Abstract
Long non-coding RNAs (lncRNAs) are of fundamental biological importance; however, their functional role is often unclear or loosely defined as experimental characterization is challenging and bioinformatic methods are limited. We developed a novel integrated method protocol for the annotation and detailed functional characterization of lncRNAs within the genome. It combines annotation, normalization and gene expression with sequence-structure conservation, functional interactome and promoter analysis. Our protocol allows an analysis based on the tissue and biological context, and is powerful in functional characterization of experimental and clinical RNA-Seq datasets including existing lncRNAs. This is demonstrated on the uncharacterized lncRNA GATA6-AS1 in dilated cardiomyopathy.
Highlights
In recent years, long non-coding RNAs have been identified as functional players that regulate important biological processes and signaling pathways associated with pathogenesis and disease progression [1,2,3,4,5,6]
We developed a method protocol for combined annotation and functional analysis of Long non-coding RNAs (lncRNAs)
In the following we focus on the experimentally uncharacterized lncRNA GATA6-AS1
Summary
Long non-coding RNAs (lncRNAs) have been identified as functional players that regulate important biological processes and signaling pathways associated with pathogenesis and disease progression [1,2,3,4,5,6]. Hundreds of lncRNAs were annotated, but only few are experimentally characterized due to the fact that lncRNAs have complex regulatory functions, such as binding of mRNAs, miRNAs and proteins [3, 7]. Bioinformatics approaches, such as phylogenetic and functional interaction analysis, are helpful to comprehensively understand lncRNA functions for experimental characterization [3]. Meik Kunz is group leader at the Chair of Medical Informatics, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany. Jan Christoph is postdoc at the Chair of Medical Informatics, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany. Submitted: 21 December 2018; Received (in revised form): 29 April 2019
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