title: From benchmarking HITS-CLIP peak detection programs to a new method for identification of miRNA-binding sites from Ago2-CLIP data.
abstract: Experimental evidence indicates that about 60% of miRNA-binding activity does not follow the canonical rule about the seed matching between miRNA and target mRNAs, but rather a non-canonical miRNA targeting activity outside the seed or with a seed-like motifs. Here, we propose a new unbiased method to identify canonical and non-canonical miRNA-binding sites from peaks identified by Ago2 Cross-Linked ImmunoPrecipitation associated to high-throughput sequencing (CLIP-seq). Since the quality of peaks is of pivotal importance for the final output of the proposed method, we provide a comprehensive benchmarking of four peak detection programs, namely CIMS, PIPE-CLIP, Piranha and Pyicoclip, on four publicly available Ago2-HITS-CLIP datasets and one unpublished in-house Ago2-dataset in stem cells. We measured the sensitivity, the specificity and the position accuracy toward miRNA binding sites identification, and the agreement with TargetScan. Secondly, we developed a new pipeline, called miRBShunter, to identify canonical and non-canonical miRNA-binding sites based on de novo motif identification from Ago2 peaks and prediction of miRNA::RNA heteroduplexes. miRBShunter was tested and experimentally validated on the in-house Ago2-dataset and on an Ago2-PAR-CLIP dataset in human stem cells. Overall, we provide guidelines to choose a suitable peak detection program and a new method for miRNA-target identification.
authors.affiliation: Université Côte d'Azur, Inserm, C3M, Nice, 06204, France.
authors.forename: Silvia
authors.initials: S
authors.lastname: Bottini
authors.affiliation: Université Côte d'Azur, Inserm, C3M, Nice, 06204, France.
authors.forename: Nedra
authors.initials: N
authors.lastname: Hamouda-Tekaya
authors.affiliation: Stanford University School of Medicine, 265 Campus Drive, LLSCR Building, Stanford, CA 94305, USA.
authors.forename: Bogdan
authors.initials: B
authors.lastname: Tanasa
authors.affiliation: Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560, France.
authors.forename: Laure-Emmanuelle
authors.initials: LE
authors.lastname: Zaragosi
authors.affiliation: Université Côte d'Azur, Inserm, C3M, Nice, 06204, France.
authors.forename: Valerie
authors.initials: V
authors.lastname: Grandjean
authors.affiliation: Université Côte d'Azur, Inserm, C3M, Nice, 06204, France.
authors.forename: Emanuela
authors.initials: E
authors.lastname: Repetto
authors.affiliation: Université Côte d'Azur, Inserm, C3M, Nice, 06204, France.
authors.forename: Michele
authors.initials: M
authors.lastname: Trabucchi
mesh_terms: D020816:Amino Acid Motifs; D060565:Argonaute Proteins / Q000737:chemistry / Q000235:genetics; D019985:Benchmarking; D001665:Binding Sites; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D012680:Sensitivity and Specificity; D012984:Software
chemical_list: C466422:AGO2 protein, human; D060565:Argonaute Proteins; D035683:MicroRNAs