Structural mapping of the whole transcriptome from the halophile archaea Halobacterium salinarum NRC-1 using footprinting techniques

• Grant number: 12/13520-0
• Support Opportunities: Scholarships in Brazil - Master
• Start date: January 01, 2013
• End date: December 31, 2013
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal Investigator: Tie Koide
• Grantee: José Vicente Gomes Filho
• Host Institution: Faculdade de Medicina de Ribeirão Preto (FMRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil

Abstract

One of the main players in the genetic landscape the RNA shows an amazing diversity of structures that are directly related to their informational or regulatory functions. However, the structural information related to this class of biomolecule is still limited. The increasing reports of new ncRNAs of unknown function demands the identification of they targets and their mechanisms of function, the structure of the RNAs is extremely important for those studies. In this project we propose the structural mapping of the whole transcriptome from the halophile archaea Halobacterium salinarum NRC-1. This organism has showed an interesting model for the study of genetic regulation in the archaea domain. For the structural mapping we will use footprinting methodologies which consists in evaluate the reactivity of the nucleotides of a RNA molecule when exposed to enzymes or chemicals, and by the relative reactivity analyze structural features. We will use footprinting methodologies based on hydroxyl radicals cleavage, DMS modification and nuclease treatment. For the high-throughput analysis we will use the PARS (Parallel Analysis of RNA Structures), which consists in enzymatic footprinting followed by RNA-sequencing methodologies. The experimental data will be compared with in silico predictions, aiming to improve the prediction models and to have better structural definition for RNAs in this archaea.