{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T01:35:19Z","timestamp":1777426519216,"version":"3.51.4"},"reference-count":81,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2013,9,30]],"date-time":"2013-09-30T00:00:00Z","timestamp":1380499200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecular Microbiology"],"published-print":{"date-parts":[[2013,11]]},"abstract":"<jats:title>Summary<\/jats:title><jats:p>Spatial relationships within the eukaryotic nucleus are essential for proper nuclear function. In <jats:italic><jats:styled-content style=\"fixed-case\">P<\/jats:styled-content>lasmodium falciparum<\/jats:italic>, the repositioning of chromosomes has been implicated in the regulation of the expression of genes responsible for antigenic variation, and the formation of a single, peri\u2010nuclear nucleolus results in the clustering of <jats:styled-content style=\"fixed-case\">rDNA<\/jats:styled-content>. Nevertheless, the precise spatial relationships between chromosomes remain poorly understood, because, until recently, techniques with sufficient resolution have been lacking. Here we have used chromosome conformation capture and second\u2010generation sequencing to study changes in chromosome folding and spatial positioning that occur during switches in <jats:styled-content style=\"fixed-case\"><jats:italic>var<\/jats:italic><\/jats:styled-content> gene expression. We have generated maps of chromosomal spatial affinities within the <jats:italic><jats:styled-content style=\"fixed-case\">P<\/jats:styled-content>.\u2009falciparum<\/jats:italic> nucleus at 25\u2009Kb resolution, revealing a structured nucleolus, an absence of chromosome territories, and confirming previously identified clustering of heterochromatin foci. We show that switches in <jats:styled-content style=\"fixed-case\"><jats:italic>var<\/jats:italic><\/jats:styled-content> gene expression do not appear to involve interaction with a distant enhancer, but do result in local changes at the active locus. These maps reveal the folding properties of malaria chromosomes, validate known physical associations, and characterize the global landscape of spatial interactions. Collectively, our data provide critical information for a better understanding of gene expression regulation and antigenic variation in malaria parasites.<\/jats:p>","DOI":"10.1111\/mmi.12381","type":"journal-article","created":{"date-parts":[[2013,8,28]],"date-time":"2013-08-28T10:34:28Z","timestamp":1377686068000},"page":"519-537","source":"Crossref","is-referenced-by-count":54,"title":["Genome\u2010wide profiling of chromosome interactions in <i><scp>P<\/scp>lasmodium falciparum<\/i> characterizes nuclear architecture and reconfigurations associated with antigenic variation"],"prefix":"10.1111","volume":"90","author":[{"given":"Jacob E.","family":"Lemieux","sequence":"first","affiliation":[{"name":"Weatherall Institute of Molecular Medicine  Headington Oxford OX3 9DS UK"},{"name":"National Institute of Allergy and Infectious Disease, NIH  Rockville MD 20892 USA"}]},{"given":"Sue A.","family":"Kyes","sequence":"additional","affiliation":[{"name":"Weatherall Institute of Molecular Medicine  Headington Oxford OX3 9DS UK"}]},{"given":"Thomas D.","family":"Otto","sequence":"additional","affiliation":[{"name":"Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus  Hinxton Cambridge CB10 1SA UK"}]},{"given":"Avi I.","family":"Feller","sequence":"additional","affiliation":[{"name":"Department of Statistics Harvard University  1 Oxford Street Cambridge MA 02138 USA"}]},{"given":"Richard T.","family":"Eastman","sequence":"additional","affiliation":[{"name":"National Institute of Allergy and Infectious Disease, NIH  Rockville MD 20892 USA"}]},{"given":"Robert A.","family":"Pinches","sequence":"additional","affiliation":[{"name":"Weatherall Institute of Molecular Medicine  Headington Oxford OX3 9DS UK"}]},{"given":"Matthew","family":"Berriman","sequence":"additional","affiliation":[{"name":"Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus  Hinxton Cambridge CB10 1SA UK"}]},{"given":"Xin\u2010zhuan","family":"Su","sequence":"additional","affiliation":[{"name":"National Institute of Allergy and Infectious Disease, NIH  Rockville MD 20892 USA"}]},{"given":"Chris I.","family":"Newbold","sequence":"additional","affiliation":[{"name":"Weatherall Institute of Molecular Medicine  Headington Oxford OX3 9DS UK"},{"name":"Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus  Hinxton Cambridge CB10 1SA UK"}]}],"member":"311","published-online":{"date-parts":[[2013,9,30]]},"reference":[{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1214572109"},{"key":"e_1_2_6_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0169-4758(00)01755-5"},{"key":"e_1_2_6_4_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1001223"},{"key":"e_1_2_6_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(95)90054-3"},{"key":"e_1_2_6_6_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.2517-6161.1995.tb02031.x"},{"key":"e_1_2_6_7_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0000005"},{"key":"e_1_2_6_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2008.11.010"},{"key":"e_1_2_6_9_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0040138"},{"key":"e_1_2_6_10_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2011-12-6-r56"},{"key":"e_1_2_6_11_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M213065200"},{"key":"e_1_2_6_12_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2004.04388.x"},{"key":"e_1_2_6_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.09.043"},{"key":"e_1_2_6_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/35091146"},{"key":"e_1_2_6_15_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1067799"},{"key":"e_1_2_6_16_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature08973"},{"key":"e_1_2_6_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2005.01.036"},{"key":"e_1_2_6_18_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.0020022"},{"key":"e_1_2_6_19_1","doi-asserted-by":"publisher","DOI":"10.1038\/sj.embor.7401063"},{"key":"e_1_2_6_20_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1070919"},{"key":"e_1_2_6_21_1","doi-asserted-by":"publisher","DOI":"10.1038\/35039531"},{"key":"e_1_2_6_22_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2005.01.037"},{"key":"e_1_2_6_23_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.gde.2012.01.006"},{"key":"e_1_2_6_24_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature08497"},{"key":"e_1_2_6_25_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2007.06.023"},{"key":"e_1_2_6_26_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000214"},{"key":"e_1_2_6_27_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature01097"},{"key":"e_1_2_6_28_1","doi-asserted-by":"publisher","DOI":"10.1128\/EC.00314-10"},{"key":"e_1_2_6_29_1","doi-asserted-by":"publisher","DOI":"10.1209\/0295-5075\/23\/5\/012"},{"key":"e_1_2_6_30_1","doi-asserted-by":"publisher","DOI":"10.1051\/jphys:0198800490120209500"},{"key":"e_1_2_6_31_1","doi-asserted-by":"publisher","DOI":"10.1128\/EC.00023\u201013"},{"key":"e_1_2_6_32_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-0-387-21606-5"},{"key":"e_1_2_6_33_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0074-7696(08)60235-1"},{"key":"e_1_2_6_34_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-5822.2012.01803.x"},{"key":"e_1_2_6_35_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0402347101"},{"key":"e_1_2_6_36_1","doi-asserted-by":"publisher","DOI":"10.2307\/1390807"},{"key":"e_1_2_6_37_1","doi-asserted-by":"publisher","DOI":"10.1186\/2046-1682-4-8"},{"key":"e_1_2_6_38_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2011.09.049"},{"key":"e_1_2_6_39_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.092759.109"},{"key":"e_1_2_6_40_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0166-6851(99)00193-0"},{"key":"e_1_2_6_41_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.micro.55.1.673"},{"key":"e_1_2_6_42_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2007.05587.x"},{"key":"e_1_2_6_43_1","doi-asserted-by":"publisher","DOI":"10.2307\/3280287"},{"key":"e_1_2_6_44_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/11.24.8703"},{"key":"e_1_2_6_45_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1087025"},{"key":"e_1_2_6_46_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0811829106"},{"key":"e_1_2_6_47_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature09333"},{"key":"e_1_2_6_48_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1181369"},{"key":"e_1_2_6_49_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1123191"},{"key":"e_1_2_6_50_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkj517"},{"key":"e_1_2_6_51_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr1032"},{"key":"e_1_2_6_52_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2006.06.035"},{"key":"e_1_2_6_53_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2007.06009.x"},{"key":"e_1_2_6_54_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2008.12.012"},{"key":"e_1_2_6_55_1","doi-asserted-by":"publisher","DOI":"10.1038\/emboj.2009.375"},{"key":"e_1_2_6_56_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2011.03.040"},{"key":"e_1_2_6_57_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1417"},{"key":"e_1_2_6_58_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1001045107"},{"key":"e_1_2_6_59_1","doi-asserted-by":"publisher","DOI":"10.1002\/bies.20226"},{"key":"e_1_2_6_60_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng1423"},{"key":"e_1_2_6_61_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-13-1"},{"key":"e_1_2_6_62_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1814"},{"key":"e_1_2_6_63_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0408883102"},{"key":"e_1_2_6_64_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1001306"},{"key":"e_1_2_6_65_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.fgb.2009.07.006"},{"key":"e_1_2_6_66_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.129692.111"},{"key":"e_1_2_6_67_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/16.10.944"},{"key":"e_1_2_6_68_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.2003.03570.x"},{"key":"e_1_2_6_69_1","doi-asserted-by":"publisher","DOI":"10.1093\/emboj\/17.18.5418"},{"key":"e_1_2_6_70_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.micro.61.080706.093134"},{"key":"e_1_2_6_71_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1089122"},{"key":"e_1_2_6_72_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.01.010"},{"key":"e_1_2_6_73_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng1896"},{"key":"e_1_2_6_74_1","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(95)90056-X"},{"key":"e_1_2_6_75_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg1688"},{"key":"e_1_2_6_76_1","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(95)90055-1"},{"key":"e_1_2_6_77_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.781840"},{"key":"e_1_2_6_78_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1621"},{"key":"e_1_2_6_79_1","doi-asserted-by":"publisher","DOI":"10.1038\/342438a0"},{"key":"e_1_2_6_80_1","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.129.6.1601"},{"key":"e_1_2_6_81_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.947"},{"key":"e_1_2_6_82_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng1891"}],"container-title":["Molecular Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1111%2Fmmi.12381","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/mmi.12381","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/mmi.12381","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/mmi.12381","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,2]],"date-time":"2023-10-02T21:26:18Z","timestamp":1696281978000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/mmi.12381"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,9,30]]},"references-count":81,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2013,11]]}},"alternative-id":["10.1111\/mmi.12381"],"URL":"https:\/\/doi.org\/10.1111\/mmi.12381","archive":["Portico"],"relation":{},"ISSN":["0950-382X","1365-2958"],"issn-type":[{"value":"0950-382X","type":"print"},{"value":"1365-2958","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,9,30]]}}}