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Systems biology of long non-coding RNAs

Grant number: 12/19278-6
Support type:Research Grants - Young Investigators Grants
Duration: December 01, 2013 - November 30, 2018
Field of knowledge:Interdisciplinary Subjects
Principal Investigator:Helder Takashi Imoto Nakaya
Grantee:Helder Takashi Imoto Nakaya
Home Institution: Faculdade de Ciências Farmacêuticas (FCF). Universidade de São Paulo (USP). São Paulo , SP, Brazil
Assoc. researchers:Marina Baquerizo Martinez ; Mario Hiroyuki Hirata ; Vinicius Ramos Henriques Maracajá Coutinho
Associated grant(s):18/14933-2 - Integrative biology applied to human health, AP.JP2
17/50137-3 - Long noncoding RNA interplay with the host microbiome may determine mucosal influenza vaccine immunogenicity, AP.R
14/50308-4 - Transcriptomic meta-analysis of positionally conserved long noncoding RNAs, AP.R
Associated scholarship(s):14/19323-7 - Long noncoding RNAs as potential biomarkers of arthritis, BP.IC

Abstract

It is estimated that thousands of long non-coding RNAs (lncRNAs) are transcribed in the genome of several organisms. Yet, only a small fraction of them have been functionally characterized. One of the main reasons for this lies in our poor understanding of their expression patterns under different biological conditions, and the difficulty in identifying their possible gene targets. Most of the high-throughput techniques, such as microarrays and next-generation sequencing (RNA-seq), aim to monitor the expression of protein-coding genes. Some of this data, although unexplored in the original publications, are derived from lncRNAs. In this project, we propose to utilize publicly-available high-throughput data to study the systems biology of lncRNAs under different perturbations and the implication of lncRNAs in the regulation of candidate target genes. For example, we re-annotated the most used Affymetrix chip, with which more than 2,300 studies have been published, and revealed the existence of 10,248 probe sets of putative lncRNAs. Studying the expression profile of lncRNAs and how their expression correlates with the expression of protein-coding genes in various tissues and conditions will reveal interesting mechanisms of gene regulation. These analyses will involve the identification of co-expression modules, the prediction of transcription factors responsible for lncRNA transcription, and the association of lncRNAs to diseases and infections. We also propose to validate the regulatory role of some of these lncRNAs. (AU)

Articles published in Agência FAPESP Newsletter about the research grant
Acute chikungunya infection studied at the molecular level in Brazilian patients 
Study identifies a key cellular mechanism that triggers pneumonia in humans 
Articles published in other media outlets (27 total):
More itemsLess items
Acute Chikungunya Infection Studied at the Molecular Level in Brazilian Patients 
Acute chikungunya infection studied with AI 
Acute chikungunya infection studied at the molecular level in Brazilian patients 
Acute chikungunya infection studied at the molecular level in Brazilian patients 
Acute chikungunya infection studied at the molecular level in Brazilian patients 
Acute chikungunya infection studied at the molecular level in Brazilian patients 
Acute chikungunya infection studied at the molecular level in brazilian patients 
Acute chikungunya infection studied at the molecular level in Brazilian patients 
Acute chikungunya infection studied at the molecular level in Brazilian patients 
Acute Chikungunya Infection Studied at Molecular Level in Brazilian Patients 
Infecção aguda pelo chikungunya é estudada em nível molecular em pacientes brasileiros 
Infecção aguda pelo chikungunya é estudada em nível molecular em pacientes brasileiros 
Infecção aguda pelo chikungunya é estudada em pacientes brasileiros 
Infecção aguda pelo chikungunya é estudada em nível molecular em pacientes brasileiros 
Infecção aguda pelo chikungunya é estudada em nível molecular em pacientes brasileiros 
Infecção aguda pelo chikungunya é estudada em nível molecular em pacientes brasileiros 
Infecção aguda pelo chikungunya é estudada em nível molecular em pacientes brasileiros 
Infecção aguda pelo chikungunya é estudada em nível molecular em pacientes brasileiros 
Infecção aguda pelo chikungunya é estudada em nível molecular em pacientes brasileiros 
Infecção aguda pelo chikungunya é estudada em nível molecular em pacientes brasileiros 
Pesquisadores brasileiros analisam células sanguíneas de pacientes infectados pelo vírus chikungunya 
Infecção aguda pelo chikungunya é estudada em pacientes brasileiros 
Infecção aguda pelo chikungunya é estudada em nível molecular em pacientes brasileiros 
Infecção aguda pelo chikungunya é estudada em nível molecular em pacientes brasileiros 
Infecção aguda pelo chikungunya é estudada em nível molecular em pacientes brasileiros 
Pesquisadores brasileiros estudam chikungunya molecular 
Infecção aguda pelo chikungunya é estudada em nível molecular em pacientes brasileiros 

Scientific publications (11)
(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)
GONCALVES, ANDRE N. A.; LEVER, MELISSA; RUSSO, PEDRO S. T.; GOMES-CORREIA, BRUNO; URBANSKI, ALYSSON H.; POLLARA, GABRIELE; NOURSADEGHI, MAHDAD; MARACAJA-COUTINHO, VINICIUS; NAKAYA, I, HELDER. Assessing the Impact of Sample Heterogeneity on Transcriptome Analysis of Human Diseases Using MDP Webtool. FRONTIERS IN GENETICS, v. 10, OCT 24 2019. Web of Science Citations: 0.
DE LIMA, DIOGENES S.; CARDOZO, LUCAS E.; MARACAJA-COUTINHO, VINICIUS; SUHRBIER, ANDREAS; MANE, KARIM; JEFFRIES, DAVID; SILVEIRA, EDUARDO L. V.; AMARAL, PAULO P.; RAPPUOLI, RINO; DE SILVA, THUSHAN I.; NAKAYA, HELDER I. Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, v. 116, n. 34, p. 17121-17126, AUG 20 2019. Web of Science Citations: 0.
MASTELIC-GAVILLET, BEATRIS; VONO, MARIA; GONZALEZ-DIAS, PATRICIA; FERREIRA, FREDERICO MORAES; CARDOZO, LUCAS; LAMBERT, PAUL-HENRI; NAKAYA, I, HELDER; SIEGRIST, CLAIRE-ANNE. Neonatal T Follicular Helper Cells Are Lodged in a Pre-T Follicular Helper Stage Favoring Innate Over Adaptive Germinal Center Responses. FRONTIERS IN IMMUNOLOGY, v. 10, AUG 13 2019. Web of Science Citations: 0.
SOARES-SCHANOSKI, ALESSANDRA; BAPTISTA CRUZ, NATALIA; DE CASTRO-JORGE, LUIZA ANTUNES; HOMEM DE CARVALHO, RENAN VILLANOVA; DOS SANTOS, CLIOMAR ALVES; DA ROS, NANCY; OLIVEIRA, URSULA; COSTA, DANUZA DUARTE; SIMOES DOS SANTOS, CECILIA LUIZA; CUNHA, MARIELTON DOS PASSOS; SARNO OLIVEIRA, MARIA LEONOR; ALVES, JULIANA CARDOSO; DE LUCENA COUTO OCEA, REGINA ADALVA; RIBEIRO, DANIELLE RODRIGUES; AQUIME GONCALVES, ANDRE NICOLAU; GONZALEZ-DIAS, PATRICIA; SUHRBIER, ANDREAS; DE ANDRADE ZANOTTO, PAOLO MARINHO; DE AZEVEDO, INACIO JUNQUEIRA; ZAMBONI, DARIO S.; ALMEIDA, ROQUE PACHECO; HO, PAULO LEE; KALIL, JORGE; NISHIYAMA, MILTON YUTAKA; NAKAYA, HELDER I. Systems analysis of subjects acutely infected with the Chikungunya virus. PLOS PATHOGENS, v. 15, n. 6 JUN 2019. Web of Science Citations: 1.
CARDOZO, LUCAS E.; RUSSO, PEDRO S. T.; GOMES-CORREIA, BRUNO; ARAUJO-PEREIRA, MARIANA; SEPULVEDA-HERMOSILLA, GONZALO; MARACAJA-COUTINHO, VINICIUS; NAKAYA, I, HELDER. webCEMiTool: Co-expression Modular Analysis Made Easy. FRONTIERS IN GENETICS, v. 10, MAR 6 2019. Web of Science Citations: 0.
JOCHEMS, SIMON P.; MARCON, FERNANDO; CARNIEL, BEATRIZ F.; HOLLOWAY, MARK; MITSI, ELENA; SMITH, EMMA; GRITZFELD, JENNA F.; SOLORZANO, CARLA; REINE, JESUS; POJAR, SHERIN; NIKOLAOU, ELISSAVET; GERMAN, ESTHER L.; HYDER-WRIGHT, ANGIE; HILL, HELEN; HALES, CAZ; PITERS, WOUTER A. A. DE STEENHUIJSEN; BOGAERT, DEBBY; ADLER, HUGH; ZAIDI, SEHER; CONNOR, VICTORIA; GORDON, STEPHEN B.; RYLANCE, JAMIE; NAKAYA, HELDER I.; FERREIRA, DANIELA M. Inflammation induced by influenza virus impairs human innate immune control of pneumococcus. NATURE IMMUNOLOGY, v. 19, n. 12, p. 1299+, DEC 2018. Web of Science Citations: 10.
FUKUTANI, KIYOSHI F.; NASCIMENTO-CARVALHO, CRISTIANA M.; BOUZAS, MAIARA L.; OLIVEIRA, JULIANA R.; BARRAL, ALDINA; DIERCKX, TIM; KHOURI, RICARDO; NAKAYA, HELDER I.; ANDRADE, BRUNO B.; VAN WEYENBERGH, JOHAN; DE OLIVEIRA, CAMILA I. In situ Immune Signatures and Microbial Load at the Nasopharyngeal Interface in Children With Acute Respiratory Infection. FRONTIERS IN MICROBIOLOGY, v. 9, NOV 9 2018. Web of Science Citations: 0.
FERREIRA, GUSTAVO RODRIGUES; NAKAYA, HELDER IMOTO; COSTA, LUCIANO DA FONTOURA. Gene regulatory and signaling networks exhibit distinct topological distributions of motifs. Physical Review E, v. 97, n. 4 APR 27 2018. Web of Science Citations: 0.
RUSSO, PEDRO S. T.; FERREIRA, GUSTAVO R.; CARDOZO, LUCAS E.; BUERGER, MATHEUS C.; ARIAS-CARRASCO, RAUL; MARUYAMA, SANDRA R.; HIRATA, THIAGO D. C.; LIMA, DIOGENES S.; PASSOS, FERNANDO M.; FUKUTANI, KIYOSHI F.; LEVER, MELISSA; SILVA, JOAO S.; MARACAJA-COUTINHO, VINICIUS; NAKAYA, HELDER I. CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses. BMC Bioinformatics, v. 19, FEB 20 2018. Web of Science Citations: 13.
ARIAS-CARRASCO, RAUL; VASQUEZ-MORAN, YESSENIA; NAKAYA, HELDER I.; MARACAJA-COUTINHO, VINICIUS. StructRNAfinder: an automated pipeline and web server for RNA families prediction. BMC Bioinformatics, v. 19, FEB 17 2018. Web of Science Citations: 3.
BLOHMKE, CHRISTOPH J.; HILL, JENNIFER; DARTON, THOMAS C.; CARVALHO-BURGER, MATHEUS; EUSTACE, ANDREW; JONES, CLAIRE; SCHREIBER, FERNANDA; GOODIER, MARTIN R.; DOUGAN, GORDON; NAKAYA, HELDER I.; POLLARD, ANDREW J. Induction of Cell Cycle and NK Cell Responses by Live-Attenuated Oral Vaccines against Typhoid Fever. FRONTIERS IN IMMUNOLOGY, v. 8, OCT 12 2017. Web of Science Citations: 4.

Please report errors in scientific publications list by writing to: cdi@fapesp.br.