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

Grant number: 21/12469-0
Support type:Scholarships in Brazil - Post-Doctorate
Effective date (Start): November 01, 2021
Effective date (End): March 31, 2023
Field of knowledge:Biological Sciences - Parasitology - Protozoology of Parasites
Cooperation agreement: MRC, UKRI ; Newton Fund, with FAPESP as a partner institution in Brazil
Principal researcher:Julia Pinheiro Chagas da Cunha
Grantee:Camila Gachet de Castro
Home 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


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)

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