Single cell expression and chromatin accessibility of the Toxoplasma gondii lytic cycle identifies AP2XII-8 as an essential ribosome regulon driver

Authors	Jingjing Lou, Yasaman Rezvani, Argenis Arriojas, Yihan Wu, David Degras, Caroline Keroack, Manoj T Duraisingh, Kourosh Zarringhalam, Marc‑Jan Gubbels.
Journal	Nature Communications, 15(1), 7419 (2024)
PubMed	39198388
DOI	10.1038/s41467-024-51011-7

Abstract

The apicomplexan parasite Toxoplasma gondii undergoes a lytic replication cycle that is characterized by a coordinated gene expression program orchestrated by stage-specific transcription factors. Here, we generated and analyzed comprehensive single-cell multi-omic profiles (scRNA-seq and scATAC-seq) across the lytic cycle to understand the regulatory mechanisms governing this complex developmental process. Our analysis identified distinct cell states corresponding to G1, S/M, and cytokinesis phases with specific transcriptional signatures. By integrating chromatin accessibility and gene expression data, we identified key regulatory elements and transcription factor binding sites. We characterized the essential ApiAP2 transcription factor AP2XII-8 using CUT&RUN and conditional knockdown approaches, revealing its role as a master regulator of ribosomal gene expression. AP2XII-8 depletion causes severe growth defects and dysregulation of hundreds of genes, particularly affecting ribosome biogenesis. This study provides unprecedented insights into the regulatory mechanisms underlying T. gondii development and highlights AP2XII-8 as a critical regulator of ribosome biosynthesis, establishing a foundation for understanding apicomplexan developmental biology through multi-omic approaches.

Key Points

• Comprehensive single-cell multi-omic atlas of T. gondii lytic cycle
• Integration of scRNA-seq and scATAC-seq data reveals regulatory dynamics
• Identification of AP2XII-8 as a master regulator of ribosomal gene expression
• CUT&RUN and conditional knockdown validate AP2XII-8 function
• Novel computational approaches for analyzing parasite developmental trajectories

Supporting Materials

• Toxoplasma Cell Atlas
• Code Repository
• Datasets

Citation

@article{lou2024single,
  title={Single cell expression and chromatin accessibility of the Toxoplasma gondii lytic cycle identifies AP2XII-8 as an essential ribosome regulon driver},
  author={Lou, Jingjing and Rezvani, Yasaman and Arriojas, Argenis and Wu, Yihan and Shankar, Nachiket and Degras, David and Keroack, Caroline D and Duraisingh, Manoj T and Zarringhalam, Kourosh and Gubbels, Marc-Jan},
  journal={Nature Communications},
  volume={15},
  number={1},
  pages={7419},
  year={2024},
  publisher={Nature Publishing Group},
  doi={10.1038/s41467-024-51011-7},
  pmid={39198388},
  pmcid={PMC11358496}
}