Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets
- Thalia A. Farazi1,5,
- Carl S. Leonhardt1,5,
- Neelanjan Mukherjee2,
- Aleksandra Mihailovic1,
- Song Li3,
- Klaas E.A. Max1,
- Cindy Meyer1,
- Masashi Yamaji1,
- Pavol Cekan1,
- Nicholas C. Jacobs2,
- Stefanie Gerstberger1,
- Claudia Bognanni1,
- Erik Larsson4,
- Uwe Ohler2 and
- Thomas Tuschl1,6
- 1Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
- 2Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
- 3Biology Department, Duke University, Durham, North Carolina 27708, USA
- 4Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, SE-405 30, Sweden
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↵5 These authors contributed equally to this work.
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.
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Footnotes
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↵6 Corresponding author
E-mail ttuschl{at}rockefeller.edu
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Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.045005.114.
- Received February 24, 2014.
- Accepted April 6, 2014.
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