title: miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction.
abstract: Identifying the interaction partners of noncoding RNAs is essential for elucidating their functions. We have developed an approach, termed microRNA crosslinking and immunoprecipitation (miR-CLIP), using pre-miRNAs modified with psoralen and biotin to capture their targets in cells. Photo-crosslinking and Argonaute 2 immunopurification followed by streptavidin affinity purification of probe-linked RNAs provided selectivity in the capture of targets, which were identified by deep sequencing. miR-CLIP with pre-miR-106a, a miR-17-5p family member, identified hundreds of putative targets in HeLa cells, many carrying conserved sequences complementary to the miRNA seed but also many that were not predicted computationally. miR-106a overexpression experiments confirmed that miR-CLIP captured functional targets, including H19, a long noncoding RNA that is expressed during skeletal muscle cell differentiation. We showed that miR-17-5p family members bind H19 in HeLa cells and myoblasts. During myoblast differentiation, levels of H19, miR-17-5p family members and mRNA targets changed in a manner suggesting that H19 acts as a 'sponge' for these miRNAs.
authors.affiliation: Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland.
authors.forename: Jochen
authors.identifier: 0000000163752240
authors.initials: J
authors.lastname: Imig
authors.affiliation: Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland.
authors.forename: Andreas
authors.identifier: 0000000244011495
authors.initials: A
authors.lastname: Brunschweiger
authors.affiliation: Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland.
authors.forename: Anneke
authors.initials: A
authors.lastname: Brümmer
authors.affiliation: Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland.
authors.forename: Boris
authors.initials: B
authors.lastname: Guennewig
authors.affiliation: Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland.
authors.forename: Nitish
authors.initials: N
authors.lastname: Mittal
authors.affiliation: Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland.
authors.forename: Shivendra
authors.initials: S
authors.lastname: Kishore
authors.affiliation: Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland.
authors.forename: Panagiota
authors.initials: P
authors.lastname: Tsikrika
authors.affiliation: Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK.
authors.forename: André P
authors.initials: AP
authors.lastname: Gerber
authors.affiliation: Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland.
authors.forename: Mihaela
authors.initials: M
authors.lastname: Zavolan
authors.affiliation: Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Hall
mesh_terms: D001483:Base Sequence; D001710:Biotin / Q000378:metabolism; D018929:Cell Culture Techniques; D002454:Cell Differentiation / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D005363:Ficusin / Q000378:metabolism; D006367:HeLa Cells; D006801:Humans; D047468:Immunoprecipitation; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D032342:Muscle Cells / Q000166:cytology / Q000378:metabolism; D032446:Myoblasts / Q000166:cytology / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D059467:Transcriptome
chemical_list: C094335:H19 long non-coding RNA; C542541:MIRN106 microRNA, human; D035683:MicroRNAs; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D001710:Biotin; D005363:Ficusin