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Characterization and comparison of promoter and enhancer regions of toxin genes between two populations of Agkistrodon piscivorus using RNA-seq, ATAC-seq, and CUT&RUN sequencing methods

Grant number: 22/04988-0
Support Opportunities:Scholarships abroad - Research Internship - Post-doctor
Effective date (Start): October 01, 2022
Effective date (End): April 30, 2023
Field of knowledge:Biological Sciences - Genetics - Animal Genetics
Principal Investigator:Inácio de Loiola Meirelles Junqueira de Azevedo
Grantee:Pedro Gabriel Nachtigall
Supervisor: Darin Rokyta
Host Institution: Instituto Butantan. Secretaria da Saúde (São Paulo - Estado). São Paulo , SP, Brazil
Research place: Florida State University, United States  
Associated to the scholarship:18/26520-4 - Characterization of the interrelationship between transcriptomes, miRNomes and proteomes from the venom glands of Bothrops fonsecai and Bothrops cotiara, BP.PD


Differences in venom composition produced by snake species can result from distinct regulatory mechanisms acting in each species. However, comparative analysis among snake species focusing on identifying regulatory regions and elements that led to distinct venom composition are still scarce. Among venomous snakes, Agkistrodon piscivorus may represent an ideal model to test complement our understanding of regulatory mechanisms controlling the venom production. The species presents an intraspecific variation in its venom phenotype that correlates with the genetic structure of the population, which indicates that regulatory regions, such as promoters and enhancers, may be responsible for the toxins expressed in specific populations. To test this hypothesis, we propose to investigate the roles of chromatin accessibility in these regions to regulate the snake venom variation observed in two distinct populations of A. piscivorus. Then, we will integrate RNA-seq, ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput sequencing), and Cut&Run (Cleavage Under Targets and Release Using Nuclease) methodologies to identify the accessible regulatory regions of toxin genes followed by a comparative analysis between the two populations of A. piscivorus. The RNA-seq allows to identify transcribed genes and its expression levels, whereas ATAC-seq and CUT&RUN are cutting-edge approaches that allow the detection of chromatin accessibility and regions interacting with proteins, respectively. The integration of these methods allows the characterization of promoter and enhancer regions of expressed genes, which may be used to identify cis-regulatory elements. The present project will help to bring novel insights into the regulatory mechanisms responsible for toxin expression and venom variation and represents an outstanding opportunity for the candidate to learn and apply these gold-standard techniques in future research. (AU)

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