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

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]

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

• 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