title: Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation.
abstract: BACKGROUND
  Post-transcriptional RNA regulons ensure coordinated expression of monocistronic mRNAs encoding functionally related proteins. In this study, we employ a combination of RIP-seq and short- and long-wave individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) technologies in Drosophila cells to identify transcripts associated with cytoplasmic ribonucleoproteins (RNPs) containing the RNA-binding protein Imp.
  
  
  RESULTS
  We find extensive binding of Imp to 3' UTRs of transcripts that are involved in F-actin formation. A common denominator of the RNA-protein interface is the presence of multiple motifs with a central UA-rich element flanked by CA-rich elements. Experiments in single cells and intact flies reveal compromised actin cytoskeletal dynamics associated with low Imp levels. The former shows reduced F-actin formation and the latter exhibits abnormal neuronal patterning. This demonstrates a physiological significance of the defined RNA regulon.
  
  
  CONCLUSIONS
  Our data imply that Drosophila Imp RNPs may function as cytoplasmic mRNA assemblages that encode proteins which participate in actin cytoskeletal remodeling. Thus, they may facilitate coordinated protein expression in sub-cytoplasmic locations such as growth cones.
authors.affiliation: Department of Biology, Center for Computational and Applied Transcriptomics, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen, Denmark. hhansen@bio.ku.dk.
authors.forename: Heidi Theil
authors.initials: HT
authors.lastname: Hansen
authors.affiliation: Department of Biology, Center for Computational and Applied Transcriptomics, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen, Denmark. simras@binf.ku.dk.
authors.forename: Simon Horskjær
authors.initials: SH
authors.lastname: Rasmussen
authors.affiliation: Department of Biology, Center for Computational and Applied Transcriptomics, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen, Denmark. sidselka@yahoo.dk.
authors.forename: Sidsel Kramshøj
authors.initials: SK
authors.lastname: Adolph
authors.affiliation: Department of Biology, Center for Computational and Applied Transcriptomics, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen, Denmark. mplass@binf.ku.dk.
authors.forename: Mireya
authors.initials: M
authors.lastname: Plass
authors.affiliation: Department of Biology, Center for Computational and Applied Transcriptomics, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen, Denmark. akrogh@bio.ku.dk.
authors.forename: Anders
authors.initials: A
authors.lastname: Krogh
authors.affiliation: MCD Biology, University of California, Santa Cruz, CA, 95064, USA. jsanfor2@ucsc.edu.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Sanford
authors.affiliation: Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, 2100, Copenhagen, Denmark. cilius@me.com.
authors.forename: Finn Cilius
authors.initials: FC
authors.lastname: Nielsen
authors.affiliation: Department of Biology, Center for Computational and Applied Transcriptomics, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen, Denmark. janchr@bio.ku.dk.
authors.forename: Jan
authors.initials: J
authors.lastname: Christiansen
mesh_terms: D020413:3' Untranslated Regions; D008841:Actin Cytoskeleton / Q000378:metabolism; D000199:Actins / Q000378:metabolism*; D000818:Animals; D002478:Cells, Cultured; D003594:Cytoplasmic Granules / Q000737:chemistry; D004330:Drosophila / Q000196:embryology / Q000235:genetics / Q000378:metabolism; D029721:Drosophila Proteins / Q000032:analysis / Q000037:antagonists & inhibitors / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing; D047468:Immunoprecipitation; D008297:Male; D009420:Nervous System / Q000196:embryology; D012333:RNA, Messenger / Q000032:analysis / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000032:analysis / Q000037:antagonists & inhibitors / Q000378:metabolism*; D012261:Ribonucleoproteins / Q000378:metabolism*; D017423:Sequence Analysis, RNA
chemical_list: D020413:3' Untranslated Regions; D000199:Actins; D029721:Drosophila Proteins; C498778:Imp protein, Drosophila; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D012261:Ribonucleoproteins