{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T13:15:33Z","timestamp":1785417333022,"version":"3.56.0"},"posted":{"date-parts":[[2025,8,28]]},"group-title":"Genomics","reference-count":95,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,8,28]],"date-time":"2025-08-28T00:00:00Z","timestamp":1756339200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"award":["R35GM144135"],"award-info":[{"award-number":["R35GM144135"]}],"id":[{"id":"https:\/\/ror.org\/04q48ey07","id-type":"ROR","asserted-by":"publisher"}]},{"award":["T32GM152354"],"award-info":[{"award-number":["T32GM152354"]}],"id":[{"id":"https:\/\/ror.org\/04q48ey07","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,8,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  The interdependence of chromatin states and transcription factor (TF) binding in eukaryotic genomes is critical for the proper regulation of gene expression. In this study, we explore the connection between TFs and chromatin states in the human malaria parasite,\n                  <jats:italic>Plasmodium falciparum<\/jats:italic>\n                  , throughout its 48-hour asexual intraerythrocytic developmental cycle (IDC). Most\n                  <jats:italic>P. falciparum<\/jats:italic>\n                  genes are expressed in a periodic manner during the IDC, accompanied by dynamic shifts in histone modifications and chromatin accessibility. Leveraging genome-wide profiles of chromatin accessibility, histone modifications, and Heterochromatin Protein 1 (HP1) occupancy, we characterize chromatin state dynamics during the IDC. Our results indicate that several chromatin states remain stable throughout the lifecycle, while others are dynamic and are linked to gene activation or repression. We further characterize chromatin state dynamics at the genome-wide DNA binding sites for a selection of\n                  <jats:italic>Plasmodium<\/jats:italic>\n                  TFs, allowing us to group TFs according to their chromatin preferences. By correlating changes in chromatin accessibility, histone modifications, and TF binding, we provide a global overview of the chromatin state dynamics that coordinate\n                  <jats:italic>P. falciparum<\/jats:italic>\n                  asexual blood stage development.\n                <\/jats:p>","DOI":"10.1101\/2025.08.22.671872","type":"posted-content","created":{"date-parts":[[2025,8,29]],"date-time":"2025-08-29T00:45:33Z","timestamp":1756428333000},"source":"Crossref","is-referenced-by-count":0,"title":["Chromatin state dynamics during the\n                  <i>Plasmodium falciparum<\/i>\n                  intraerythrocytic development cycle"],"prefix":"10.64898","author":[{"suffix":"Jr.","given":"Alan S.","family":"Brown","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6173-5882","authenticated-orcid":false,"given":"Manuel","family":"Llin\u00e1s","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2641-1807","authenticated-orcid":false,"given":"Shaun","family":"Mahony","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2025090218251174000_2025.08.22.671872v1.1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0007936"},{"key":"2025090218251174000_2025.08.22.671872v1.2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu638"},{"key":"2025090218251174000_2025.08.22.671872v1.3","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki709"},{"key":"2025090218251174000_2025.08.22.671872v1.4","doi-asserted-by":"publisher","DOI":"10.1016\/S1471-4922(03)00086-2"},{"key":"2025090218251174000_2025.08.22.671872v1.5","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1001223"},{"key":"2025090218251174000_2025.08.22.671872v1.6","doi-asserted-by":"publisher","DOI":"10.1038\/sj.emboj.7601926"},{"key":"2025090218251174000_2025.08.22.671872v1.7","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-11-34"},{"key":"2025090218251174000_2025.08.22.671872v1.8","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"2025090218251174000_2025.08.22.671872v1.9","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae585"},{"key":"2025090218251174000_2025.08.22.671872v1.10","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0000005"},{"key":"2025090218251174000_2025.08.22.671872v1.11","doi-asserted-by":"publisher","DOI":"10.1101\/gr.172155.114"},{"key":"2025090218251174000_2025.08.22.671872v1.12","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-04295-5"},{"key":"2025090218251174000_2025.08.22.671872v1.13","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2013.01.038"},{"key":"2025090218251174000_2025.08.22.671872v1.14","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2021.102444"},{"key":"2025090218251174000_2025.08.22.671872v1.15","doi-asserted-by":"publisher","DOI":"10.1186\/s13072-023-00478-7"},{"key":"2025090218251174000_2025.08.22.671872v1.16","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-020-06787-5"},{"key":"2025090218251174000_2025.08.22.671872v1.17","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2010.07324.x"},{"key":"2025090218251174000_2025.08.22.671872v1.18","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-00687-7"},{"key":"2025090218251174000_2025.08.22.671872v1.19","doi-asserted-by":"publisher","DOI":"10.1186\/s13072-021-00393-9"},{"key":"2025090218251174000_2025.08.22.671872v1.20","doi-asserted-by":"publisher","DOI":"10.1101\/gr.2218604"},{"key":"2025090218251174000_2025.08.22.671872v1.21","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1016071107"},{"key":"2025090218251174000_2025.08.22.671872v1.22","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr539"},{"key":"2025090218251174000_2025.08.22.671872v1.23","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2015.09.007"},{"key":"2025090218251174000_2025.08.22.671872v1.24","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts635"},{"key":"2025090218251174000_2025.08.22.671872v1.25","doi-asserted-by":"publisher","DOI":"10.1126\/science.1105136"},{"key":"2025090218251174000_2025.08.22.671872v1.26","doi-asserted-by":"publisher","DOI":"10.1038\/nature11247"},{"key":"2025090218251174000_2025.08.22.671872v1.27","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1906"},{"key":"2025090218251174000_2025.08.22.671872v1.28","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3157"},{"key":"2025090218251174000_2025.08.22.671872v1.29","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2017.124"},{"key":"2025090218251174000_2025.08.22.671872v1.30","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000784"},{"key":"2025090218251174000_2025.08.22.671872v1.31","doi-asserted-by":"publisher","DOI":"10.1007\/s00018-006-6095-6"},{"key":"2025090218251174000_2025.08.22.671872v1.32","doi-asserted-by":"publisher","DOI":"10.1038\/nature01097"},{"key":"2025090218251174000_2025.08.22.671872v1.33","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1804663115"},{"key":"2025090218251174000_2025.08.22.671872v1.34","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1003170"},{"key":"2025090218251174000_2025.08.22.671872v1.35","doi-asserted-by":"publisher","DOI":"10.1002\/iub.2195"},{"key":"2025090218251174000_2025.08.22.671872v1.36","doi-asserted-by":"publisher","DOI":"10.1038\/nature07829"},{"key":"2025090218251174000_2025.08.22.671872v1.37","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1937"},{"key":"2025090218251174000_2025.08.22.671872v1.38","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks1284"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