Genome-wide approaches to reveal epigenomic structure in trypanosomes subjected to metabolic states changes and during cell cycle

• Grant number: 21/12469-0
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: November 01, 2021
• End date: December 31, 2022
• Field of knowledge: Biological Sciences - Parasitology - Protozoology of Parasites
• Agreement: MRC, UKRI ; Newton Fund, with FAPESP as a partner institution in Brazil
• Principal Investigator: Julia Pinheiro Chagas da Cunha
• Grantee: Camila Gachet de Castro
• Host Institution: Instituto Butantan. Secretaria da Saúde (São Paulo - Estado). São Paulo , SP, Brazil
• Associated research grant: 18/14432-3 - A network for an integrative biology in neglected diseases: bridging epigenetics, metabolism and cell cycle in pathogenic trypanosomatids, AP.TEM

Abstract

Parasites will be subject to different metabolic backgrounds, such as severe metabolic stress by incubating them in deprivation of nutrients (PBS buffer) or under metabolic stress conditions with single carbon and energy sources for maintenance (PBS supplemented with glucose, proline, histidine or leucine). In parallel, parasites in different cell cycle stages will be obtained by cell sorting or after HU synchronization. To evaluate changes in their epigenome, we will take advantage of two genome-wide high resolution techniques that allows the identification of nucleosomes position as well as putative regulatory sequences, possibly associated to highly active transcribed regions. Nucleosome positioning will be accessed by MNase-seq, a procedure where unprotected DNA sequences is cleaved by Micrococcus nuclease resulting in loci of high nucleosome occupancy. Open chromatin regions will be accessed either by FAIRE-seq or ATAC-seq methodologies. These two approaches will be complementary and will be possible to discriminate unbiased important genomic regions associated either with metabolic states or cell cycle.To this end, an intense bioinformatic approach to integrate these datasets as well as to explore functional annotation available at public datasets will also be implemented. In addition, comparison between T.cruzi and Leishmania data will be a valuable resource to better understand similarities and differences inherent to their biology. (AU)

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

MENEZES, ANA PAULA; MURILLO, ANA MILENA; DE CASTRO, CAMILA GACHET; BELLINI, NATALIA KARLA; TOSI, LUIZ RICARDO ORSINI; THIEMANN, OTAVIO HENRIQUE; ELIAS, MARIA CAROLINA; SILBER, ARIEL MARIANO; DA CUNHA, JULIA PINHEIRO CHAGAS. Navigating the boundaries between metabolism and epigenetics in trypanosomes. Trends in Parasitology, v. 39, n. 8, p. 14-pg., 2023-08-01. (21/12469-0, 18/14432-3, 18/15553-9, 21/03219-0, 19/21354-1, 20/00694-6)