title: Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets.
abstract: Recent studies implicated the RNA-binding protein with multiple splicing (RBPMS) family of proteins in oocyte, retinal ganglion cell, heart, and gastrointestinal smooth muscle development. These RNA-binding proteins contain a single RNA recognition motif (RRM), and their targets and molecular function have not yet been identified. We defined transcriptome-wide RNA targets using photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) in HEK293 cells, revealing exonic mature and intronic pre-mRNA binding sites, in agreement with the nuclear and cytoplasmic localization of the proteins. Computational and biochemical approaches defined the RNA recognition element (RRE) as a tandem CAC trinucleotide motif separated by a variable spacer region. Similar to other mRNA-binding proteins, RBPMS family of proteins relocalized to cytoplasmic stress granules under oxidative stress conditions suggestive of a support function for mRNA localization in large and/or multinucleated cells where it is preferentially expressed.
authors.affiliation: Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA.
authors.forename: Thalia A
authors.initials: TA
authors.lastname: Farazi
authors.affiliation: Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA.
authors.forename: Carl S
authors.initials: CS
authors.lastname: Leonhardt
authors.affiliation: Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
authors.forename: Neelanjan
authors.initials: N
authors.lastname: Mukherjee
authors.affiliation: Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA.
authors.forename: Aleksandra
authors.initials: A
authors.lastname: Mihailovic
authors.affiliation: Biology Department, Duke University, Durham, North Carolina 27708, USA.
authors.forename: Song
authors.initials: S
authors.lastname: Li
authors.affiliation: Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA.
authors.forename: Klaas E A
authors.initials: KE
authors.lastname: Max
authors.affiliation: Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA.
authors.forename: Cindy
authors.initials: C
authors.lastname: Meyer
authors.affiliation: Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA.
authors.forename: Masashi
authors.initials: M
authors.lastname: Yamaji
authors.affiliation: Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA.
authors.forename: Pavol
authors.initials: P
authors.lastname: Cekan
authors.affiliation: Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
authors.forename: Nicholas C
authors.initials: NC
authors.lastname: Jacobs
authors.affiliation: Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Gerstberger
authors.affiliation: Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA.
authors.forename: Claudia
authors.initials: C
authors.lastname: Bognanni
authors.affiliation: Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, SE-405 30, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Larsson
authors.affiliation: Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
authors.forename: Uwe
authors.initials: U
authors.lastname: Ohler
authors.affiliation: Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Tuschl
mesh_terms: D000328:Adult; D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D002478:Cells, Cultured; D005260:Female; D020869:Gene Expression Profiling; D057809:HEK293 Cells; D006801:Humans; D008297:Male; D051379:Mice; D008969:Molecular Sequence Data; D005810:Multigene Family; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs / Q000235:genetics; D012313:RNA / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D017386:Sequence Homology, Amino Acid; D059467:Transcriptome
chemical_list: C101827:RBPMS protein, human; D016601:RNA-Binding Proteins; D012313:RNA
keywords: PAR-CLIP; RBPMS; RNA recognition element; RNA-binding protein