Using nanopore-based deep learning assay to map the DNA replication landscape in Trypanosoma cruzi

• Grant number: 24/00401-0
• Support Opportunities: Research Grants - Visiting Researcher Grant - International
• Start date: September 18, 2024
• End date: October 17, 2024
• Field of knowledge: Biological Sciences - Parasitology - Protozoology of Parasites
• Principal Investigator: Maria Carolina Quartim Barbosa Elias Sabbaga
• Grantee: Maria Carolina Quartim Barbosa Elias Sabbaga
• Visiting researcher: Jeziel Dener Damasceno
• Visiting researcher institution: University of Glasgow, Scotland
• Host Institution: Instituto Butantan. Secretaria da Saúde (São Paulo - Estado). São Paulo , SP, Brazil
• Associated research grant: 20/00694-6 - How DNA replication contributes for the success of infection caused by Trypanosoma cruzi, AP.TEM

Abstract

Trypanosomatid parasites, namely Trypanosoma cruzi, Leishmania spp., and Trypanosoma brucei, are the etiological agents of Chagas disease, leishmaniasis, and sleeping sickness, respectively. Collectively, these illnesses have a profound impact on public health worldwide. A hallmark of these parasites is their genomic plasticity, primarily through gene and chromosomal copy number variations. Such genome malleability is frequently linked to drug resistance, posing significant challenges to disease eradication efforts. A pivotal and yet unresolved question in trypanosomatid genome biology is the processes by which these parasites manage their genome replication. Understanding this is critical to elucidate the intricate balance they maintain between genome variability and stability.Recent advancements in Oxford Nanopore Sequencing Technology and deep learning-driven bioinformatics, exemplified by tools like D-Nascent, offer unprecedented sensitivity and resolution for analysing DNA replication at the single-molecule level in these pathogens. Dr. Damasceno, at the University of Glasgow, has developed comprehensive bioinformatics pipelines to extensively analyze D-Nascent datasets from Leishmania and T. brucei. The proposed collaboration aims to adapt these pipelines for an in-depth examination of the DNA replication landscape in T. cruzi. By utilizing existing D-Nascent datasets from T. cruzi, the activities proposed here will elucidate, for the first time, the DNA Replication Fork Directionality (RFD) and Origin Efficiency Metrics (OEM) at genome-wide scale in T. cruzi. Dr. Damasceno will also integrate the RFD and OEM analysis with both published and unpublished data sets allowing examination of how DNA replication dynamics correlates with genome sequence content, epigenetic features and transcription initiation in this parasite. The immediate availability of extensive and previously validated datasets ensures a rapid initiation and progression of this project. By uncovering the nuances of DNA replication dynamics in T. cruzi, we aim to deepen our understanding of its genome maintenance mechanisms. Furthermore, this research will lay the groundwork for comparative analyses with other trypanosomatids (L. major and T. brucei), fostering insights into their evolutionary biology and the pathobiology of the diseases they engender. (AU)