article-title":"RNase H and multiple RNA biogenesis factors cooperate to prevent RNA:DNA hybrids from generating genome instability","volume":"44","author":"Wahba","year":"2011","journal-title":"Mol. Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib19","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.molcel.2012.04.009","article-title":"R\u00a0loops: from transcription byproducts to threats to genome stability","volume":"46","author":"Aguilera","year":"2012","journal-title":"Mol. Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib20","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1128\/MCB.01251-07","article-title":"Mechanism of R-loop formation at immunoglobulin class switch sequences","volume":"28","author":"Roy","year":"2008","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib21","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1126\/science.1234848","article-title":"R-loop stabilization represses antisense transcription at the Arabidopsis FLC locus","volume":"340","author":"Sun","year":"2013","journal-title":"Science"},{"key":"10.1016\/j.jmb.2019.10.025_bib22","doi-asserted-by":"crossref","first-page":"1010","DOI":"10.1101\/gad.2037511","article-title":"CpG islands and the regulation of transcription","volume":"25","author":"Deaton","year":"2011","journal-title":"Genes Dev."},{"key":"10.1016\/j.jmb.2019.10.025_bib23","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1016\/j.molcel.2012.01.017","article-title":"R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters","volume":"45","author":"Ginno","year":"2012","journal-title":"Mol. Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib24","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1016\/j.molcel.2013.10.006","article-title":"R\u00a0loops are linked to histone H3 S10 phosphorylation and chromatin condensation","volume":"52","author":"Castellano-Pozo","year":"2013","journal-title":"Mol. Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib25","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1007781","article-title":"RNase H1 directs origin-specific initiation of DNA replication in human mitochondria","volume":"15","author":"Posse","year":"2019","journal-title":"PLoS Genet."},{"key":"10.1016\/j.jmb.2019.10.025_bib26","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1016\/j.cell.2005.06.008","article-title":"Inactivation of the SR protein splicing factor ASF\/SF2 results in genomic instability","volume":"122","author":"Li","year":"2005","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib27","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1038\/nrg2960","article-title":"Mutation: the perils of transcription","volume":"12","author":"Muers","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.jmb.2019.10.025_bib28","doi-asserted-by":"crossref","first-page":"2115","DOI":"10.1038\/ncomms3115","article-title":"R-loops and nicks initiate DNA breakage and genome instability in non-growing Escherichia coli","volume":"4","author":"Wimberly","year":"2013","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jmb.2019.10.025_bib29","doi-asserted-by":"crossref","first-page":"1384","DOI":"10.1101\/gad.242990.114","article-title":"A\u00a0double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression","volume":"28","author":"Skourti-Stathaki","year":"2014","journal-title":"Genes Dev."},{"key":"10.1016\/j.jmb.2019.10.025_bib30","doi-asserted-by":"crossref","first-page":"2041","DOI":"10.1101\/gad.17010011","article-title":"R-loop-mediated genomic instability is caused by impairment of replication fork progression","volume":"25","author":"Gan","year":"2011","journal-title":"Genes Dev."},{"key":"10.1016\/j.jmb.2019.10.025_bib31","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1038\/embor.2012.119","article-title":"R-loops cause replication impairment and genome instability during meiosis","volume":"13","author":"Castellano-Pozo","year":"2012","journal-title":"EMBO Rep."},{"key":"10.1016\/j.jmb.2019.10.025_bib32","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1004318","article-title":"R-loops associated with triplet repeat expansions promote gene silencing in Friedreich ataxia and fragile X syndrome","volume":"10","author":"Groh","year":"2014","journal-title":"PLoS Genet."},{"key":"10.1016\/j.jmb.2019.10.025_bib33","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1038\/nature13787","article-title":"R-loops induce repressive chromatin marks over mammalian gene terminators","volume":"516","author":"Skourti-Stathaki","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2019.10.025_bib34","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":"Sollier","year":"2014","journal-title":"Mol. Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib35","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1126\/science.1279808","article-title":"Stability and properties of double and triple helices: dramatic effects of RNA or DNA backbone composition","volume":"258","author":"Roberts","year":"1992","journal-title":"Science"},{"key":"10.1016\/j.jmb.2019.10.025_bib36","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1016\/S0092-8674(03)00554-3","article-title":"Loading Rho to terminate transcription","volume":"114","author":"Richardson","year":"2003","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib37","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1016\/j.dnarep.2011.04.013","article-title":"Human DHX9 helicase preferentially unwinds RNA-containing displacement loops (R-loops) and G-quadruplexes","volume":"10","author":"Chakraborty","year":"2011","journal-title":"DNA Repair (Amst)"},{"key":"10.1016\/j.jmb.2019.10.025_bib38","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1016\/j.cell.2012.09.041","article-title":"Senataxin associates with replication forks to protect fork integrity across RNA-polymerase-II-transcribed genes","volume":"151","author":"Alzu","year":"2012","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib39","doi-asserted-by":"crossref","first-page":"1494","DOI":"10.1111\/j.1742-4658.2009.06908.x","article-title":"Ribonuclease H: the enzymes in eukaryotes","volume":"276","author":"Cerritelli","year":"2009","journal-title":"FEBS J."},{"key":"10.1016\/j.jmb.2019.10.025_bib40","doi-asserted-by":"crossref","first-page":"4927","DOI":"10.1111\/j.1742-4658.2011.08394.x","article-title":"Analysis of subunit assembly and function of the Saccharomyces cerevisiae RNase H2 complex","volume":"278","author":"Nguyen","year":"2011","journal-title":"FEBS J."},{"key":"10.1016\/j.jmb.2019.10.025_bib41","doi-asserted-by":"crossref","first-page":"10530","DOI":"10.1074\/jbc.M110.177394","article-title":"The structure of the human RNase H2 complex defines key interaction interfaces relevant to enzyme function and human disease","volume":"286","author":"Reijns","year":"2011","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jmb.2019.10.025_bib42","doi-asserted-by":"crossref","first-page":"1546","DOI":"10.1101\/gad.573310","article-title":"Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis","volume":"24","author":"El Hage","year":"2010","journal-title":"Genes Dev."},{"key":"10.1016\/j.jmb.2019.10.025_bib43","doi-asserted-by":"crossref","first-page":"692","DOI":"10.1073\/pnas.0909740107","article-title":"R\u00a0loops stimulate genetic instability of CTG.CAG repeats","volume":"107","author":"Lin","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jmb.2019.10.025_bib44","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/0300-9084(93)90033-O","article-title":"Substrate specificity of human RNase H1 and its role in excision repair of ribose residues misincorporated in DNA","volume":"75","author":"Eder","year":"1993","journal-title":"Biochimie"},{"key":"10.1016\/j.jmb.2019.10.025_bib45","doi-asserted-by":"crossref","first-page":"8361","DOI":"10.1128\/MCB.19.12.8361","article-title":"Saccharomyces cerevisiae RNase H(35) functions in RNA primer removal during lagging-strand DNA synthesis, most efficiently in cooperation with Rad27 nuclease","volume":"19","author":"Qiu","year":"1999","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib46","doi-asserted-by":"crossref","first-page":"16654","DOI":"10.1073\/pnas.262591699","article-title":"Excision of misincorporated ribonucleotides in DNA by RNase H (type 2) and FEN-1 in cell-free extracts","volume":"99","author":"Rydberg","year":"2002","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jmb.2019.10.025_bib47","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1004630","article-title":"Out of balance: R-loops in human disease","volume":"10","author":"Groh","year":"2014","journal-title":"PLoS Genet."},{"key":"10.1016\/j.jmb.2019.10.025_bib48","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0003397","article-title":"A\u00a0literature review of economic evaluations for a neglected tropical disease: human African trypanosomiasis (\u201csleeping sickness\u201d)","volume":"9","author":"Sutherland","year":"2015","journal-title":"PLoS Negl. Trop. Dis."},{"key":"10.1016\/j.jmb.2019.10.025_bib49","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1017\/S003118200004717X","article-title":"Identification, purification and properties of clone-specific glycoprotein antigens constituting the surface coat of Trypanosoma brucei","volume":"71","author":"Cross","year":"1975","journal-title":"Parasitology"},{"key":"10.1016\/j.jmb.2019.10.025_bib50","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/0014-4894(85)90062-1","article-title":"Trypanosoma brucei: immunogenicity of the variant surface coat glycoprotein of virulent and avirulent subspecies","volume":"59","author":"Diffley","year":"1985","journal-title":"Exp. Parasitol."},{"key":"10.1016\/j.jmb.2019.10.025_bib51","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":"Cross","year":"2014","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.jmb.2019.10.025_bib52","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1038\/s41586-018-0619-8","article-title":"Genome organization and DNA accessibility control antigenic variation in trypanosomes","volume":"563","author":"M\u00fcller","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2019.10.025_bib53","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1101\/gr.5147406","article-title":"Hemizygous subtelomeres of an African trypanosome chromosome may account for over 75% of chromosome length","volume":"16","author":"Callejas","year":"2006","journal-title":"Genome Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib54","doi-asserted-by":"crossref","first-page":"4856","DOI":"10.1093\/nar\/gkg673","article-title":"The sequence and analysis of Trypanosoma brucei chromosome II","volume":"31","author":"El-Sayed","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib55","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/S0166-6851(00)00388-1","article-title":"Diversity and dynamics of the minichromosomal karyotype in Trypanosoma brucei","volume":"113","author":"Alsford","year":"2001","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.jmb.2019.10.025_bib56","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/299417a0","article-title":"Genomic environment of T.\u00a0brucei VSG genes: presence of a minichromosome","volume":"299","author":"Williams","year":"1982","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2019.10.025_bib57","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0166-6851(90)90107-W","article-title":"Structure of a telomeric expression site for variant specific surface antigens in Trypanosoma brucei","volume":"42","author":"Crozatier","year":"1990","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.jmb.2019.10.025_bib58","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/0166-6851(90)90101-Q","article-title":"Bloodstream and metacyclic variant surface glycoprotein gene expression sites of Trypanosoma brucei gambiense","volume":"41","author":"Barnes","year":"1990","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.jmb.2019.10.025_bib59","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":"Hertz-Fowler","year":"2008","journal-title":"PLoS One"},{"key":"10.1016\/j.jmb.2019.10.025_bib60","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1038\/299451a0","article-title":"Genomic environment of the expression-linked extra copies of genes for surface antigens of Trypanosoma brucei resembles the end of a chromosome","volume":"299","author":"de Lange","year":"1982","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2019.10.025_bib61","doi-asserted-by":"crossref","first-page":"119","DOI":"10.2174\/1389202918666170911161831","article-title":"Transcriptional regulation of telomeric expression sites and antigenic variation in trypanosomes","volume":"19","author":"Cestari","year":"2018","journal-title":"Curr. Genomics"},{"key":"10.1016\/j.jmb.2019.10.025_bib62","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1016\/j.gene.2014.09.047","article-title":"Mono-allelic VSG expression by RNA polymerase I in Trypanosoma brucei: expression site control from both ends?","volume":"556","author":"Gunzl","year":"2015","journal-title":"Gene"},{"key":"10.1016\/j.jmb.2019.10.025_bib63","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1042\/bse0480201","article-title":"Epigenetics and transcriptional control in African trypanosomes","volume":"48","author":"Rudenko","year":"2010","journal-title":"Essays Biochem."},{"key":"10.1016\/j.jmb.2019.10.025_bib64","doi-asserted-by":"crossref","first-page":"7673","DOI":"10.1093\/nar\/gkt562","article-title":"Silencing subtelomeric VSGs by Trypanosoma brucei RAP1 at the insect stage involves chromatin structure changes","volume":"41","author":"Pandya","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib65","doi-asserted-by":"crossref","first-page":"2981","DOI":"10.1093\/nar\/gks1469","article-title":"TDP1 is an HMG chromatin protein facilitating RNA polymerase I transcription in African trypanosomes","volume":"41","author":"Narayanan","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib66","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1003010","article-title":"Histone H1 plays a role in heterochromatin formation and VSG expression site silencing in Trypanosoma brucei","volume":"8","author":"Povelones","year":"2012","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.jmb.2019.10.025_bib67","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1128\/EC.00281-09","article-title":"Active VSG expression sites in Trypanosoma brucei are depleted of nucleosomes","volume":"9","author":"Stanne","year":"2010","journal-title":"Eukaryot. Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib68","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1128\/EC.00282-09","article-title":"Nucleosomes are depleted at the VSG expression site transcribed by RNA polymerase I in African trypanosomes","volume":"9","author":"Figueiredo","year":"2010","journal-title":"Eukaryot. Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib69","doi-asserted-by":"crossref","first-page":"2400","DOI":"10.1038\/sj.emboj.7601678","article-title":"A\u00a0novel ISWI is involved in VSG expression site downregulation in African trypanosomes","volume":"26","author":"Hughes","year":"2007","journal-title":"EMBO J."},{"key":"10.1016\/j.jmb.2019.10.025_bib70","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1111\/mmi.12812","article-title":"FACT plays a major role in histone dynamics affecting VSG expression site control in Trypanosoma brucei","volume":"94","author":"Denninger","year":"2014","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.jmb.2019.10.025_bib71","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1111\/j.1365-2958.2010.07350.x","article-title":"The FACT subunit TbSpt16 is involved in cell cycle specific control of VSG expression sites in Trypanosoma brucei","volume":"78","author":"Denninger","year":"2010","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.jmb.2019.10.025_bib72","doi-asserted-by":"crossref","first-page":"2265","DOI":"10.1093\/emboj\/18.8.2265","article-title":"Trypanosoma brucei variant surface glycoprotein regulation involves coupled activation\/inactivation and chromatin remodeling of expression sites","volume":"18","author":"Navarro","year":"1999","journal-title":"EMBO J."},{"key":"10.1016\/j.jmb.2019.10.025_bib73","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1005762","article-title":"Base J and H3.V regulate transcriptional termination in Trypanosoma brucei","volume":"12","author":"Schulz","year":"2016","journal-title":"PLoS Genet."},{"key":"10.1016\/j.jmb.2019.10.025_bib74","doi-asserted-by":"crossref","first-page":"8943","DOI":"10.1073\/pnas.1404873111","article-title":"Transcription is initiated on silent variant surface glycoprotein expression sites despite monoallelic expression in Trypanosoma brucei","volume":"111","author":"Kassem","year":"2014","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jmb.2019.10.025_bib75","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1046\/j.1365-2958.2000.01844.x","article-title":"Differential RNA elongation controls the variant surface glycoprotein gene expression sites of Trypanosoma brucei","volume":"36","author":"Vanhamme","year":"2000","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.jmb.2019.10.025_bib76","doi-asserted-by":"crossref","DOI":"10.1128\/MCB.00395-18","article-title":"Nuclear phosphatidylinositol 5-phosphatase is essential for allelic exclusion of variant surface glycoprotein genes in trypanosomes","volume":"39","author":"Cestari","year":"2019","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib77","doi-asserted-by":"crossref","first-page":"E2803","DOI":"10.1073\/pnas.1501206112","article-title":"Inositol phosphate pathway controls transcription of telomeric expression sites in trypanosomes","volume":"112","author":"Cestari","year":"2015","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jmb.2019.10.025_bib78","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.1001287","article-title":"NUP-1 Is a large coiled-coil nucleoskeletal protein in trypanosomes with lamin-like functions","volume":"10","author":"DuBois","year":"2012","journal-title":"PLoS Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib79","doi-asserted-by":"crossref","first-page":"10554","DOI":"10.1093\/nar\/gkw751","article-title":"Co-dependence between trypanosome nuclear lamina components in nuclear stability and control of gene expression","volume":"44","author":"Maishman","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib80","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1004545","article-title":"SUMOylation by the E3 ligase TbSIZ1\/PIAS1 positively regulates VSG expression in Trypanosoma brucei","volume":"10","author":"Lopez-Farfan","year":"2014","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.jmb.2019.10.025_bib81","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1111\/mmi.12093","article-title":"Trypanosoma brucei Orc1 is essential for nuclear DNA replication and affects both VSG silencing and VSG switching","volume":"87","author":"Benmerzouga","year":"2013","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.jmb.2019.10.025_bib82","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":"Tiengwe","year":"2012","journal-title":"Cell Rep."},{"key":"10.1016\/j.jmb.2019.10.025_bib83","article-title":"MCM-BP is required for repression of life-cycle specific genes transcribed by RNA polymerase I in the mammalian infectious form of Trypanosoma brucei","volume":"8","author":"Kim","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.jmb.2019.10.025_bib84","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1093\/nar\/gky1088","article-title":"Genome-wide function of MCM-BP in Trypanosoma brucei DNA replication and transcription","volume":"47","author":"Kim","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib85","doi-asserted-by":"crossref","first-page":"3023","DOI":"10.1038\/s41467-019-10823-8","article-title":"Monoallelic expression and epigenetic inheritance sustained by a Trypanosoma brucei variant surface glycoprotein exclusion complex","volume":"10","author":"Faria","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jmb.2019.10.025_bib86","doi-asserted-by":"crossref","first-page":"7225","DOI":"10.1073\/pnas.1600344113","article-title":"VEX1 controls the allelic exclusion required for antigenic variation in trypanosomes","volume":"113","author":"Glover","year":"2016","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jmb.2019.10.025_bib87","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.cell.2009.01.037","article-title":"RAP1 is essential for silencing telomeric variant surface glycoprotein genes in Trypanosoma brucei","volume":"137","author":"Yang","year":"2009","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib88","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1007\/BF00531626","article-title":"Loss of variable antigen during transformation of trypanosoma brucei rhodesiense from bloodstream to procyclic forms in the tsetse fly","volume":"74","author":"Turner","year":"1988","journal-title":"Parasitol. Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib89","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1242\/jcs.87.2.363","article-title":"Onset of expression of the variant surface glycoproteins of Trypanosoma brucei in the tsetse fly studied using immunoelectron microscopy","volume":"87","author":"Tetley","year":"1987","journal-title":"J.\u00a0Cell Sci."},{"key":"10.1016\/j.jmb.2019.10.025_bib90","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.molbiopara.2017.07.002","article-title":"Metacyclic VSG expression site promoters are recognized by the same general transcription factor that is required for RNA polymerase I transcription of bloodstream expression sites","volume":"216","author":"Kolev","year":"2017","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.jmb.2019.10.025_bib91","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.molbiopara.2015.04.001","article-title":"Synchronous expression of individual metacyclic variant surface glycoprotein genes in Trypanosoma brucei","volume":"200","author":"Ramey-Butler","year":"2015","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.jmb.2019.10.025_bib92","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/S0166-6851(99)00128-0","article-title":"A\u00a0structural and transcription pattern for variant surface glycoprotein gene expression sites used in metacyclic stage Trypanosoma brucei","volume":"103","author":"Graham","year":"1999","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.jmb.2019.10.025_bib93","doi-asserted-by":"crossref","first-page":"16876","DOI":"10.1074\/jbc.274.24.16876","article-title":"The anatomy and transcription of a monocistronic expression site for a metacyclic variant surface glycoprotein gene in Trypanosoma brucei","volume":"274","author":"Pedram","year":"1999","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jmb.2019.10.025_bib94","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.1128\/MCB.18.3.1137","article-title":"Activity of a trypanosome metacyclic variant surface glycoprotein gene promoter is dependent upon life cycle stage and chromosomal context","volume":"18","author":"Graham","year":"1998","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib95","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/S0166-6851(97)00193-X","article-title":"VSG gene control and infectivity strategy of metacyclic stage Trypanosoma brucei","volume":"91","author":"Barry","year":"1998","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.jmb.2019.10.025_bib96","doi-asserted-by":"crossref","first-page":"1985","DOI":"10.1093\/nar\/26.8.1985","article-title":"A\u00a0trypanosome metacyclic VSG gene promoter with two functionally distinct, life cycle stage-specific activities","volume":"26","author":"Graham","year":"1998","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib97","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.02324","article-title":"Expression site attenuation mechanistically links antigenic variation and development in Trypanosoma brucei","volume":"3","author":"Batram","year":"2014","journal-title":"Elife"},{"key":"10.1016\/j.jmb.2019.10.025_bib98","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/0092-8674(84)90206-X","article-title":"Antigenic variation in African trypanosomes by gene replacement or activation of alternative telomeres","volume":"39","author":"Myler","year":"1984","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib99","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1038\/309282a0","article-title":"Two mechanisms of expression of a variant antigen gene of Trypanosoma brucei","volume":"309","author":"Myler","year":"1984","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2019.10.025_bib100","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.MDNA3-0016-2014","article-title":"DNA recombination strategies during antigenic variation in the African trypanosome","volume":"3","author":"McCulloch","year":"2015","journal-title":"Microbiol. Spectr."},{"key":"10.1016\/j.jmb.2019.10.025_bib101","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/316562a0","article-title":"Telomeric reciprocal recombination as a possible mechanism for antigenic variation in trypanosomes","volume":"316","author":"Pays","year":"1985","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2019.10.025_bib102","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/0166-6851(96)02669-2","article-title":"Telomere exchange can be an important mechanism of variant surface glycoprotein gene switching in Trypanosoma brucei","volume":"80","author":"Rudenko","year":"1996","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.jmb.2019.10.025_bib103","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":"McCulloch","year":"1997","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib104","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1016\/0092-8674(83)90371-9","article-title":"Gene conversion as a mechanism for antigenic variation in trypanosomes","volume":"34","author":"Pays","year":"1983","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib105","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1016\/0092-8674(83)90370-7","article-title":"At least two transposed sequences are associated in the expression site of a surface antigen gene in different trypanosome clones","volume":"34","author":"Pays","year":"1983","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib106","doi-asserted-by":"crossref","first-page":"8149","DOI":"10.1093\/nar\/11.23.8149","article-title":"Telomere conversion in trypanosomes","volume":"11","author":"de Lange","year":"1983","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib107","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1016\/j.tig.2018.04.002","article-title":"Break-induced replication: the where, the why, and the how","volume":"34","author":"Kramara","year":"2018","journal-title":"Trends Genet."},{"key":"10.1016\/j.jmb.2019.10.025_bib108","doi-asserted-by":"crossref","first-page":"9375","DOI":"10.1073\/pnas.86.23.9375","article-title":"Active late-appearing variable surface antigen genes in Trypanosoma equiperdum are constructed entirely from pseudogenes","volume":"86","author":"Roth","year":"1989","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.jmb.2019.10.025_bib109","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":"Marcello","year":"2007","journal-title":"Genome Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib110","doi-asserted-by":"crossref","first-page":"2690","DOI":"10.1128\/IAI.73.5.2690-2697.2005","article-title":"Trypanosomes expressing a mosaic variant surface glycoprotein coat escape early detection by the immune system","volume":"73","author":"Dubois","year":"2005","journal-title":"Infect. Immun."},{"key":"10.1016\/j.jmb.2019.10.025_bib111","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":"Mugnier","year":"2015","journal-title":"Science"},{"key":"10.1016\/j.jmb.2019.10.025_bib112","doi-asserted-by":"crossref","first-page":"12899","DOI":"10.1093\/nar\/gku942","article-title":"Suppression of subtelomeric VSG switching by Trypanosoma brucei TRF requires its TTAGGG repeat-binding activity","volume":"42","author":"Jehi","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib113","doi-asserted-by":"crossref","first-page":"1724","DOI":"10.1111\/j.1462-5822.2009.01383.x","article-title":"Antigenic variation in the African trypanosome: molecular mechanisms and phenotypic complexity","volume":"11","author":"Morrison","year":"2009","journal-title":"Cell Microbiol."},{"key":"10.1016\/j.jmb.2019.10.025_bib114","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1000992","article-title":"TOPO3alpha influences antigenic variation by monitoring expression-site-associated VSG switching in Trypanosoma brucei","volume":"6","author":"Kim","year":"2010","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.jmb.2019.10.025_bib115","article-title":"Identification of Trypanosoma brucei RMI1\/BLAP75 homologue and its roles in antigenic variation","volume":"6","author":"Kim","year":"2011","journal-title":"PLoS One"},{"key":"10.1016\/j.jmb.2019.10.025_bib116","doi-asserted-by":"crossref","first-page":"2875","DOI":"10.1101\/gad.13.21.2875","article-title":"A\u00a0role for RAD51 and homologous recombination in Trypanosoma brucei antigenic variation","volume":"13","author":"McCulloch","year":"1999","journal-title":"Genes Dev."},{"key":"10.1016\/j.jmb.2019.10.025_bib117","doi-asserted-by":"crossref","first-page":"6906","DOI":"10.1093\/nar\/gki996","article-title":"Distinct roles for two RAD51-related genes in Trypanosoma brucei antigenic variation","volume":"33","author":"Proudfoot","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib118","doi-asserted-by":"crossref","first-page":"1237","DOI":"10.1111\/j.1365-2958.2008.06230.x","article-title":"Trypanosoma brucei BRCA2 acts in antigenic variation and has undergone a recent expansion in BRC repeat number that is important during homologous recombination","volume":"68","author":"Hartley","year":"2008","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.jmb.2019.10.025_bib119","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.12765","article-title":"Mapping replication dynamics in Trypanosoma brucei reveals a link with telomere transcription and antigenic variation","volume":"5","author":"Devlin","year":"2016","journal-title":"Elife"},{"key":"10.1016\/j.jmb.2019.10.025_bib120","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0156746","article-title":"Trypanosoma brucei TIF2 and TRF suppress VSG switching using overlapping and independent mechanisms","volume":"11","author":"Jehi","year":"2016","journal-title":"PLoS One"},{"key":"10.1016\/j.jmb.2019.10.025_bib121","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":"Jehi","year":"2014","journal-title":"Cell Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib122","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1002900","article-title":"Telomere length affects the frequency and mechanism of antigenic variation in Trypanosoma brucei","volume":"8","author":"Hovel-Miner","year":"2012","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.jmb.2019.10.025_bib123","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1007321","article-title":"Evaluation of mechanisms that may generate DNA lesions triggering antigenic variation in African trypanosomes","volume":"14","author":"da Silva","year":"2018","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.jmb.2019.10.025_bib124","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1042\/ETLS20170104","article-title":"Emerging challenges in understanding trypanosome antigenic variation","volume":"1","author":"McCulloch","year":"2017","journal-title":"Emerg. Top. Life Sci."},{"key":"10.1016\/j.jmb.2019.10.025_bib125","doi-asserted-by":"crossref","first-page":"2820","DOI":"10.1093\/nar\/gky028","article-title":"TelAP1 links telomere complexes with developmental expression site silencing in African trypanosomes","volume":"46","author":"Reis","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib126","doi-asserted-by":"crossref","first-page":"2100","DOI":"10.1101\/gad.1346005","article-title":"Shelterin: the protein complex that shapes and safeguards human telomeres","volume":"19","author":"de Lange","year":"2005","journal-title":"Genes Dev."},{"key":"10.1016\/j.jmb.2019.10.025_bib127","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1038\/nrm.2016.171","article-title":"Telomeres in cancer: tumour suppression and genome instability","volume":"18","author":"Maciejowski","year":"2017","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib128","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1016\/j.tibs.2015.06.003","article-title":"Replicating through telomeres: a means to an end","volume":"40","author":"Mart\u00ednez","year":"2015","journal-title":"Trends Biochem. Sci."},{"key":"10.1016\/j.jmb.2019.10.025_bib129","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1146\/annurev-genet-032918-021921","article-title":"Shelterin-mediated telomere protection","volume":"52","author":"de Lange","year":"2018","journal-title":"Annu. Rev. Genet."},{"key":"10.1016\/j.jmb.2019.10.025_bib130","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.biochi.2007.07.022","article-title":"Telomeric position effect: from the yeast paradigm to human pathologies?","volume":"90","author":"Ottaviani","year":"2008","journal-title":"Biochimie"},{"key":"10.1016\/j.jmb.2019.10.025_bib131","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.mad.2017.09.001","article-title":"Regulated expression of the lncRNA TERRA and its impact on telomere biology","volume":"167","author":"Oliva-Rico","year":"2017","journal-title":"Mech. Ageing Dev."},{"key":"10.1016\/j.jmb.2019.10.025_bib132","doi-asserted-by":"crossref","first-page":"4536","DOI":"10.1093\/nar\/gki769","article-title":"Telomere structure and shortening in telomerase-deficient Trypanosoma brucei","volume":"33","author":"Dreesen","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib133","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1038\/cr.2013.35","article-title":"A\u00a0trans-spliced telomerase RNA dictates telomere synthesis in Trypanosoma brucei","volume":"23","author":"Sandhu","year":"2013","journal-title":"Cell Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib134","doi-asserted-by":"crossref","first-page":"1399","DOI":"10.1016\/j.febslet.2013.03.017","article-title":"The Trypanosoma brucei Telomerase RNA (TER) homologue binds core proteins of the C\/D snoRNA family","volume":"587","author":"Gupta","year":"2013","journal-title":"FEBS Lett."},{"key":"10.1016\/j.jmb.2019.10.025_bib135","doi-asserted-by":"crossref","first-page":"5011","DOI":"10.1128\/MCB.25.12.5011-5021.2005","article-title":"Trypanosome telomeres are protected by a homologue of mammalian TRF2","volume":"25","author":"Li","year":"2005","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib136","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1083\/jcb.108.2.737","article-title":"Procyclin gene expression and loss of the variant surface glycoprotein during differentiation of Trypanosoma brucei","volume":"108","author":"Roditi","year":"1989","journal-title":"J.\u00a0Cell Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib137","doi-asserted-by":"crossref","first-page":"2633","DOI":"10.1002\/j.1460-2075.1989.tb08403.x","article-title":"Transcription of telomere repeats in protozoa","volume":"8","author":"Rudenko","year":"1989","journal-title":"EMBO J."},{"key":"10.1016\/j.jmb.2019.10.025_bib138","doi-asserted-by":"crossref","first-page":"798","DOI":"10.1126\/science.1147182","article-title":"Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends","volume":"318","author":"Azzalin","year":"2007","journal-title":"Science"},{"key":"10.1016\/j.jmb.2019.10.025_bib139","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1038\/ncb1685","article-title":"Developmentally regulated transcription of mammalian telomeres by DNA-dependent RNA polymerase II","volume":"10","author":"Schoeftner","year":"2008","journal-title":"Nat. Cell Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib140","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1016\/j.molcel.2008.10.019","article-title":"The Rat1p 5\u2032 to 3\u2032 exonuclease degrades telomeric repeat-containing RNA and promotes telomere elongation in Saccharomyces cerevisiae","volume":"32","author":"Luke","year":"2008","journal-title":"Mol. Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib141","doi-asserted-by":"crossref","first-page":"2995","DOI":"10.1093\/nar\/gkr1153","article-title":"The telomeric transcriptome of Schizosaccharomyces pombe","volume":"40","author":"Bah","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib142","doi-asserted-by":"crossref","first-page":"2956","DOI":"10.1093\/nar\/gkr1155","article-title":"Non-coding telomeric and subtelomeric transcripts are differentially regulated by telomeric and heterochromatin assembly factors in fission yeast","volume":"40","author":"Greenwood","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib143","doi-asserted-by":"crossref","first-page":"2186","DOI":"10.1261\/rna.1748309","article-title":"CpG-island promoters drive transcription of human telomeres","volume":"15","author":"Nergadze","year":"2009","journal-title":"RNA"},{"key":"10.1016\/j.jmb.2019.10.025_bib144","doi-asserted-by":"crossref","first-page":"5379","DOI":"10.1038\/ncomms6379","article-title":"Functional characterization of the TERRA transcriptome at damaged telomeres","volume":"5","author":"Porro","year":"2014","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jmb.2019.10.025_bib145","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.ymeth.2016.08.004","article-title":"A\u00a0practical qPCR approach to detect TERRA, the elusive telomeric repeat-containing RNA","volume":"114","author":"Feretzaki","year":"2017","journal-title":"Methods"},{"key":"10.1016\/j.jmb.2019.10.025_bib146","doi-asserted-by":"crossref","first-page":"4165","DOI":"10.1038\/emboj.2012.266","article-title":"A\u00a0role for CTCF and cohesin in subtelomere chromatin organization, TERRA transcription, and telomere end protection","volume":"31","author":"Deng","year":"2012","journal-title":"EMBO J."},{"key":"10.1016\/j.jmb.2019.10.025_bib147","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1038\/nsmb.3432","article-title":"PAR-TERRA directs homologous sex chromosome pairing","volume":"24","author":"Chu","year":"2017","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib148","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1002747","article-title":"TERRA promotes telomere shortening through exonuclease 1-mediated resection of chromosome ends","volume":"8","author":"Pfeiffer","year":"2012","journal-title":"PLoS Genet."},{"key":"10.1016\/j.jmb.2019.10.025_bib149","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1000986","article-title":"siRNA-mediated methylation of Arabidopsis telomeres","volume":"6","author":"Vrbsky","year":"2010","journal-title":"PLoS Genet."},{"key":"10.1016\/j.jmb.2019.10.025_bib150","doi-asserted-by":"crossref","first-page":"12534","DOI":"10.1038\/ncomms12534","article-title":"Telomeric RNAs are essential to maintain telomeres","volume":"7","author":"Montero","year":"2016","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jmb.2019.10.025_bib151","doi-asserted-by":"crossref","first-page":"4723","DOI":"10.1038\/ncomms5723","article-title":"Identification of TERRA locus unveils a telomere protection role through association to nearly all chromosomes","volume":"5","author":"Lopez de Silanes","year":"2014","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jmb.2019.10.025_bib152","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1016\/j.cell.2017.06.017","article-title":"TERRA RNA antagonizes ATRX and protects telomeres","volume":"170","author":"Chu","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib153","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1038\/nature09772","article-title":"TERRA and hnRNPA1 orchestrate an RPA-to-POT1 switch on telomeric single-stranded DNA","volume":"471","author":"Flynn","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2019.10.025_bib154","doi-asserted-by":"crossref","first-page":"316","DOI":"10.7150\/ijbs.10528","article-title":"Role of TERRA in the regulation of telomere length","volume":"11","author":"Wang","year":"2015","journal-title":"Int. J. Biol. Sci."},{"key":"10.1016\/j.jmb.2019.10.025_bib155","doi-asserted-by":"crossref","first-page":"938","DOI":"10.1080\/15476286.2015.1065374","article-title":"Telomere elongation chooses TERRA ALTernatives","volume":"12","author":"Arora","year":"2015","journal-title":"RNA Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib156","doi-asserted-by":"crossref","first-page":"999","DOI":"10.15252\/embr.201541708","article-title":"TERRA promotes telomerase-mediated telomere elongation in Schizosaccharomyces pombe","volume":"17","author":"Moravec","year":"2016","journal-title":"EMBO Rep."},{"key":"10.1016\/j.jmb.2019.10.025_bib157","doi-asserted-by":"crossref","first-page":"5797","DOI":"10.1093\/nar\/gkq296","article-title":"The non-coding RNA TERRA is a natural ligand and direct inhibitor of human telomerase","volume":"38","author":"Redon","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib158","doi-asserted-by":"crossref","first-page":"3377","DOI":"10.1073\/pnas.1307415111","article-title":"Telomeric transcripts stimulate telomere recombination to suppress senescence in cells lacking telomerase","volume":"111","author":"Yu","year":"2014","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jmb.2019.10.025_bib159","doi-asserted-by":"crossref","first-page":"143","DOI":"10.3389\/fgene.2015.00143","article-title":"Telomeric repeat-containing RNA TERRA: a noncoding RNA connecting telomere biology to genome integrity","volume":"6","author":"Cusanelli","year":"2015","journal-title":"Front. Genet."},{"key":"10.1016\/j.jmb.2019.10.025_bib160","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1534\/genetics.119.302606","article-title":"RNA-DNA hybrids support recombination-based telomere maintenance in fission yeast","volume":"213","author":"Hu","year":"2019","journal-title":"Genetics"},{"key":"10.1016\/j.jmb.2019.10.025_bib161","doi-asserted-by":"crossref","DOI":"10.3390\/cells8030246","article-title":"The emerging roles of TERRA in telomere maintenance and genome stability","volume":"8","author":"Bettin","year":"2019","journal-title":"Cells"},{"key":"10.1016\/j.jmb.2019.10.025_bib162","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":"Berriman","year":"2005","journal-title":"Science"},{"key":"10.1016\/j.jmb.2019.10.025_bib163","doi-asserted-by":"crossref","first-page":"459","DOI":"10.2217\/fmb.11.20","article-title":"Trans-splicing in trypanosomes: machinery and its impact on the parasite transcriptome","volume":"6","author":"Michaeli","year":"2011","journal-title":"Future Microbiol."},{"key":"10.1016\/j.jmb.2019.10.025_bib164","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/j.ijmm.2012.07.004","article-title":"mRNA splicing in trypanosomes","volume":"302","author":"Preu\u00dfer","year":"2012","journal-title":"Int. J. Med. Microbiol."},{"key":"10.1016\/j.jmb.2019.10.025_bib165","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1590\/0074-02760170054","article-title":"Evidence for regulated expression of Telomeric Repeat-containing RNAs (TERRA) in parasitic trypanosomatids","volume":"112","author":"Damasceno","year":"2017","journal-title":"Mem. Inst. Oswaldo Cruz"},{"key":"10.1016\/j.jmb.2019.10.025_bib166","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/0022-1759(86)90040-2","article-title":"Characterization of monoclonal antibody to DNA.RNA and its application to immunodetection of hybrids","volume":"89","author":"Boguslawski","year":"1986","journal-title":"J.\u00a0Immunol. Methods"},{"key":"10.1016\/j.jmb.2019.10.025_bib167","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1038\/nsmb.2662","article-title":"Telomeric RNA-DNA hybrids affect telomere-length dynamics and senescence","volume":"20","author":"Balk","year":"2013","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib168","doi-asserted-by":"crossref","first-page":"5220","DOI":"10.1038\/ncomms6220","article-title":"RNaseH1 regulates TERRA-telomeric DNA hybrids and telomere maintenance in ALT tumour cells","volume":"5","author":"Arora","year":"2014","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jmb.2019.10.025_bib169","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1111\/febs.14700","article-title":"FANCD2 protects genome stability by recruiting RNA processing enzymes to resolve R-loops during mild replication stress","volume":"286","author":"Okamoto","year":"2019","journal-title":"FEBS J."},{"key":"10.1016\/j.jmb.2019.10.025_bib170","doi-asserted-by":"crossref","first-page":"4346","DOI":"10.1038\/s41467-018-06677-1","article-title":"DHX9 helicase promotes R-loop formation in cells with impaired RNA splicing","volume":"9","author":"Chakraborty","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.jmb.2019.10.025_bib171","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/S0166-6851(00)00182-1","article-title":"Trypanosoma brucei RNase HI requires its divergent spacer subdomain for enzymatic function and its conserved RNA binding motif for nuclear localization","volume":"107","author":"Kobil","year":"2000","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.jmb.2019.10.025_bib172","doi-asserted-by":"crossref","first-page":"11789","DOI":"10.1093\/nar\/gky928","article-title":"Genome-wide mapping reveals conserved and diverged R-loop activities in the unusual genetic landscape of the African trypanosome genome","volume":"46","author":"Briggs","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib173","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":"Campbell","year":"1984","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib174","doi-asserted-by":"crossref","first-page":"3161","DOI":"10.1093\/nar\/13.9.3161","article-title":"(TAA)n within sequences flanking several intrachromosomal variant surface glycoprotein genes in Trypanosoma brucei","volume":"13","author":"Aline","year":"1985","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib175","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/0022-2836(91)80178-W","article-title":"Variant specific glycoprotein of Trypanosoma brucei consists of two domains each having an independently conserved pattern of cysteine residues","volume":"221","author":"Carrington","year":"1991","journal-title":"J.\u00a0Mol. Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib176","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.molbiopara.2012.01.008","article-title":"Trypanosomal histone gammaH2A and the DNA damage response","volume":"183","author":"Glover","year":"2012","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.jmb.2019.10.025_bib177","doi-asserted-by":"crossref","first-page":"822","DOI":"10.1016\/S0959-437X(97)80046-9","article-title":"Chromosome ends: all the same under their caps","volume":"7","author":"Pryde","year":"1997","journal-title":"Curr. Opin. Genet. Dev."},{"key":"10.1016\/j.jmb.2019.10.025_bib178","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1038\/nrg727","article-title":"The complex structure and dynamic evolution of human subtelomeres","volume":"3","author":"Mefford","year":"2002","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.jmb.2019.10.025_bib179","doi-asserted-by":"crossref","first-page":"156","DOI":"10.3389\/fonc.2012.00156","article-title":"Telomere components as potential therapeutic targets for treating microbial pathogen infections","volume":"2","author":"Li","year":"2012","journal-title":"Front. Oncol."},{"key":"10.1016\/j.jmb.2019.10.025_bib180","doi-asserted-by":"crossref","first-page":"R151","DOI":"10.1186\/gb-2007-8-7-r151","article-title":"Human subtelomeric duplicon structure and organization","volume":"8","author":"Ambrosini","year":"2007","journal-title":"Genome Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib181","doi-asserted-by":"crossref","first-page":"e73","DOI":"10.1093\/nar\/gkx017","article-title":"High-throughput single-molecule mapping links subtelomeric variants and long-range haplotypes with specific telomeres","volume":"45","author":"Young","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib182","doi-asserted-by":"crossref","first-page":"9173","DOI":"10.1038\/s41598-017-09471-z","article-title":"Genetic basis of mycotoxin susceptibility differences between budding yeast isolates","volume":"7","author":"Quispe","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.jmb.2019.10.025_bib183","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1534\/genetics.107.083196","article-title":"Molecular population genetics of Drosophila subtelomeric DNA","volume":"178","author":"Anderson","year":"2008","journal-title":"Genetics"},{"key":"10.1016\/j.jmb.2019.10.025_bib184","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1534\/genetics.105.055202","article-title":"Natural variation in a subtelomeric region of Arabidopsis: implications for the genomic dynamics of a chromosome end","volume":"173","author":"Kuo","year":"2006","journal-title":"Genetics"},{"key":"10.1016\/j.jmb.2019.10.025_bib185","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.01470-17","article-title":"Mechanisms of surface antigenic variation in the human pathogenic fungus Pneumocystis jirovecii","volume":"8","author":"Schmid-Siegert","year":"2017","journal-title":"mBio"},{"key":"10.1016\/j.jmb.2019.10.025_bib186","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1111\/j.1574-6968.2007.00812.x","article-title":"Telomeres in the rice blast fungus Magnaporthe oryzae: the world of the end as we know it","volume":"273","author":"Farman","year":"2007","journal-title":"FEMS Microbiol. Lett."},{"key":"10.1016\/j.jmb.2019.10.025_bib187","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/S0166-6851(00)00316-9","article-title":"The molecular karyotype of the megabase chromosomes of Trypanosoma brucei stock 427","volume":"111","author":"Melville","year":"2000","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.jmb.2019.10.025_bib188","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1023\/A:1009247315947","article-title":"Multiple causes of size variation in the diploid megabase chromosomes of African trypanosomes","volume":"7","author":"Melville","year":"1999","journal-title":"Chromosome Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib189","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/S0092-8674(00)80932-0","article-title":"TRF2 protects human telomeres from end-to-end fusions","volume":"92","author":"van Steensel","year":"1998","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib190","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1038\/ncb1275","article-title":"DNA processing is not required for ATM-mediated telomere damage response after TRF2 deletion","volume":"7","author":"Celli","year":"2005","journal-title":"Nat. Cell Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib191","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1016\/j.cell.2015.11.054","article-title":"Chromothripsis and kataegis induced by telomere crisis","volume":"163","author":"Maciejowski","year":"2015","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib192","doi-asserted-by":"crossref","first-page":"1698","DOI":"10.1042\/BST0381698","article-title":"Different outcomes of telomere-dependent anaphase bridges","volume":"38","author":"Tusell","year":"2010","journal-title":"Biochem. Soc. Trans."},{"key":"10.1016\/j.jmb.2019.10.025_bib193","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1016\/j.cell.2004.10.011","article-title":"Homologous recombination generates T-loop-sized deletions at human telomeres","volume":"119","author":"Wang","year":"2004","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib194","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1091\/mbc.e10-02-0173","article-title":"Telomeric recombination induced by dysfunctional telomeres","volume":"22","author":"Brault","year":"2011","journal-title":"Mol. Biol. Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib195","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1038\/nature14513","article-title":"Cell death during crisis is mediated by mitotic telomere deprotection","volume":"522","author":"Hayashi","year":"2015","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2019.10.025_bib196","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1016\/0092-8674(93)90234-H","article-title":"An alternative pathway for yeast telomere maintenance rescues est1- senescence","volume":"73","author":"Lundblad","year":"1993","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib197","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1093\/genetics\/152.1.143","article-title":"RAD50 and RAD51 define two pathways that collaborate to maintain telomeres in the absence of telomerase","volume":"152","author":"Le","year":"1999","journal-title":"Genetics"},{"key":"10.1016\/j.jmb.2019.10.025_bib198","doi-asserted-by":"crossref","first-page":"1819","DOI":"10.1128\/MCB.21.5.1819-1827.2001","article-title":"Two survivor pathways that allow growth in the absence of telomerase are generated by distinct telomere recombination events","volume":"21","author":"Chen","year":"2001","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib199","doi-asserted-by":"crossref","first-page":"8716","DOI":"10.1073\/pnas.0501886102","article-title":"Variant surface glycoprotein RNA interference triggers a precytokinesis cell cycle arrest in African trypanosomes","volume":"102","author":"Sheader","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"10.1016\/j.jmb.2019.10.025_bib200","doi-asserted-by":"crossref","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":"Glover","year":"2013","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.jmb.2019.10.025_bib201","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1038\/nature07982","article-title":"A\u00a0yeast-endonuclease-generated DNA break induces antigenic switching in Trypanosoma brucei","volume":"459","author":"Boothroyd","year":"2009","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2019.10.025_bib202","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":"Dreesen","year":"2006","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib203","doi-asserted-by":"crossref","first-page":"872","DOI":"10.1093\/nar\/gkl1100","article-title":"Deletion of a trypanosome telomere leads to loss of silencing and progressive loss of terminal DNA in the absence of cell cycle arrest","volume":"35","author":"Glover","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib204","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1016\/j.tig.2017.09.003","article-title":"Alternative lengthening of telomeres: DNA repair pathways converge","volume":"33","author":"Sobinoff","year":"2017","journal-title":"Trends Genet."},{"key":"10.1016\/j.jmb.2019.10.025_bib205","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1007\/s00294-018-0822-z","article-title":"Chromosome ends as adaptive beginnings: the potential role of dysfunctional telomeres in subtelomeric evolvability","volume":"64","author":"Mason","year":"2018","journal-title":"Curr. Genet."},{"key":"10.1016\/j.jmb.2019.10.025_bib206","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1534\/genetics.117.300607","article-title":"Mild telomere dysfunction as a force for altering the adaptive potential of subtelomeric genes","volume":"208","author":"Mason","year":"2018","journal-title":"Genetics"},{"key":"10.1016\/j.jmb.2019.10.025_bib207","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1005994","article-title":"A\u00a0conserved DNA repeat promotes selection of a diverse repertoire of Trypanosoma brucei surface antigens from the genomic archive","volume":"12","author":"Hovel-Miner","year":"2016","journal-title":"PLoS Genet."},{"key":"10.1016\/j.jmb.2019.10.025_bib208","doi-asserted-by":"crossref","DOI":"10.1002\/bies.201700229","article-title":"DNA repair: the search for homology","volume":"40","author":"Haber","year":"2018","journal-title":"Bioessays"},{"key":"10.1016\/j.jmb.2019.10.025_bib209","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1038\/303592a0","article-title":"Growth of chromosome ends in multiplying trypanosomes","volume":"303","author":"Bernards","year":"1983","journal-title":"Nature"},{"key":"10.1016\/j.jmb.2019.10.025_bib210","doi-asserted-by":"crossref","first-page":"4534","DOI":"10.1093\/nar\/gkf572","article-title":"Slipped-strand DNAs formed by long (CAG)*(CTG) repeats: slipped-out repeats and slip-out junctions","volume":"30","author":"Pearson","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib211","doi-asserted-by":"crossref","first-page":"41715","DOI":"10.1074\/jbc.M406415200","article-title":"Hairpin structure-forming propensity of the (CCTG.CAGG) tetranucleotide repeats contributes to the genetic instability associated with myotonic dystrophy type 2","volume":"279","author":"Dere","year":"2004","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jmb.2019.10.025_bib212","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1146\/annurev.bb.23.060194.003415","article-title":"G-quartet structures in telomeric DNA","volume":"23","author":"Williamson","year":"1994","journal-title":"Annu. Rev. Biophys. Biomol. Struct."},{"key":"10.1016\/j.jmb.2019.10.025_bib213","doi-asserted-by":"crossref","first-page":"16784","DOI":"10.1074\/jbc.271.28.16784","article-title":"TTA.TAA triplet repeats in plasmids form a non-H bonded structure","volume":"271","author":"Ohshima","year":"1996","journal-title":"J.\u00a0Biol. Chem."},{"key":"10.1016\/j.jmb.2019.10.025_bib214","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":"Sfeir","year":"2009","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib215","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1016\/j.cell.2010.05.032","article-title":"TRF2 and apollo cooperate with topoisomerase 2alpha to protect human telomeres from replicative damage","volume":"142","author":"Ye","year":"2010","journal-title":"Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib216","doi-asserted-by":"crossref","first-page":"2050","DOI":"10.1101\/gad.194282.112","article-title":"Telomere-binding protein Taz1 controls global replication timing through its localization near late replication origins in fission yeast","volume":"26","author":"Tazumi","year":"2012","journal-title":"Genes Dev."},{"key":"10.1016\/j.jmb.2019.10.025_bib217","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/j.gde.2012.11.009","article-title":"Replication stress and genome rearrangements: lessons from yeast models","volume":"23","author":"Lambert","year":"2013","journal-title":"Curr. Opin. Genet. Dev."},{"key":"10.1016\/j.jmb.2019.10.025_bib218","doi-asserted-by":"crossref","first-page":"2223","DOI":"10.1016\/j.celrep.2017.10.103","article-title":"Impediment of replication forks by long non-coding RNA provokes chromosomal rearrangements by error-prone restart","volume":"21","author":"Watanabe","year":"2017","journal-title":"Cell Rep."},{"key":"10.1016\/j.jmb.2019.10.025_bib219","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/nrm.2016.88","article-title":"Transcription-replication conflicts: how they occur and how they are resolved","volume":"17","author":"Garc\u00eda-Muse","year":"2016","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib220","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":"Gunzl","year":"2003","journal-title":"Eukaryot. Cell"},{"key":"10.1016\/j.jmb.2019.10.025_bib221","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":"Wierdl","year":"1996","journal-title":"Genetics"},{"key":"10.1016\/j.jmb.2019.10.025_bib222","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":"Gottipati","year":"2008","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.jmb.2019.10.025_bib223","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":"Alsford","year":"2007","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.jmb.2019.10.025_bib224","doi-asserted-by":"crossref","first-page":"166","DOI":"10.3389\/fpubh.2019.00166","article-title":"Chagas disease: from discovery to a worldwide health problem","volume":"7","author":"Lidani","year":"2019","journal-title":"Front. Public Health"},{"key":"10.1016\/j.jmb.2019.10.025_bib225","doi-asserted-by":"crossref","DOI":"10.3390\/pathogens8030119","article-title":"Therapeutic interventions for countering Leishmaniasis and Chagas's disease: from traditional sources to nanotechnological systems","volume":"8","author":"Souto","year":"2019","journal-title":"Pathogens"},{"key":"10.1016\/j.jmb.2019.10.025_bib226","doi-asserted-by":"crossref","first-page":"2451","DOI":"10.1093\/nar\/27.12.2451","article-title":"Identification of the telomere in Trypanosoma cruzi reveals highly heterogeneous telomere lengths in different parasite strains","volume":"27","author":"Freitas-Junior","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib227","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1126\/science.1112680","article-title":"The genome of the kinetoplastid parasite, Leishmania major","volume":"309","author":"Ivens","year":"2005","journal-title":"Science"},{"key":"10.1016\/j.jmb.2019.10.025_bib228","doi-asserted-by":"crossref","first-page":"D457","DOI":"10.1093\/nar\/gkp851","article-title":"TriTrypDB: a functional genomic resource for the Trypanosomatidae","volume":"38","author":"Aslett","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jmb.2019.10.025_bib229","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1186\/1471-2180-10-136","article-title":"The Leishmania amazonensis TRF (TTAGGG repeat-binding factor) homologue binds and co-localizes with telomeres","volume":"10","author":"da Silva","year":"2010","journal-title":"BMC Microbiol."},{"key":"10.1016\/j.jmb.2019.10.025_bib230","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1111\/j.1365-2249.2006.03118.x","article-title":"Interaction of natural killer cells with Trypanosoma cruzi-infected fibroblasts","volume":"145","author":"Lieke","year":"2006","journal-title":"Clin. Exp. Immunol."},{"key":"10.1016\/j.jmb.2019.10.025_bib231","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/0166-6851(86)90081-2","article-title":"Partial inhibition of trypomastigote entry into cultured mammalian cells by monoclonal antibodies against a surface glycoprotein of Trypanosoma cruzi","volume":"21","author":"Alves","year":"1986","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.jmb.2019.10.025_bib232","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/0166-6851(89)90209-0","article-title":"A\u00a0surface antigen of Trypanosoma cruzi involved in cell invasion (Tc-85) is heterogeneous in expression and molecular constitution","volume":"35","author":"Abuin","year":"1989","journal-title":"Mol. Biochem. Parasitol."},{"key":"10.1016\/j.jmb.2019.10.025_bib233","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0004099","article-title":"Trypanosoma cruzi binds to cytokeratin through conserved peptide motifs found in the Laminin-G-like domain of the gp85\/Trans-sialidase proteins","volume":"9","author":"Teixeira","year":"2015","journal-title":"PLoS Negl. Trop. Dis."},{"key":"10.1016\/j.jmb.2019.10.025_bib234","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/j.micinf.2016.08.003","article-title":"Decreased cruzipain and gp85\/trans-sialidase family protein expression contributes to loss of Trypanosoma cruzi trypomastigote virulence","volume":"19","author":"San Francisco","year":"2017","journal-title":"Microbes Infect."},{"key":"10.1016\/j.jmb.2019.10.025_bib235","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1016\/j.gene.2004.10.014","article-title":"Telomere and subtelomere of Trypanosoma cruzi chromosomes are enriched in (pseudo)genes of retrotransposon hot spot and trans-sialidase-like gene families: the origins of T.\u00a0cruzi telomeres","volume":"346","author":"Kim","year":"2005","journal-title":"Gene"}],"container-title":["Journal of Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0022283619306217?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0022283619306217?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T02:39:37Z","timestamp":1777430377000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0022283619306217"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,7]]},"references-count":235,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2020,7]]}},"alternative-id":["S0022283619306217"],"URL":"https:\/\/doi.org\/10.1016\/j.jmb.2019.10.025","relation":{},"ISSN":["0022-2836"],"issn-type":[{"value":"0022-2836","type":"print"}],"subject":[],"published":{"date-parts":[[2020,7]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Telomere and Subtelomere R-loops and Antigenic Variation in Trypanosomes","name":"articletitle","label":"Article Title"},{"value":"Journal of Molecular Biology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jmb.2019.10.025","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2019 Elsevier Ltd. All rights reserved.","name":"copyright","label":"Copyright"}]}}