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By employing three complementary approaches we provide a high-resolution map of ORIs in Plasmodium falciparum, the deadliest human malaria parasite. We profiled the distribution of origin of recognition complex (ORC) binding sites by ChIP-seq of two PfORC subunits and mapped active ORIs using NFS and SNS-seq. We show that ORIs lack sequence specificity but are not randomly distributed, and group in clusters. Licensing is biased towards regions of higher GC content and associated with G-quadruplex forming sequences (G4FS). While strong transcription likely enhances firing, active origins are depleted from transcription start sites. Instead, most accumulate in transcriptionally active gene bodies. Single molecule analysis of nanopore reads containing multiple initiation events, which could have only come from individual nuclei, showed a relationship between the replication fork pace and the distance to the nearest origin. While some similarities were drawn with the canonic eukaryote model, the distribution of ORIs in P. falciparum is likely shaped by unique genomic features such as extreme AT-richness\u2014a product of evolutionary pressure imposed by the parasitic lifestyle.<\/jats:p>","DOI":"10.1093\/nar\/gkad1103","type":"journal-article","created":{"date-parts":[[2023,12,1]],"date-time":"2023-12-01T12:16:27Z","timestamp":1701432987000},"page":"660-676","source":"Crossref","is-referenced-by-count":23,"title":["The genetic landscape of origins of replication in <i>P.\u00a0falciparum<\/i>"],"prefix":"10.1093","volume":"52","author":[{"given":"Casilda Mu\u00f1oz","family":"Castellano","sequence":"first","affiliation":[{"name":"LPHI, CNRS, Universit\u00e9 de Montpellier , 34095\u00a0 Montpellier , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6382-9057","authenticated-orcid":false,"given":"Laurent","family":"Lacroix","sequence":"additional","affiliation":[{"name":"Institut de Biologie de l\u2019Ecole Normale Sup\u00e9rieure (IBENS) , Ecole Normale Sup\u00e9rieure, CNRS, INSERM, Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emilie","family":"Mathis","sequence":"additional","affiliation":[{"name":"LPHI, CNRS, Universit\u00e9 de Montpellier , 34095\u00a0 Montpellier , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paulina","family":"Prorok","sequence":"additional","affiliation":[{"name":"Institute of Human Genetics , CNRS, 34396\u00a0 Montpellier , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0352-2790","authenticated-orcid":false,"given":"Magali","family":"Hennion","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris Cit\u00e9 , CNRS, Epigenetics and Cell Fate, F-75013\u00a0 Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose-Juan","family":"Lopez-Rubio","sequence":"additional","affiliation":[{"name":"LPHI, CNRS, Universit\u00e9 de Montpellier , 34095\u00a0 Montpellier , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcel","family":"M\u00e9chali","sequence":"additional","affiliation":[{"name":"Institute of Human Genetics , CNRS, 34396\u00a0 Montpellier , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7684-8815","authenticated-orcid":false,"given":"Ana\u00a0Rita","family":"Gomes","sequence":"additional","affiliation":[{"name":"LPHI, CNRS, Universit\u00e9 de Montpellier , 34095\u00a0 Montpellier , France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,12,1]]},"reference":[{"key":"2024012516143399700_B1","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1146\/annurev.genet.41.110306.130308","article-title":"Cell cycle regulation of DNA replication","volume":"41","author":"Sclafani","year":"2007","journal-title":"Annu. 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Biol."},{"key":"2024012516143399700_B65","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1101\/gr.142331.112","article-title":"Genome-wide mapping of human DNA-replication origins: levels of transcription at ORC1 sites regulate origin selection and replication timing","volume":"23","author":"Dellino","year":"2013","journal-title":"Genome Res."},{"key":"2024012516143399700_B66","doi-asserted-by":"crossref","first-page":"8489","DOI":"10.1073\/pnas.0503525102","article-title":"Structural basis of the Sir1\u2013origin recognition complex interaction in transcriptional silencing","volume":"102","author":"Hou","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2024012516143399700_B67","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1038\/381251a0","article-title":"Role of interactions between the origin recognition complex and SIR1 in transcriptional silencing","volume":"381","author":"Triolo","year":"1996","journal-title":"Nature"},{"key":"2024012516143399700_B68","doi-asserted-by":"crossref","first-page":"1774","DOI":"10.1016\/j.celrep.2016.07.007","article-title":"Transcriptionally driven DNA replication program of the Human parasite Leishmania major","volume":"16","author":"Lombra\u00f1a","year":"2016","journal-title":"Cell Rep."},{"key":"2024012516143399700_B69","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1186\/s13059-020-02013-3","article-title":"FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing","volume":"21","author":"Hennion","year":"2020","journal-title":"Genome Biol."},{"key":"2024012516143399700_B70","doi-asserted-by":"crossref","first-page":"23142","DOI":"10.1038\/srep23142","article-title":"Single-molecule analysis of DNA replication reveals novel features in the divergent eukaryotes Leishmania and Trypanosoma brucei versus mammalian cells","volume":"6","author":"Stanojcic","year":"2016","journal-title":"Sci. Rep."},{"key":"2024012516143399700_B71","doi-asserted-by":"crossref","first-page":"858","DOI":"10.1016\/j.pt.2017.08.002","article-title":"Nuclear DNA replication in trypanosomatids: there are No easy methods for solving difficult problems","volume":"33","author":"da\u00a0Silva","year":"2017","journal-title":"Trends Parasitol."},{"key":"2024012516143399700_B72","doi-asserted-by":"crossref","first-page":"1433","DOI":"10.1093\/nar\/29.7.1433","article-title":"Monitoring S phase progression globally and locally using BrdU incorporation in TK+ yeast strains","volume":"29","author":"Lengronne","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2024012516143399700_B73","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1126\/science.1103717","article-title":"A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses","volume":"307","author":"Hall","year":"2005","journal-title":"Science"},{"key":"2024012516143399700_B74","first-page":"1889","article-title":"Extreme mutation bias and high AT content in Plasmodium falciparum","volume":"45","author":"Hamilton","year":"2017","journal-title":"Nucleic Acids Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/52\/2\/660\/56418879\/gkad1103.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/52\/2\/660\/56418879\/gkad1103.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,25]],"date-time":"2024-01-25T17:13:53Z","timestamp":1706202833000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/52\/2\/660\/7457016"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,12,1]]},"references-count":74,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2023,12,1]]},"published-print":{"date-parts":[[2024,1,25]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkad1103","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,1,25]]},"published":{"date-parts":[[2023,12,1]]}}}