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A major characterization of human intragenic long non-coding RNAs expression and expression regulation

Grant number: 19/26582-2
Support type:Scholarships abroad - Research Internship - Doctorate (Direct)
Effective date (Start): July 01, 2020
Effective date (End): June 30, 2021
Field of knowledge:Interdisciplinary Subjects
Principal Investigator:Pedro Alexandre Favoretto Galante
Grantee:Felipe Rodolfo Camargo dos Santos
Supervisor abroad: Chung Chau Hon
Home Institution: Hospital Sírio-Libanês. Sociedade Beneficente de Senhoras (SBSHSL). São Paulo , SP, Brazil
Local de pesquisa : RIKEN, Japan  
Associated to the scholarship:17/18246-7 - Overlapped genes: mutual regulation of coding and noncoding genes biogenesis, BP.DD

Abstract

Over the last decade, advances in bioinformatics and deep sequencing technology have allowed major descriptive analyses of long noncoding RNAs (lncRNAs). In the human genome, they have been added to approximately 18,000 lncRNAs, and some of them were clearly associated with biological processes and dysregulation of gene expression in diseases. Although many lncRNAs are positionally independent of protein coding genes (i.e., intergenic lncRNA, or lincRNAs), a significant fraction of lncRNAs are transcribed from within or proximal to the genic regions of protein coding genes (i.e. intragenic lncRNAs). While most studies focused on lincRNAs, attributed to the simplicity of interpretation, little is known about intragenic lncRNAs. Even major questions such as whether intragenic lncRNAs are just noise of their own host gene transcription or functional transcripts have not been fully addressed. Here we propose a comprehensive study of expression and expression regulation of lncRNAs located within or proximal to protein coding genes by using ample sets of data (e.g., RNA-seq, sc-RNA-seq, CAGE-seq, ATAC-seq, Hi-C, and other data of expression regulation and conservation). Using these datasets in combination with robust computation methodologies, we aim to properly define the existence and regulatory potential of intragenic lncRNAs in the human genome and clarify the relationship between these lncRNAs and their host genes. These approaches rely on analyzing the original dataset (from RIKEN), never used to study intragenic lncRNAs and the expertise of our groups in analyzing lncRNA and intragenic ones. In the end, we expect to bring novel and ultimate information regarding intragenic lncRNA, clearly stating several aspects of their functionality. (AU)