Dimitrios Anastasakis, Daniel Benhalevy, Markus Hafner
{"title":"Proximity-CLIP and Expedited Non-Radioactive Library Preparation of Small RNA Footprints for Next-Generation Sequencing.","authors":"Dimitrios Anastasakis, Daniel Benhalevy, Markus Hafner","doi":"10.1002/cpmb.120","DOIUrl":"10.1002/cpmb.120","url":null,"abstract":"<p><p>During the course of their life cycle, most RNAs move between several cellular environments where they associate with different RNA binding proteins (RBPs). Reciprocally, a significant portion of RBPs reside in more than a single cellular compartment, where they can interact with discrete RNAs and even exert distinct biological roles. Proximity-CLIP combines proximity biotinylation of proteins with photoactivatable ribonucleoside-enhanced protein-RNA crosslinking to simultaneously profile the proteome, including RBPs and the RBP-bound transcriptome, in any given subcellular compartment. Here we provide a detailed experimental protocol for Proximity-CLIP along with a simplified non-radioactive, small-RNA cDNA library preparation protocol. Published 2020 U.S. Government. Basic Protocol 1: Cell culture, 4SU labeling, proximity biotinylation, and crosslinking Basic Protocol 2: Cell extraction, streptavidin affinity purification, and on-beads trypsinization Basic Protocol 3: RNA footprints cDNA library preparation Support Protocol: Preparation of RNA-seq libraries from intact RNA.</p>","PeriodicalId":10734,"journal":{"name":"Current Protocols in Molecular Biology","volume":"131 1","pages":"e120"},"PeriodicalIF":0.0,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpmb.120","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37960565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marta Vazquez-Vilar, Mónica Gandía, Victor García-Carpintero, Eric Marqués, Alejandro Sarrion-Perdigones, Lynne Yenush, Julio Polaina, Paloma Manzanares, Jose F. Marcos, Diego Orzaez
Justin A. Bosch, Shannon Knight, Oguz Kanca, Jonathan Zirin, Donghui Yang-Zhou, Yanhui Hu, Jonathan Rodiger, Gabriel Amador, Hugo J. Bellen, Norbert Perrimon, Stephanie E. Mohr