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Systems biology of the extremophile Halobacterium salinarum: role of the non-coding RNAs in the global gene regulatory network model

Abstract

Systems approaches have been developed in the post-genomic era to have a global understanding of the cell. In this framework, the use of computational, mathematical and statistical tools, together with new technologies in biology allow the development of global models with predictive power. These global models usually take into account mRNA and protein levels. However, there is an increasingly important category of regulatory molecules that are not considered in these models: the non-coding RNAs (ncRNAs). To identify the influence of these molecules in the global gene regulatory network, we propose the study of ncRNAs in Halobacterium salinarum, a model extremophile in systems biology. Top-down and bottom-up approaches will be combined, together with bioinformatics tools to characterize these molecules and their role in gene regulation. The characterization of the global regulatory networks in this organism will contribute to the development of technologies to reengineering and potential applications in biotechnology. (AU)

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Scientific publications (4)
(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)
ZARAMELA, LIVIA S.; VENCIO, RICARDO Z. N.; TEN-CATEN, FELIPE; BALIGA, NITIN S.; KOIDE, TIE. Transcription Start Site Associated RNAs (TSSaRNAs) Are Ubiquitous in All Domains of Life. PLoS One, v. 9, n. 9, . (11/14455-4, 11/07487-7, 09/09532-0)
SILVA-ROCHA, RAFAEL; PONTELLI, MARJORIE CORNEJO; FURTADO, GILVAN PESSOA; ZARAMELA, LIVIA SOARES; KOIDE, TIE. Development of New Modular Genetic Tools for Engineering the Halophilic Archaeon Halobacterium salinarum. PLoS One, v. 10, n. 6, . (13/04125-2, 11/07487-7, 13/23712-6, 09/09532-0)
LORENZETTI, ALAN P. R.; KUSEBAUCH, ULRIKE; ZARAMELA, LIVIA S.; WU, WEI-JU; DE ALMEIDA, JOAO P. P.; TURKARSLAN, SERDAR; L. G. DE LOMANA, ADRIAN; GOMES-FILHO, JOSE V.; VENCIO, RICARDO Z. N.; MORITZ, ROBERT L.; et al. A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon. MSYSTEMS, v. 8, n. 2, p. 22-pg., . (17/03052-2, 15/21038-1, 11/07487-7, 19/13440-5, 13/21522-5, 09/09532-0)
GOMES-FILHO, JOSE VICENTE; ZARAMELA, LIVIA SOARES; DA SILVA ITALIANI, VALERIA CRISTINA; BALIGA, NITIN S.; VENCIO, RICARDO Z. N.; KOIDE, TIE. Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea. RNA BIOLOGY, v. 12, n. 5, p. 490-500, . (13/21522-5, 10/10195-5, 11/07487-7, 09/09532-0)

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