A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs

Kunz, Meik (Chair of Medical Informatics, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany) ; Wolf, Beat (School of Engineering and Architecture (HEIA-FR), HES-SO // University of Applied Sciences Western Switzerland) ; Fuchs, Maximilian (Functional Genomics and Systems Biology Group, department of Bioinformatics, University of Würzburg, Germany) ; Christoph, Jan (Chair of Medical Informatics, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany) ; Xiao, Ke (Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany) ; Thum, Thomas (Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Jannover Medical School, Hannover, Germany) ; Atlan, David (Phenosystems SA, Braine le Château, Belgium) ; Prokosch, Hans-Ulrich (Chair of Medical Informatics, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany) ; Dandekar, Thomas (Functional Genomics and Systems Biology Group, department of Bioinformatics, University of Würzburg, Germany)

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.


Keywords:
Article Type:
scientifique
Faculty:
Ingénierie et Architecture
School:
HEIA-FR
Institute:
iCoSys - Institut des systèmes complexes
Date:
2019-10
Pagination:
6 p.
Published in:
Briefings in Bioinformatics
DOI:
ISSN:
1477-4054
Appears in Collection:



 Record created 2019-12-17, last modified 2020-01-07

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