title: TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins.
abstract: RNA transcripts are bound and regulated by RNA-binding proteins (RBPs). Current methods for identifying in vivo targets of an RBP are imperfect and not amenable to examining small numbers of cells. To address these issues, we developed TRIBE (targets of RNA-binding proteins identified by editing), a technique that couples an RBP to the catalytic domain of the Drosophila RNA-editing enzyme ADAR and expresses the fusion protein in vivo. RBP targets are marked with novel RNA editing events and identified by sequencing RNA. We have used TRIBE to identify the targets of three RBPs (Hrp48, dFMR1, and NonA). TRIBE compares favorably to other methods, including CLIP, and we have identified RBP targets from as little as 150 specific fly neurons. TRIBE can be performed without an antibody and in small numbers of specific cells.
authors.affiliation: Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA.
authors.forename: Aoife C
authors.initials: AC
authors.lastname: McMahon
authors.affiliation: Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA.
authors.forename: Reazur
authors.initials: R
authors.lastname: Rahman
authors.affiliation: Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA.
authors.forename: Hua
authors.initials: H
authors.lastname: Jin
authors.affiliation: Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA.
authors.forename: James L
authors.initials: JL
authors.lastname: Shen
authors.affiliation: Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA.
authors.forename: Allegra
authors.initials: A
authors.lastname: Fieldsend
authors.affiliation: Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA.
authors.forename: Weifei
authors.initials: W
authors.lastname: Luo
authors.affiliation: Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA. Electronic address: rosbash@brandeis.edu.
authors.forename: Michael
authors.initials: M
authors.lastname: Rosbash
mesh_terms: D020413:3' Untranslated Regions; D000243:Adenosine Deaminase / Q000378:metabolism*; D000818:Animals; D029721:Drosophila Proteins / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000201:enzymology*; D005821:Genetic Techniques; D034441:Heterogeneous-Nuclear Ribonucleoproteins / Q000378:metabolism; D017393:RNA Editing; D016601:RNA-Binding Proteins
chemical_list: D020413:3' Untranslated Regions; D029721:Drosophila Proteins; D034441:Heterogeneous-Nuclear Ribonucleoproteins; C487427:Hrb27C protein, Drosophila; D016601:RNA-Binding Proteins; C567956:Adar protein, Drosophila; D000243:Adenosine Deaminase