title: Elucidation of transcriptome-wide microRNA binding sites in human cardiac tissues by Ago2 HITS-CLIP.
abstract: MicroRNAs (miRs) have emerged as key biological effectors in human health and disease. These small noncoding RNAs are incorporated into Argonaute (Ago) proteins, where they direct post-transcriptional gene silencing via base-pairing with target transcripts. Although miRs have become intriguing biological entities and attractive therapeutic targets, the translational impacts of miR research remain limited by a paucity of empirical miR targeting data, particularly in human primary tissues. Here, to improve our understanding of the diverse roles miRs play in cardiovascular function and disease, we applied high-throughput methods to globally profile miR:target interactions in human heart tissues. We deciphered Ago2:RNA interactions using crosslinking immunoprecipitation coupled with high-throughput sequencing (HITS-CLIP) to generate the first transcriptome-wide map of miR targeting events in human myocardium, detecting 4000 cardiac Ago2 binding sites across >2200 target transcripts. Our initial exploration of this interactome revealed an abundance of miR target sites in gene coding regions, including several sites pointing to new miR-29 functions in regulating cardiomyocyte calcium, growth and metabolism. Also, we uncovered several clinically-relevant interactions involving common genetic variants that alter miR targeting events in cardiomyopathy-associated genes. Overall, these data provide a critical resource for bolstering translational miR research in heart, and likely beyond.
authors.affiliation: Department of Internal Medicine, Carver College of Medicine; Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA 52242, USA.
authors.forename: Ryan M
authors.initials: RM
authors.lastname: Spengler
authors.affiliation: Department of Internal Medicine, Carver College of Medicine; Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA 52242, USA.
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Zhang
authors.affiliation: The Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
authors.forename: Congsheng
authors.initials: C
authors.lastname: Cheng
authors.affiliation: Department of Internal Medicine, Carver College of Medicine; Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA 52242, USA.
authors.forename: Jared M
authors.initials: JM
authors.lastname: McLendon
authors.affiliation: Department of Internal Medicine, Carver College of Medicine; Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA 52242, USA.
authors.forename: Jessica M
authors.initials: JM
authors.lastname: Skeie
authors.affiliation: Department of Internal Medicine, Carver College of Medicine; Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA 52242, USA.
authors.forename: Frances L
authors.initials: FL
authors.lastname: Johnson
authors.affiliation: The Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA Department of Pathology and Laboratory Medicine, the University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Beverly L
authors.initials: BL
authors.lastname: Davidson
authors.affiliation: Department of Internal Medicine, Carver College of Medicine; Abboud Cardiovascular Research Center, University of Iowa, Iowa City, IA 52242, USA ryan-boudreau@uiowa.edu.
authors.forename: Ryan L
authors.initials: RL
authors.lastname: Boudreau
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D060565:Argonaute Proteins / Q000235:genetics* / Q000378:metabolism*; D001665:Binding Sites; D002118:Calcium / Q000378:metabolism; D009202:Cardiomyopathies / Q000235:genetics; D003432:Cross-Linking Reagents; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D047468:Immunoprecipitation; D035683:MicroRNAs / Q000378:metabolism*; D009206:Myocardium / Q000166:cytology / Q000378:metabolism*; D016366:Open Reading Frames / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D013379:Substrate Specificity; D059467:Transcriptome / Q000235:genetics*
chemical_list: D020413:3' Untranslated Regions; C466422:AGO2 protein, human; D060565:Argonaute Proteins; D003432:Cross-Linking Reagents; D035683:MicroRNAs; D002118:Calcium