Journal
METHODS
Volume 63, Issue 1, Pages 32-40Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ymeth.2013.03.022
Keywords
CLIP; Protein-RNA interactions; Next-generation sequencing; Bioinformatics
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An emergent strategy for the transcriptome-wide study of protein-RNA interactions is CLIP-seq (cross-linking and immunoprecipitation followed by high-throughput sequencing). We combined CLIP-seq and mRNA-seq to identify direct RNA binding sites of eIF4AIII in human cells. This RNA helicase is a core constituant of the Exon Junction Complex (EJC), a multifunctional protein complex associated with spliced mRNAs in metazoans. Here, we describe the successive steps of the CLIP protocol and the computational tools and strategies we employed to map the physiological targets of eIF4AIII on human RNAs. (C) 2013 Elsevier Inc. All rights reserved.
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