{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T21:48:00Z","timestamp":1792100880906,"version":"4.4.0"},"reference-count":90,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T00:00:00Z","timestamp":1762300800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T00:00:00Z","timestamp":1762300800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Commun"],"DOI":"10.1038\/s41467-025-64751-x","type":"journal-article","created":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T13:35:45Z","timestamp":1762349745000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Toxoplasma gondii chromatin remodeler SWI\/SNF controls parasite division and gene expression"],"prefix":"10.1038","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9917-4817","authenticated-orcid":false,"given":"Dandan","family":"Hu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuan","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiayi","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueqin","family":"Zou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongbin","family":"Si","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0668-8187","authenticated-orcid":false,"given":"Xun","family":"Suo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0680-2771","authenticated-orcid":false,"given":"Xingju","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,11,5]]},"reference":[{"key":"64751_CR1","doi-asserted-by":"publisher","first-page":"1965","DOI":"10.1016\/S0140-6736(04)16412-X","volume":"363","author":"JG Montoya","year":"2004","unstructured":"Montoya, J. G. & Liesenfeld, O. Toxoplasmosis. Lancet 363, 1965\u20131976 (2004).","journal-title":"Lancet"},{"key":"64751_CR2","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1146\/annurev-micro-091014-104100","volume":"69","author":"IJ Blader","year":"2015","unstructured":"Blader, I. J., Coleman, B. I., Chen, C. T. & Gubbels, M. J. Lytic cycle of Toxoplasma gondii: 15 years later. Annu Rev. Microbiol. 69, 463\u2013485 (2015).","journal-title":"Annu Rev. Microbiol."},{"key":"64751_CR3","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1038\/nrmicro3184","volume":"12","author":"ME Francia","year":"2014","unstructured":"Francia, M. E. & Striepen, B. Cell division in apicomplexan parasites. Nat. Rev. Microbiol. 12, 125\u2013136 (2014).","journal-title":"Nat. Rev. Microbiol."},{"key":"64751_CR4","doi-asserted-by":"publisher","first-page":"877","DOI":"10.1016\/j.ijpara.2009.01.005","volume":"39","author":"JP Dubey","year":"2009","unstructured":"Dubey, J. P. History of the discovery of the life cycle of Toxoplasma gondii. Int J. Parasitol. 39, 877\u2013882 (2009).","journal-title":"Int J. Parasitol."},{"key":"64751_CR5","doi-asserted-by":"publisher","first-page":"570","DOI":"10.1038\/s41564-020-0674-4","volume":"5","author":"DC Farhat","year":"2020","unstructured":"Farhat, D. C. et al. A MORC-driven transcriptional switch controls Toxoplasma developmental trajectories and sexual commitment.Nat. Microbiol. 5, 570\u2013583 (2020).","journal-title":"Nat. Microbiol."},{"key":"64751_CR6","doi-asserted-by":"publisher","first-page":"1448","DOI":"10.1126\/science.1221472","volume":"336","author":"G Moissiard","year":"2012","unstructured":"Moissiard, G. et al. MORC family ATPases required for heterochromatin condensation and gene silencing. Science 336, 1448\u20131451 (2012).","journal-title":"Science"},{"key":"64751_CR7","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-023-02939-4","volume":"24","author":"Z Zhong","year":"2023","unstructured":"Zhong, Z. et al. MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions. Genome Biol. 24, 96 (2023).","journal-title":"Genome Biol."},{"key":"64751_CR8","doi-asserted-by":"publisher","first-page":"700","DOI":"10.1016\/j.molcel.2019.07.032","volume":"75","author":"H Kim","year":"2019","unstructured":"Kim, H. et al. The gene-silencing protein MORC-1 topologically entraps DNA and forms multimeric assemblies to cause DNA compaction. Mol. Cell 75, 700\u2013710. e706 (2019).","journal-title":"Mol. Cell"},{"key":"64751_CR9","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/s41586-023-06821-y","volume":"625","author":"AV Antunes","year":"2024","unstructured":"Antunes, A. V. et al. In vitro production of cat-restricted Toxoplasma pre-sexual stages. Nature 625, 366\u2013376 (2024).","journal-title":"Nature"},{"key":"64751_CR10","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-44967-z","volume":"15","author":"J Wang","year":"2024","unstructured":"Wang, J. et al. The transcription factor AP2XI-2 is a key negative regulator of Toxoplasma gondii merogony. Nat. Commun. 15, 793 (2024).","journal-title":"Nat. Commun."},{"key":"64751_CR11","doi-asserted-by":"publisher","first-page":"e01785","DOI":"10.1128\/mbio.01785-23","volume":"14","author":"F Fan","year":"2023","unstructured":"Fan, F., Xue, L., Yin, X., Gupta, N. & Shen, B. AP2XII-1 is a negative regulator of merogony and presexual commitment in Toxoplasma gondii. mBio 14, e01785\u201301723 (2023).","journal-title":"mBio"},{"key":"64751_CR12","doi-asserted-by":"publisher","first-page":"5527","DOI":"10.3390\/ijms25105527","volume":"25","author":"Y Jiang","year":"2024","unstructured":"Jiang, Y., Shi, Y., Xue, Y., Hu, D. & Song, X. AP2XII-1 and AP2XI-2 suppress schizogony gene expression in Toxoplasma gondii. Int J. Mol. Sci. 25, 5527 (2024).","journal-title":"Int J. Mol. Sci."},{"key":"64751_CR13","doi-asserted-by":"publisher","first-page":"e2412000","DOI":"10.1002\/advs.202412000","volume":"12","author":"L Xue","year":"2024","unstructured":"Xue, L. et al. A novel nuclear protein complex controlling the expression of developmentally regulated genes in Toxoplasma Gondii. Adv. Sci. 12, e2412000 (2024).","journal-title":"Adv. Sci."},{"key":"64751_CR14","doi-asserted-by":"publisher","first-page":"e00606","DOI":"10.1128\/msphere.00606-22","volume":"8","author":"S Srivastava","year":"2023","unstructured":"Srivastava, S., Holmes, M. J., White, M. W. & Sullivan, J.rW. J. Toxoplasma gondii AP2XII-2 contributes to transcriptional repression for sexual commitment. mSphere 8, e00606\u2013e00622 (2023).","journal-title":"mSphere"},{"key":"64751_CR15","doi-asserted-by":"publisher","first-page":"e00542","DOI":"10.1128\/mSphere.00542-20","volume":"5","author":"S Srivastava","year":"2020","unstructured":"Srivastava, S., White, M. W. & Sullivan, W. J. Jr Toxoplasma gondii AP2XII-2 contributes to proper progression through S-Phase of the cell cycle. mSphere 5, e00542\u201300520 (2020).","journal-title":"mSphere"},{"key":"64751_CR16","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1146\/annurev.biochem.77.062706.153223","volume":"78","author":"CR Clapier","year":"2009","unstructured":"Clapier, C. R. & Cairns, B. R. The biology of chromatin remodeling complexes. Annu Rev. Biochem 78, 273\u2013304 (2009).","journal-title":"Annu Rev. Biochem"},{"key":"64751_CR17","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1146\/annurev-biophys-051013-022819","volume":"45","author":"CY Zhou","year":"2016","unstructured":"Zhou, C. Y., Johnson, S. L., Gamarra, N. I. & Narlikar, G. J. Mechanisms of ATP-dependent chromatin remodeling motors. Annu Rev. Biophys. 45, 153\u2013181 (2016).","journal-title":"Annu Rev. Biophys."},{"key":"64751_CR18","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1016\/j.sbi.2016.01.006","volume":"36","author":"G Hauk","year":"2016","unstructured":"Hauk, G. & Berger, J. M. The role of ATP-dependent machines in regulating genome topology. Curr. Opin. Struct. Biol. 36, 85\u201396 (2016).","journal-title":"Curr. Opin. Struct. Biol."},{"key":"64751_CR19","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1038\/cr.2011.32","volume":"21","author":"DC Hargreaves","year":"2011","unstructured":"Hargreaves, D. C. & Crabtree, G. R. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Cell Res. 21, 396\u2013420 (2011).","journal-title":"Cell Res."},{"key":"64751_CR20","doi-asserted-by":"publisher","first-page":"e00140","DOI":"10.1128\/msphere.00140-24","volume":"9","author":"M Kalamuddin","year":"2024","unstructured":"Kalamuddin, M. et al. MYST regulates DNA repair and forms a NuA4-like complex in the malaria parasite Plasmodium falciparum. mSphere 9, e00140\u201300124 (2024).","journal-title":"mSphere"},{"key":"64751_CR21","doi-asserted-by":"publisher","first-page":"2400","DOI":"10.1038\/sj.emboj.7601678","volume":"26","author":"K Hughes","year":"2007","unstructured":"Hughes, K. et al. A novel ISWI is involved in VSG expression site downregulation in African trypanosomes. EMBO J. 26, 2400\u20132410 (2007).","journal-title":"EMBO J."},{"key":"64751_CR22","doi-asserted-by":"publisher","first-page":"e2303432120","DOI":"10.1073\/pnas.2303432120","volume":"120","author":"I Kaneko","year":"2023","unstructured":"Kaneko, I., Nishi, T., Iwanaga, S. & Yuda, M. Differentiation of Plasmodium male gametocytes is initiated by the recruitment of a chromatin remodeler to a male-specific cis-element. Proc. Natl. Acad. Sci. USA 120, e2303432120 (2023).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"64751_CR23","doi-asserted-by":"publisher","first-page":"5624","DOI":"10.1093\/nar\/gkae207","volume":"52","author":"T Nishi","year":"2024","unstructured":"Nishi, T., Kaneko, I., Iwanaga, S. & Yuda, M. PbARID-associated chromatin remodeling events are essential for gametocyte development in Plasmodium. Nucleic Acids Res 52, 5624\u20135642 (2024).","journal-title":"Nucleic Acids Res"},{"key":"64751_CR24","doi-asserted-by":"publisher","first-page":"e1010514","DOI":"10.1371\/journal.ppat.1010514","volume":"18","author":"T Vellmer","year":"2022","unstructured":"Vellmer, T. et al. A novel SNF2 ATPase complex in Trypanosoma brucei with a role in H2A. Z-mediated chromatin remodelling. PLoS Pathog. 18, e1010514 (2022).","journal-title":"PLoS Pathog."},{"key":"64751_CR25","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13071-020-3918-5","volume":"13","author":"W-F Wang","year":"2020","unstructured":"Wang, W.-F. & Zhang, Y.-L. PfSWIB, a potential chromatin regulator for var gene regulation and parasite development in Plasmodium falciparum. Parasit. Vectors 13, 1\u201315 (2020).","journal-title":"Parasit. Vectors"},{"key":"64751_CR26","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s00436-002-0814-1","volume":"90","author":"WJ Sullivan","year":"2003","unstructured":"Sullivan, W. J. et al. Molecular cloning and characterization of an SRCAP chromatin remodeling homologue in Toxoplasma gondii. Parasitol. Res 90, 1\u20138 (2003).","journal-title":"Parasitol. Res"},{"key":"64751_CR27","doi-asserted-by":"publisher","first-page":"e19570","DOI":"10.1371\/journal.pone.0019570","volume":"6","author":"PJ Rooney","year":"2011","unstructured":"Rooney, P. J., Neal, L. M. & Knoll, L. J. Involvement of a Toxoplasma gondii chromatin remodeling complex ortholog in developmental regulation. PLoS One 6, e19570 (2011).","journal-title":"PLoS One"},{"key":"64751_CR28","doi-asserted-by":"publisher","first-page":"1156","DOI":"10.1038\/s41564-025-01980-2","volume":"10","author":"B Pachano","year":"2025","unstructured":"Pachano, B. et al. An ISWI-related chromatin remodeller regulates stage-specific gene expression in Toxoplasma gondii. Nat. Microbiol 10, 1156\u20131170 (2025).","journal-title":"Nat. Microbiol"},{"key":"64751_CR29","doi-asserted-by":"publisher","first-page":"5757","DOI":"10.1038\/s41467-025-60795-1","volume":"16","author":"Y Zhu","year":"2025","unstructured":"Zhu, Y. et al. Regulation of the developmental programs in Toxoplasma by a novel SNF2L-containing chromatin remodeling complex. Nat. Commun. 16, 5757 (2025).","journal-title":"Nat. Commun."},{"key":"64751_CR30","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1016\/j.mrfmmm.2006.10.006","volume":"618","author":"Y Bao","year":"2007","unstructured":"Bao, Y. & Shen, X. INO80 subfamily of chromatin remodeling complexes. Mutat. Res. 618, 18\u201329 (2007).","journal-title":"Mutat. Res."},{"key":"64751_CR31","doi-asserted-by":"publisher","first-page":"1423","DOI":"10.1016\/j.cell.2016.08.019","volume":"166","author":"SM Sidik","year":"2016","unstructured":"Sidik, S. M. et al. A genome-wide CRISPR screen in Toxoplasma identifies essential Apicomplexan genes. Cell 166, 1423\u20131435 (2016).","journal-title":"Cell"},{"key":"64751_CR32","doi-asserted-by":"publisher","first-page":"00375","DOI":"10.1128\/mBio.00375-17","volume":"8","author":"KM Brown","year":"2017","unstructured":"Brown, K. M., Long, S. & Sibley, L. D. Plasma membrane association by N-acylation governs PKG function in Toxoplasma gondii. mBio 8, 00375\u201300317 (2017).","journal-title":"mBio"},{"key":"64751_CR33","doi-asserted-by":"publisher","first-page":"269","DOI":"10.3389\/fcimb.2020.00269","volume":"10","author":"M-J Gubbels","year":"2020","unstructured":"Gubbels, M.-J. et al. Fussing about fission: defining variety among mainstream and exotic apicomplexan cell division modes. Front Cell Infect. Microbiol. 10, 269 (2020).","journal-title":"Front Cell Infect. Microbiol."},{"key":"64751_CR34","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1091\/mbc.01-06-0309","volume":"13","author":"K Hu","year":"2002","unstructured":"Hu, K. et al. Daughter cell assembly in the protozoan parasite Toxoplasma gondii. Mol. Biol. Cell 13, 593\u2013606 (2002).","journal-title":"Mol. Biol. Cell"},{"key":"64751_CR35","doi-asserted-by":"publisher","first-page":"1559","DOI":"10.1242\/jcs.021089","volume":"121","author":"M Nishi","year":"2008","unstructured":"Nishi, M., Hu, K., Murray, J. M. & Roos, D. S. Organellar dynamics during the cell cycle of Toxoplasma gondii. J. Cell Sci. 121, 1559\u20131568 (2008).","journal-title":"J. Cell Sci."},{"key":"64751_CR36","doi-asserted-by":"publisher","first-page":"e1002093","DOI":"10.1371\/journal.pbio.1002093","volume":"13","author":"ES Suvorova","year":"2015","unstructured":"Suvorova, E. S., Francia, M., Striepen, B. & White, M. W. A novel bipartite centrosome coordinates the apicomplexan cell cycle. PLoS Biol. 13, e1002093 (2015).","journal-title":"PLoS Biol."},{"key":"64751_CR37","doi-asserted-by":"publisher","first-page":"1474","DOI":"10.1038\/s41598-018-37671-8","volume":"9","author":"C Ramakrishnan","year":"2019","unstructured":"Ramakrishnan, C. et al. An experimental genetically attenuated live vaccine to prevent transmission of Toxoplasma gondii by cats. Sci. Rep. 9, 1474 (2019).","journal-title":"Sci. Rep."},{"key":"64751_CR38","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1186\/s12864-015-1225-x","volume":"16","author":"AB Hehl","year":"2015","unstructured":"Hehl, A. B. et al. Asexual expansion of Toxoplasma gondii merozoites is distinct from tachyzoites and entails expression of non-overlapping gene families to attach, invade, and replicate within feline enterocytes. BMC Genomics 16, 66 (2015).","journal-title":"BMC Genomics"},{"key":"64751_CR39","doi-asserted-by":"publisher","first-page":"2868","DOI":"10.1016\/j.celrep.2017.11.024","volume":"21","author":"F Angrisano","year":"2017","unstructured":"Angrisano, F. et al. Targeting the conserved fusion loop of HAP2 inhibits the transmission of Plasmodium berghei and falciparum. Cell Rep. 21, 2868\u20132878 (2017).","journal-title":"Cell Rep."},{"key":"64751_CR40","doi-asserted-by":"publisher","first-page":"1051","DOI":"10.1101\/gad.1656508","volume":"22","author":"Y Liu","year":"2008","unstructured":"Liu, Y. et al. The conserved plant sterility gene HAP2 functions after attachment of fusogenic membranes in Chlamydomonas and Plasmodium gametes. Genes Dev. 22, 1051\u20131068 (2008).","journal-title":"Genes Dev."},{"key":"64751_CR41","doi-asserted-by":"publisher","first-page":"e1012269","DOI":"10.1371\/journal.ppat.1012269","volume":"20","author":"CG Baptista","year":"2024","unstructured":"Baptista, C. G. et al. The Toxoplasma gondii F-Box Protein L2 functions as a repressor of stage specific gene expression. PLoS Pathog. 20, e1012269 (2024).","journal-title":"PLoS Pathog."},{"key":"64751_CR42","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1186\/1471-2164-13-685","volume":"13","author":"M Katrib","year":"2012","unstructured":"Katrib, M. et al. Stage-specific expression of protease genes in the apicomplexan parasite, Eimeria tenella. BMC Genomics 13, 685 (2012).","journal-title":"BMC Genomics"},{"key":"64751_CR43","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1186\/s12864-015-1298-6","volume":"16","author":"RA Walker","year":"2015","unstructured":"Walker, R. A. et al. RNA Seq analysis of the Eimeria tenella gametocyte transcriptome reveals clues about the molecular basis for sexual reproduction and oocyst biogenesis. BMC Genomics 16, 94 (2015).","journal-title":"BMC Genomics"},{"key":"64751_CR44","doi-asserted-by":"publisher","first-page":"350","DOI":"10.1186\/1471-2164-15-350","volume":"15","author":"MS Behnke","year":"2014","unstructured":"Behnke, M. S., Zhang, T. P., Dubey, J. P. & Sibley, L. D. Toxoplasma gondii merozoite gene expression analysis with comparison to the life cycle discloses a unique expression state during enteric development. BMC Genomics 15, 350 (2014).","journal-title":"BMC Genomics"},{"key":"64751_CR45","doi-asserted-by":"publisher","first-page":"e1011707","DOI":"10.1371\/journal.ppat.1011707","volume":"19","author":"RR Pasquarelli","year":"2023","unstructured":"Pasquarelli, R. R., Back, P. S., Sha, J., Wohlschlegel, J. A. & Bradley, P. J. Identification of IMC43, a novel IMC protein that collaborates with IMC32 to form an essential daughter bud assembly complex in Toxoplasma gondii. PLoS Pathog. 19, e1011707 (2023).","journal-title":"PLoS Pathog."},{"key":"64751_CR46","doi-asserted-by":"publisher","first-page":"e1012411","DOI":"10.1371\/journal.ppat.1012411","volume":"20","author":"RR Pasquarelli","year":"2024","unstructured":"Pasquarelli, R. R., Sha, J., Wohlschlegel, J. A. & Bradley, P. J. BCC0 collaborates with IMC32 and IMC43 to form the Toxoplasma gondii essential daughter bud assembly complex. PLoS Pathog. 20, e1012411 (2024).","journal-title":"PLoS Pathog."},{"key":"64751_CR47","doi-asserted-by":"publisher","first-page":"e0304222","DOI":"10.1128\/mbio.03042-22","volume":"14","author":"PS Back","year":"2023","unstructured":"Back, P. S. et al. IMC29 plays an important role in Toxoplasma endodyogeny and reveals new components of the daughter-enriched IMC proteome. mBio 14, e0304222 (2023).","journal-title":"mBio"},{"key":"64751_CR48","doi-asserted-by":"publisher","first-page":"e1001094","DOI":"10.1371\/journal.ppat.1001094","volume":"6","author":"JR Beck","year":"2010","unstructured":"Beck, J. R. et al. A novel family of Toxoplasma IMC proteins displays a hierarchical organization and functions in coordinating parasite division. PLoS Pathog. 6, e1001094 (2010).","journal-title":"PLoS Pathog."},{"key":"64751_CR49","doi-asserted-by":"crossref","unstructured":"Vigetti, L. et al. The BCC7 protein contributes to the Toxoplasma basal pole by interfacing between the MyoC motor and the IMC membrane network. Int, J. Mol. Sci. 23, 5995 (2022).","DOI":"10.3390\/ijms23115995"},{"key":"64751_CR50","doi-asserted-by":"publisher","first-page":"4644","DOI":"10.1038\/s41467-022-32151-0","volume":"13","author":"K Engelberg","year":"2022","unstructured":"Engelberg, K., Bechtel, T., Michaud, C., Weerapana, E. & Gubbels, M. J. Proteomic characterization of the Toxoplasma gondii cytokinesis machinery portrays an expanded hierarchy of its assembly and function. Nat. Commun. 13, 4644 (2022).","journal-title":"Nat. Commun."},{"key":"64751_CR51","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1016\/j.chom.2014.04.002","volume":"15","author":"RD Etheridge","year":"2014","unstructured":"Etheridge, R. D. et al. The Toxoplasma pseudokinase ROP5 forms complexes with ROP18 and ROP17 kinases that synergize to control acute virulence in mice. Cell Host Microbe 15, 537\u2013550 (2014).","journal-title":"Cell Host Microbe"},{"key":"64751_CR52","doi-asserted-by":"crossref","unstructured":"Fox, B. A. et al. The Toxoplasma gondii rhoptry kinome is essential for chronic infection. mBio 7, 193 (2016).","DOI":"10.1128\/mBio.00193-16"},{"key":"64751_CR53","doi-asserted-by":"publisher","first-page":"00409","DOI":"10.1128\/mSphere.00409-17","volume":"2","author":"R Dubey","year":"2017","unstructured":"Dubey, R. et al. Differential roles for inner membrane complex proteins across Toxoplasma gondii and Sarcocystis neurona development. mSphere 2, 00409\u201300417 (2017).","journal-title":"mSphere"},{"key":"64751_CR54","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1016\/j.ijpara.2003.11.024","volume":"34","author":"D Ferguson","year":"2004","unstructured":"Ferguson, D. Use of molecular and ultrastructural markers to evaluate stage conversion of Toxoplasma gondii in both the intermediate and definitive host. Int J. Parasitol. 34, 347\u2013360 (2004).","journal-title":"Int J. Parasitol."},{"key":"64751_CR55","doi-asserted-by":"crossref","unstructured":"Sugi, T., Tu, V., Ma, Y., Tomita, T. & Weiss, L. M. Toxoplasma gondii requires glycogen phosphorylase for balancing amylopectin storage and for efficient production of brain cysts. mBio 8, 1289 (2017).","DOI":"10.1128\/mBio.01289-17"},{"key":"64751_CR56","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1128\/CMR.11.2.267","volume":"11","author":"JP Dubey","year":"1998","unstructured":"Dubey, J. P., Lindsay, D. S. & Speer, C. A. Structures of Toxoplasma gondii tachyzoites, bradyzoites, and sporozoites and biology and development of tissue cysts. Clin. Microbiol Rev. 11, 267\u2013299 (1998).","journal-title":"Clin. Microbiol Rev."},{"key":"64751_CR57","doi-asserted-by":"crossref","unstructured":"Ferguson, D. J. & Dubremetz, J.-F. The ultrastructure of Toxoplasma gondii. In: Toxoplasma gondii). (Academic Press, 2014).","DOI":"10.1016\/B978-0-12-396481-6.00002-7"},{"key":"64751_CR58","doi-asserted-by":"publisher","first-page":"670","DOI":"10.1016\/j.chom.2015.11.004","volume":"18","author":"AD Uboldi","year":"2015","unstructured":"Uboldi, A. D. et al. Regulation of starch stores by a Ca(2+)-dependent protein kinase is essential for viable cyst development in Toxoplasma gondii. Cell Host Microbe 18, 670\u2013681 (2015).","journal-title":"Cell Host Microbe"},{"key":"64751_CR59","doi-asserted-by":"publisher","first-page":"e3002791","DOI":"10.1371\/journal.pbio.3002791","volume":"22","author":"AS Khelifa","year":"2024","unstructured":"Khelifa, A. S. et al. PP1 phosphatase controls both daughter cell formation and amylopectin levels in Toxoplasma gondii. PLoS Biol. 22, e3002791 (2024).","journal-title":"PLoS Biol."},{"key":"64751_CR60","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-35267-5","volume":"13","author":"JL Wang","year":"2022","unstructured":"Wang, J. L. et al. The protein phosphatase 2A holoenzyme is a key regulator of starch metabolism and bradyzoite differentiation in Toxoplasma gondii. Nat. Commun. 13, 7560 (2022).","journal-title":"Nat. Commun."},{"key":"64751_CR61","doi-asserted-by":"publisher","first-page":"200384","DOI":"10.1098\/rsob.200384","volume":"11","author":"C Lyu","year":"2021","unstructured":"Lyu, C. et al. Role of amylopectin synthesis in Toxoplasma gondii and its implication in vaccine development against toxoplasmosis. Open Biol. 11, 200384 (2021).","journal-title":"Open Biol."},{"key":"64751_CR62","doi-asserted-by":"publisher","first-page":"2085","DOI":"10.1002\/pro.3932","volume":"29","author":"K Imamura","year":"2020","unstructured":"Imamura, K. et al. Structural analysis and reaction mechanism of the disproportionating enzyme (D-enzyme) from potato. Protein Sci.: a Publ. Protein Soc. 29, 2085\u20132100 (2020).","journal-title":"Protein Sci.: a Publ. Protein Soc."},{"key":"64751_CR63","doi-asserted-by":"publisher","first-page":"2057","DOI":"10.1111\/1751-7915.13668","volume":"13","author":"J Yang","year":"2020","unstructured":"Yang, J. et al. Toxoplasma gondii \u03b1-amylase deletion mutant is a promising vaccine against acute and chronic toxoplasmosis. Microb. Biotechnol. 13, 2057\u20132069 (2020).","journal-title":"Microb. Biotechnol."},{"key":"64751_CR64","doi-asserted-by":"publisher","first-page":"752","DOI":"10.1016\/j.chom.2020.09.011","volume":"28","author":"K Barylyuk","year":"2020","unstructured":"Barylyuk, K. et al. A comprehensive subcellular atlas of the Toxoplasma proteome via hyperLOPIT provides spatial context for protein functions. Cell Host Microbe 28, 752\u2013766. e759 (2020).","journal-title":"Cell Host Microbe"},{"key":"64751_CR65","doi-asserted-by":"publisher","first-page":"1272","DOI":"10.1016\/j.cell.2018.09.032","volume":"175","author":"N Mashtalir","year":"2018","unstructured":"Mashtalir, N. et al. Modular organization and assembly of SWI\/SNF family chromatin remodeling complexes. Cell 175, 1272\u20131288. e1220 (2018).","journal-title":"Cell"},{"key":"64751_CR66","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1146\/annurev-arplant-102820-093218","volume":"74","author":"T Bieluszewski","year":"2023","unstructured":"Bieluszewski, T., Prakash, S., Roul\u00e9, T. & Wagner, D. The role and activity of SWI\/SNF chromatin remodelers. Annu Rev. Plant Biol. 74, 139\u2013163 (2023).","journal-title":"Annu Rev. Plant Biol."},{"key":"64751_CR67","doi-asserted-by":"publisher","first-page":"e1004273","DOI":"10.1371\/journal.ppat.1004273","volume":"10","author":"D Bargieri","year":"2014","unstructured":"Bargieri, D. et al. Host cell invasion by apicomplexan parasites: the junction conundrum. PLoS Pathog. 10, e1004273 (2014).","journal-title":"PLoS Pathog."},{"key":"64751_CR68","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1038\/s41586-020-2087-1","volume":"579","author":"Y Han","year":"2020","unstructured":"Han, Y., Reyes, A. A., Malik, S. & He, Y. Cryo-EM structure of SWI\/SNF complex bound to a nucleosome. Nature 579, 452\u2013455 (2020).","journal-title":"Nature"},{"key":"64751_CR69","doi-asserted-by":"publisher","first-page":"838","DOI":"10.1126\/science.aay0033","volume":"366","author":"Y Ye","year":"2019","unstructured":"Ye, Y. et al. Structure of the RSC complex bound to the nucleosome. Science 366, 838\u2013843 (2019).","journal-title":"Science"},{"key":"64751_CR70","doi-asserted-by":"publisher","first-page":"2124","DOI":"10.1016\/j.celrep.2017.01.058","volume":"18","author":"A Dutta","year":"2017","unstructured":"Dutta, A. et al. Composition and function of mutant SWI\/SNF complexes. Cell Rep. 18, 2124\u20132134 (2017).","journal-title":"Cell Rep."},{"key":"64751_CR71","doi-asserted-by":"publisher","first-page":"2135","DOI":"10.1016\/j.celrep.2017.02.017","volume":"18","author":"P Sen","year":"2017","unstructured":"Sen, P. et al. Loss of Snf5 Induces Formation of an Aberrant SWI\/SNF Complex. Cell Rep. 18, 2135\u20132147 (2017).","journal-title":"Cell Rep."},{"key":"64751_CR72","doi-asserted-by":"publisher","first-page":"e29391","DOI":"10.7554\/eLife.29391","volume":"6","author":"F Sindikubwabo","year":"2017","unstructured":"Sindikubwabo, F., et al. Modifications at K31 on the lateral surface of histone H4 contribute to genome structure and expression in apicomplexan parasites. Elife 6, e29391 (2017).","journal-title":"Elife"},{"key":"64751_CR73","doi-asserted-by":"publisher","first-page":"e01846","DOI":"10.1128\/mBio.01846-17","volume":"8","author":"A Dhara","year":"2017","unstructured":"Dhara, A., de Paula Baptista, R., Kissinger, J. C., Snow, E. C. & Sinai, A. P. Ablation of an ovarian tumor family deubiquitinase exposes the underlying regulation governing the plasticity of cell cycle progression in Toxoplasma gondii. mBio 8, e01846\u201301817 (2017).","journal-title":"mBio"},{"key":"64751_CR74","doi-asserted-by":"publisher","first-page":"1547","DOI":"10.1093\/molbev\/msy096","volume":"35","author":"S Kumar","year":"2018","unstructured":"Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547\u20131549 (2018).","journal-title":"Mol. Biol. Evol."},{"key":"64751_CR75","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","volume":"37","author":"BQ Minh","year":"2020","unstructured":"Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530\u20131534 (2020).","journal-title":"Mol. Biol. Evol."},{"key":"64751_CR76","doi-asserted-by":"publisher","first-page":"1733","DOI":"10.1016\/j.molp.2023.09.010","volume":"16","author":"C Chen","year":"2023","unstructured":"Chen, C. et al. TBtools-II: A \u201cone for all, all for one\u201d bioinformatics platform for biological big-data mining. Mol. Plant 16, 1733\u20131742 (2023).","journal-title":"Mol. Plant"},{"key":"64751_CR77","doi-asserted-by":"publisher","first-page":"e01336","DOI":"10.1128\/mbio.01336-24","volume":"15","author":"Y Shi","year":"2024","unstructured":"Shi, Y., Li, X., Xue, Y., Hu, D. & Song, X. Cell cycle-regulated transcription factor AP2XII-9 is a key activator for asexual division and apicoplast inheritance in Toxoplasma gondii tachyzoite. mBio 15, e01336\u201301324 (2024).","journal-title":"mBio"},{"key":"64751_CR78","doi-asserted-by":"publisher","first-page":"804","DOI":"10.1016\/j.chom.2018.10.015","volume":"24","author":"KM Brown","year":"2018","unstructured":"Brown, K. M. & Sibley, L. D. Essential cGMP signaling in toxoplasma is initiated by a hybrid P-Type ATPase-guanylate cyclase. Cell Host Microbe 24, 804\u2013816.e806 (2018).","journal-title":"Cell Host Microbe"},{"key":"64751_CR79","doi-asserted-by":"publisher","first-page":"1466","DOI":"10.1021\/acs.jproteome.2c00834","volume":"22","author":"D Kohler","year":"2023","unstructured":"Kohler, D. et al. MSstats version 4.0: Statistical analyses of quantitative mass spectrometry-based proteomic experiments with chromatography-based quantification at scale. J. Proteome Res. 22, 1466\u20131482 (2023).","journal-title":"J. Proteome Res."},{"key":"64751_CR80","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","volume":"34","author":"S Chen","year":"2018","unstructured":"Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884\u2013i890 (2018).","journal-title":"Bioinformatics"},{"key":"64751_CR81","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","volume":"37","author":"D Kim","year":"2019","unstructured":"Kim, D., Paggi, J. M., Park, C., Bennett, C. & Salzberg, S. L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol. 37, 907\u2013915 (2019).","journal-title":"Nat. Biotechnol."},{"key":"64751_CR82","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","volume":"30","author":"Y Liao","year":"2014","unstructured":"Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923\u2013930 (2014).","journal-title":"Bioinformatics"},{"key":"64751_CR83","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).","journal-title":"Genome Biol."},{"key":"64751_CR84","doi-asserted-by":"publisher","first-page":"5","DOI":"10.6026\/97320630002005","volume":"2","author":"L Kumar","year":"2007","unstructured":"Kumar, L. M EF. Mfuzz: a software package for soft clustering of microarray data. Bioinformation 2, 5\u20137 (2007).","journal-title":"Bioinformation"},{"key":"64751_CR85","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"},{"key":"64751_CR86","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The sequence alignment\/map format and SAMtools. Bioinformatics 25, 2078\u20132079 (2009).","journal-title":"Bioinformatics"},{"key":"64751_CR87","volume":"496521","author":"John M. Gaspar","year":"2018","unstructured":"Gaspar, J. M. Improved peak-calling with MACS2. BioRxiv, 496521 (2018).","journal-title":"BioRxiv"},{"key":"64751_CR88","doi-asserted-by":"publisher","first-page":"1884","DOI":"10.1002\/sim.9334","volume":"41","author":"R Singh","year":"2022","unstructured":"Singh, R., Zhang, F. & Li, Q. Assessing reproducibility of high-throughput experiments in the case of missing data. Stat. Med 41, 1884\u20131899 (2022).","journal-title":"Stat. Med"},{"key":"64751_CR89","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1093\/bib\/bbs017","volume":"14","author":"H Thorvaldsd\u00f3ttir","year":"2013","unstructured":"Thorvaldsd\u00f3ttir, H., Robinson, J. T. & Mesirov, J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14, 178\u2013192 (2013).","journal-title":"Brief. Bioinform."},{"key":"64751_CR90","unstructured":"Stark, R. & Brown, G. DiffBind: differential binding analysis of ChIP-Seq peak data. R package version 100, (2011)."}],"container-title":["Nature Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41467-025-64751-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-025-64751-x","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-025-64751-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,10]],"date-time":"2025-11-10T01:03:15Z","timestamp":1762736595000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41467-025-64751-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,5]]},"references-count":90,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["64751"],"URL":"https:\/\/doi.org\/10.1038\/s41467-025-64751-x","relation":{},"ISSN":["2041-1723"],"issn-type":[{"value":"2041-1723","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,5]]},"assertion":[{"value":"30 January 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 September 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 November 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"9777"}}