RNA-seq: segmentation and modeling of the signal

• Grant number: 11/14455-4
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• Start date: September 01, 2011
• End date: June 30, 2015
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal Investigator: Tie Koide
• Grantee: Felipe ten Caten
• Host Institution: Faculdade de Medicina de Ribeirão Preto (FMRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• Associated research grant: 09/09532-0 - Systems biology of the extremophile Halobacterium salinarum: role of the non-coding RNAs in the global gene regulatory network model, AP.JP

Abstract

New sequencing technologies are revolutionizing large-scale research in the field of transcriptome, providing data for a more comprehensive understanding of the Biology of organisms at the molecular level. The ability to sequence the full transcripts of a organism and examine how they manifest themselves in different conditions is a key step in the development of predictive models of cellular function. However, as the methodology by applying large-scale sequencing to study the transcriptome (RNA-seq) is very new, it still poses many challenges, especially in the analysis and understanding of the results. In this project are proposed approaches to the treatment of the signal generated by RNA-seq, in order to minimize the effects of noise inherent to the technique and search for information that go beyond the mere level of expression. One of these challenges is what is known in the area of signal processing as segmentation. Then we can define correctly the portions corresponding to the transcripts and define structures that may have important biological roles, such as new non-coding RNA, and RNA present in regulatory regions. The development of a model to describe the signals of interest must be defined to assist the mapping of new elements, contributing to the understanding of their roles in the dynamics and regulation of gene expression. (AU)

Scientific publications

(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, SEP 19 2014. (11/14455-4, 11/07487-7, 09/09532-0)

PEREIRA DE ALMEIDA, JOAO PAULO; VENCIO, RICARDO Z. N.; LORENZETTI, ALAN P. R.; TEN-CATEN, FELIPE; GOMES-FILHO, JOSE VICENTE; KOIDE, TIE. The Primary Antisense Transcriptome of Halobacterium salinarum NRC-1. GENES, v. 10, n. 4, APR 2019. (15/12012-9, 15/21038-1, 13/21522-5, 17/03052-2, 11/14455-4)

TEN-CATEN, FELIPE; VENCIO, RICARDO Z. N.; LORENZETTI, ALAN PERICLES R.; ZARAMELA, LIVIA SOARES; SANTANA, ANA CAROLINA; KOIDE, TIE. Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea. RNA BIOLOGY, v. 15, n. 8, p. 1119-1132, 2018. (11/14455-4, 15/21038-1, 17/03052-2, 11/07487-7, 15/12012-9)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

CATEN, Felipe ten. Pervasive transcription in the archaeon Halobacterium salinarum NRC- 1 and the identification of new transcripts.. 2017. Doctoral Thesis - Universidade de São Paulo (USP). Instituto de Matemática e Estatística (IME/SBI) São Paulo.