Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation

TY - JOUR

T1 - Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation

AU - Hansen, Heidi Theil

AU - Rasmussen, Simon Horskjær

AU - Adolph, Sidsel Kramshøj

AU - Plass, Mireya

AU - Krogh, Anders

AU - Sanford, Jeremy

AU - Nielsen, Finn Cilius

AU - Christiansen, Jan

PY - 2015/6/9

Y1 - 2015/6/9

N2 - BACKGROUND: Post-transcriptional RNA regulons ensure co-ordinated 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 co-ordinated protein expression in sub-cytoplasmic locations such as growth cones.

AB - BACKGROUND: Post-transcriptional RNA regulons ensure co-ordinated 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 co-ordinated protein expression in sub-cytoplasmic locations such as growth cones.

U2 - 10.1186/s13059-015-0687-0

DO - 10.1186/s13059-015-0687-0

M3 - Journal article

C2 - 26054396

SN - 1474-7596

VL - 16

JO - Genome Biology (Online Edition)

JF - Genome Biology (Online Edition)

M1 - 123

ER -