Overlapped genes: mutual regulation of coding and noncoding genes biogenesis

• Grant number: 17/18246-7
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• Start date: April 01, 2018
• End date: October 31, 2021
• Field of knowledge: Interdisciplinary Subjects
• Principal Investigator: Pedro Alexandre Favoretto Galante
• Grantee: Felipe Rodolfo Camargo dos Santos
• Host Institution: Hospital Sírio-Libanês. São Paulo , SP, Brazil
• Associated scholarship(s): 19/26582-2 - A major characterization of human intragenic long non-coding RNAs expression and expression regulation, BE.EP.DD

Abstract

Gene expression process has been linked to numerous cis and trans elements. Nowadays, more precise and powerful bioinformatics coupled to the DNA/RNA sequencing methods revolution improves gene regulation understanding dramatically. Evidences of increasingly strong interaction between overlapped genes, according to genomic coordinates, has been published relating biogenesis, function, expression and conservation. The combination of such mechanisms are complex and need to be analysed in a broad and integrated manner, which demands bioinformatics analysis. Intron importance has also been reviewed, mostly concerning its role and classification as a simple bypass product. Up to date it is known that the majority of small nucleolar RNAs (snoRNAs) ~90% and miRNAs (miRNAs) ~60% are intragenic. lncRNAs are still subject of characterization studies and has not reached stable numbers for intragenic/intergenic proportions, although many important functions has been attributed to them and count with significant intragenic elements according to recent studies. In this project, we propose an analysis of long noncoding RNAs (lncRNAs) collocated with coding genes (mainly in introns). In a more detailed manner we propose to: i) systematically characterize the intragenic long noncoding RNAs; ii) to study a few evolutive features; iii) to study the expression and possible coexpression of these long noncoding RNAs and their host genes; iv) and to explore the occurrence of alternative splicing in gene regions containing these lncRNAs. The expression and alternative splicing analysis will also be done in a context of health versus tumoral tissues. Overall, we hope to give a considerable contribution for the wide features of this important group of noncoding RNAs at the end of this project. (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)

DE SOUZA, ANACLETO SILVA; AMORIM, VITOR MARTINS DE FREITAS; GUARDIA, GABRIELA D. A.; DOS SANTOS, FELIPE R. C.; DOS SANTOS, FILIPE F.; DE SOUZA, ROBSON FRANCISCO; JUVENAL, GUILHERME DE ARAUJO; HUANG, YIHUA; GE, PINGJU; JIANG, YINAN; et al. Molecular Dynamics Analysis of Fast-Spreading Severe Acute Respiratory Syndrome Coronavirus 2 Variants and Their Effects on the Interaction with Human Angiotensin-Converting Enzyme 2. ACS OMEGA, v. 7, n. 35, p. 10-pg., 2022-08-24. (20/06091-1, 17/18246-7, 17/19541-2, 20/04680-0, 19/00195-2, 16/09047-8, 18/15579-8, 18/07366-4, 20/14158-9)

DE SOUZA, ANACLETO SILVA; DE FREITAS AMORIM, VITOR MARTINS; GUARDIA, GABRIELA D. A.; DOS SANTOS, FILIPE F.; ULRICH, HENNING; GALANTE, PEDRO A. F.; DE SOUZA, ROBSON FRANCISCO; GUZZO, CRISTIANE RODRIGUES. Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern: A Perspective for Emerging More Transmissible and Vaccine-Resistant Strains. Viruses-Basel, v. 14, n. 4, p. 21-pg., 2022-04-01. (18/07366-4, 20/06091-1, 19/00195-2, 16/09047-8, 20/14158-9, 20/04680-0, 17/18246-7, 17/19541-2, 18/15579-8)

DOS SANTOS, FELIPE R. C.; GUARDIA, GABRIELA D. A.; DOS SANTOS, FILIPE F.; OHARA, DANIEL T.; GALANTE, PEDRO A. F.. Reboot: a straightforward approach to identify genes and splicing isoforms associated with cancer patient prognosis. NAR CANCER, v. 3, n. 2, p. 15-pg., 2021-06-01. (17/18246-7, 18/15579-8, 17/19541-2, 17/17974-9)