title: Improved binding site assignment by high-resolution mapping of RNA-protein interactions using iCLIP.
abstract: Individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) allows the determination of crosslinking sites of RNA-binding proteins (RBPs) on RNAs. iCLIP is based on ultraviolet light crosslinking of RBPs to RNA, reverse transcription and high-throughput sequencing of fragments terminating at the site of crosslinking. As a result, start sites of iCLIP fragments are expected to cluster with a narrow distribution, typically representing the site of direct interaction between the RBP and the RNA. Here we show that for several RBPs (eIF4A3, PTB, SRSF3, SRSF4 and hnRNP L), the start sites of iCLIP fragments show a fragment length-dependent broader distribution that can be shifted to positions upstream of the known RNA-binding site. We developed an analysis tool that identifies these shifts and can improve the positioning of RBP binding sites.
authors.affiliation: Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany.|Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120 Heidelberg, Germany.|European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Hauer
authors.affiliation: European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.|University of Ljubljana, Faculty of Computer and Information Science, Vecna pot 113, SI-1000 Ljubljana, Slovenia.
authors.forename: Tomaz
authors.initials: T
authors.lastname: Curk
authors.affiliation: European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Simon
authors.identifier: http://orcid.org/0000-0003-4868-1805
authors.initials: S
authors.lastname: Anders
authors.affiliation: European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Schwarzl
authors.affiliation: European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Anne-Marie
authors.initials: AM
authors.lastname: Alleaume
authors.affiliation: Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany.|Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120 Heidelberg, Germany.
authors.forename: Jana
authors.initials: J
authors.lastname: Sieber
authors.affiliation: Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany.|Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120 Heidelberg, Germany.|European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Ina
authors.initials: I
authors.lastname: Hollerer
authors.affiliation: Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany.|Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120 Heidelberg, Germany.
authors.forename: Madhuri
authors.initials: M
authors.lastname: Bhuvanagiri
authors.affiliation: European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Huber
authors.affiliation: Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120 Heidelberg, Germany.|European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Matthias W
authors.initials: MW
authors.lastname: Hentze
authors.affiliation: Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 430, 69120 Heidelberg, Germany.|Molecular Medicine Partnership Unit (MMPU), Im Neuenheimer Feld 350, 69120 Heidelberg, Germany.
authors.forename: Andreas E
authors.initials: AE
authors.lastname: Kulozik
mesh_terms: D001665:Binding Sites; D006367:HeLa Cells; D006801:Humans; D047468:Immunoprecipitation; D021141:Nucleic Acid Amplification Techniques; D011485:Protein Binding; D012313:RNA / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D012261:Ribonucleoproteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D016601:RNA-Binding Proteins; D012261:Ribonucleoproteins; D012313:RNA