title: Bioinformatics of cardiovascular miRNA biology.
abstract: MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs and are highly conserved among species. Moreover, miRNAs regulate gene expression of a large number of genes associated with important biological functions and signaling pathways. Recently, several miRNAs have been found to be associated with cardiovascular diseases. Thus, investigating the complex regulatory effect of miRNAs may lead to a better understanding of their functional role in the heart. To achieve this, bioinformatics approaches have to be coupled with validation and screening experiments to understand the complex interactions of miRNAs with the genome. This will boost the subsequent development of diagnostic markers and our understanding of the physiological and therapeutic role of miRNAs in cardiac remodeling. In this review, we focus on and explain different bioinformatics strategies and algorithms for the identification and analysis of miRNAs and their regulatory elements to better understand cardiac miRNA biology. Starting with the biogenesis of miRNAs, we present approaches such as LocARNA and miRBase for combining sequence and structure analysis including phylogenetic comparisons as well as detailed analysis of RNA folding patterns, functional target prediction, signaling pathway as well as functional analysis. We also show how far bioinformatics helps to tackle the unprecedented level of complexity and systemic effects by miRNA, underlining the strong therapeutic potential of miRNA and miRNA target structures in cardiovascular disease. In addition, we discuss drawbacks and limitations of bioinformatics algorithms and the necessity of experimental approaches for miRNA target identification. This article is part of a Special Issue entitled 'Non-coding RNAs'.
authors.affiliation: Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, Würzburg, Germany; Institute for Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany.
authors.forename: Meik
authors.initials: M
authors.lastname: Kunz
authors.affiliation: Institute for Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany; Plant Breeding Institute, Christian-Albrechts-University of Kiel, Olshausenstr. 40, 24098 Kiel, Germany.
authors.forename: Ke
authors.initials: K
authors.lastname: Xiao
authors.affiliation: Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, Würzburg, Germany.
authors.forename: Chunguang
authors.initials: C
authors.lastname: Liang
authors.affiliation: Institute for Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany.
authors.forename: Janika
authors.initials: J
authors.lastname: Viereck
authors.affiliation: Department of Internal Medicine I, University Hospital Würzburg, Germany and Comprehensive Heart Failure Center, University of Würzburg, Germany.
authors.forename: Christina
authors.initials: C
authors.lastname: Pachel
authors.affiliation: Department of Internal Medicine I, University Hospital Würzburg, Germany and Comprehensive Heart Failure Center, University of Würzburg, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Frantz
authors.affiliation: Institute for Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany; Excellence Cluster REBIRTH, Hannover Medical School, Hannover, Germany; National Heart and Lung Institute, Imperial College London, London, UK.
authors.forename: Thomas
authors.initials: T
authors.lastname: Thum
authors.affiliation: Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, Würzburg, Germany; EMBL Heidelberg, BioComputing Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany. Electronic address: dandekar@biozentrum.uni-wuerzburg.de.
authors.forename: Thomas
authors.initials: T
authors.lastname: Dandekar
mesh_terms: D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D035683:MicroRNAs / Q000096:biosynthesis / Q000378:metabolism*; D008969:Molecular Sequence Data
chemical_list: D035683:MicroRNAs
keywords: Database; Heart; MiRNAs; Multiple sequence alignment; Omics; RNA secondary structure