A MultiOmics time-resolved systems map of gene regulation in Toxoplasma gondii
Abstract
Understanding how T. gondii builds an invasion-competent cell has been limited by its rapid, asynchronous division cycle, incomplete gene function annotation, and studies that have examined one regulator or complex at a time. Here, we placed acute perturbation of 21 transcriptional and epigenetic factors, promoter occupancy, chromatin accessibility, and molecular validation on a common single-cell clock. The resulting consensus map links the lytic-cycle programs to candidate activating and repressive inputs, organizes genes into 108 co-regulated communities, and nominates regulatory partnerships that would not have emerged from any single data type. The work bridges three longstanding gaps: it resolves perturbation responses in cell-cycle time, distinguishes promoter occupancy from perturbation-linked regulation, and turns a large multidimensional dataset into an experimentally navigable map. We indeed confirmed known factor interactions such as MORC/HDAC3 and recovered combinations such as the Cdc5/SNIP1 and DMAP1/EPL1 as coregulatory nodes (that in other systems have been described to cooperate). Furthermore, we discovered a novel apicomplexan specific combination of AAF1/AP2XI-5 that provides mechanistic insights of the unique AP2 transcription factor family.
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BibTeX
@misc{wu2026multiomics,
title = {{A MultiOmics time-resolved systems map of gene regulation in Toxoplasma gondii}},
author = {Yihan Wu and Argenis A. Arriojas and Nachiket Shankar and Shalini Aggarwal and Jingjing Lou and Prarthana Prathap and Shreya Dua and Gretchen M. Diffendall and Jiahong Li and Pamodya Pamunuwa and Prince Oppong and Omar Graia and Lee Sarah Izhaki-Tavor and Eranthie Weerapana and Mélissa Léger-Abraham and Manoj T. Duraisingh and Kourosh Zarringhalam and Marc-Jan Gubbels},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.29.762658},
url = {https://www.biorxiv.org/content/10.64898/2026.10.29.762658v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - A MultiOmics time-resolved systems map of gene regulation in Toxoplasma gondii
AU - Yihan Wu
AU - Argenis A. Arriojas
AU - Nachiket Shankar
AU - Shalini Aggarwal
AU - Jingjing Lou
AU - Prarthana Prathap
AU - Shreya Dua
AU - Gretchen M. Diffendall
AU - Jiahong Li
AU - Pamodya Pamunuwa
AU - Prince Oppong
AU - Omar Graia
AU - Lee Sarah Izhaki-Tavor
AU - Eranthie Weerapana
AU - Mélissa Léger-Abraham
AU - Manoj T. Duraisingh
AU - Kourosh Zarringhalam
AU - Marc-Jan Gubbels
PY - 2026
DA - 2026/10/29
PB - bioRxiv
DO - 10.64898/2026.10.29.762658
UR - https://www.biorxiv.org/content/10.64898/2026.10.29.762658v1
AB - Understanding how T. gondii builds an invasion-competent cell has been limited by its rapid, asynchronous division cycle, incomplete gene function annotation, and studies that have examined one regulator or complex at a time. Here, we placed acute perturbation of 21 transcriptional and epigenetic factors, promoter occupancy, chromatin accessibility, and molecular validation on a common single-cell clock. The resulting consensus map links the lytic-cycle programs to candidate activating and repressive inputs, organizes genes into 108 co-regulated communities, and nominates regulatory partnerships that would not have emerged from any single data type. The work bridges three longstanding gaps: it resolves perturbation responses in cell-cycle time, distinguishes promoter occupancy from perturbation-linked regulation, and turns a large multidimensional dataset into an experimentally navigable map. We indeed confirmed known factor interactions such as MORC/HDAC3 and recovered combinations such as the Cdc5/SNIP1 and DMAP1/EPL1 as coregulatory nodes (that in other systems have been described to cooperate). Furthermore, we discovered a novel apicomplexan specific combination of AAF1/AP2XI-5 that provides mechanistic insights of the unique AP2 transcription factor family.
SN - 2692-8205
ER -