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Deciphering the Molecular Mechanism and Function of Pore-Forming Toxins Using Leishmania major
Published on: October 28, 2022
In silico identification of conserved intercoding sequences in Leishmania genomes: unraveling putative cis-regulatory
E J R Vasconcelos1, M C Terrão, J C Ruiz
1Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Universidade de São Paulo, Ribeirão Preto, Brazil. eltonjrv@usp.br
Molecular and Biochemical Parasitology
|March 6, 2012
Summary
This study developed a computational pipeline to identify conserved intercoding sequences (CICS) in Leishmania genomes. The pipeline successfully identified potential regulatory elements and gene networks involved in Leishmania gene expression control.
Area of Science:
- Genomics
- Bioinformatics
- Parasitology
Background:
- Leishmania spp. are pathogens with complex gene expression regulation.
- Understanding gene regulation is crucial for developing new treatments.
- Conserved intercoding sequences (CICS) are potential regulatory elements.
Purpose of the Study:
- To develop and apply a computational pipeline for identifying CICS in Leishmania genomes.
- To investigate the role of CICS in gene expression control.
- To identify potential regulatory elements and regulons in Leishmania.
Main Methods:
- In silico analysis of Leishmania major, L. infantum, and L. braziliensis genomes.
- Utilized Linux-Shell, PERL, R, BLAST, MSPcrunch, SSAKE, and Pred-A-Term algorithms.
- Developed a pipeline for CICS identification, redundancy elimination, mRNA extremity prediction, and gene clustering.
Main Results:
- Successfully identified 730 LeishCICS-clusters with significant correlation to gene expression profiles.
- These clusters contained 2 to 17 genes, suggesting coordinated regulation.
- The pipeline identified potential regulatory cis-elements and putative regulons in Leishmania.
Conclusions:
- The developed computational pipeline is an effective tool for identifying regulatory elements in Leishmania.
- The study identified novel CICS and putative regulons, advancing the understanding of Leishmania gene regulation.
- Findings provide a foundation for further research into therapeutic targets for Leishmania infections.
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