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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Uncovering the mouse olfactory long non-coding transcriptome with a novel machine-learning model

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Author(s):
Camargo, Antonio P. [1, 2] ; Nakahara, Thiago S. [3, 1] ; Firmino, Luiz E. R. [3] ; Netto, Paulo H. M. [1, 2] ; do Nascimento, Joao B. P. [3] ; Donnard, Elisa R. [4] ; Galante, Pedro A. F. [4] ; Carazzolle, Marcelo F. [1] ; Malnic, Bettina [3] ; Papes, Fabio [1]
Total Authors: 10
Affiliation:
[1] Univ Estadual Campinas, Inst Biol, Dept Genet & Evolut, BR-13083862 Campinas, SP - Brazil
[2] Univ Estadual Campinas, Inst Biol, Grad Program Genet & Mol Biol, BR-13083862 Campinas, SP - Brazil
[3] Univ Sao Paulo, Inst Chem, Dept Biochem, BR-05508000 Sao Paulo, SP - Brazil
[4] Hosp Sirio Libanes, Mol Oncol Ctr, BR-01308060 Sao Paulo, SP - Brazil
Total Affiliations: 4
Document type: Journal article
Source: DNA Research; v. 26, n. 4, p. 365-378, AUG 2019.
Web of Science Citations: 0
Abstract

Very little is known about long non-coding RNAs (lncRNAs) in the mammalian olfactory sensory epithelia. Deciphering the non-coding transcriptome in olfaction is relevant because these RNAs have been shown to play a role in chromatin modification and nuclear architecture reorganization, processes that accompany olfactory differentiation and olfactory receptor gene choice, one of the most poorly understood gene regulatory processes in mammals. In this study, we used a combination of in silico and ex vivo approaches to uncover a comprehensive catalogue of olfactory lncRNAs and to investigate their expression in the mouse olfactory organs. Initially, we used a novel machine-learning lncRNA classifier to discover hundreds of annotated and unannotated lncRNAs, some of which were predicted to be preferentially expressed in the main olfactory epithelium and the vomeronasal organ, the most important olfactory structures in the mouse. Moreover, we used whole-tissue and single-cell RNA sequencing data to discover lncRNAs expressed in mature sensory neurons of the main epithelium. Candidate lncRNAs were further validated by in situ hybridization and RT-PCR, leading to the identification of lncRNAs found throughout the olfactory epithelia, as well as others exquisitely expressed in subsets of mature olfactory neurons or progenitor cells. (AU)

FAPESP's process: 11/22611-6 - Identification of non-coding RNAs expressed in the olfactory epithelium
Grantee:João Batista Placido do Nascimento
Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
FAPESP's process: 16/24471-0 - Odorant receptors: mechanisms of gene expression and signal transduction
Grantee:Bettina Malnic
Support Opportunities: Research Projects - Thematic Grants
FAPESP's process: 18/11860-4 - Epigenetic mechanisms in the regulation of gene expression: the case of odorant receptors
Grantee:Thiago Seike Picoreti Nakahara
Support Opportunities: Scholarships in Brazil - Post-Doctoral
FAPESP's process: 16/05379-6 - Analysis of the lincRNA transcriptome in the accessory olfactory system
Grantee:Antônio Pedro de Castello Branco da Rocha Camargo
Support Opportunities: Scholarships in Brazil - Master
FAPESP's process: 13/08293-7 - CCES - Center for Computational Engineering and Sciences
Grantee:Munir Salomao Skaf
Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC
FAPESP's process: 15/50371-0 - Mechanisms underkying how social experience alters hormone levels, sensory signaling and behavior
Grantee:Fabio Papes
Support Opportunities: Regular Research Grants