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An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells

Nature Structural & Molecular Biology volume 16, pages 130–137 (2009)Cite this article

Abstract

The elucidation of a code for regulated splicing has been a long-standing goal in understanding the control of post-transcriptional gene expression events that are crucial for cell survival, differentiation and development. We decoded functional RNA elements in vivo by constructing an RNA map for the cell type–specific splicing regulator FOX2 (also known as RBM9) via cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-seq) in human embryonic stem cells. The map identified a large cohort of specific FOX2 targets, many of which are themselves splicing regulators, and comparison between the FOX2 binding profile and validated splicing events revealed a general rule for FOX2-regulated exon inclusion or skipping in a position-dependent manner. These findings suggest that FOX2 functions as a critical regulator of a splicing network, and we further show that FOX2 is important for the survival of human embryonic stem cells.

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Figure 1: CLIP-seq of FOX2 in hESCs.
Figure 2: Genomic mapping and analysis of FOX2 CLIP-seq reads.
Figure 3: Clustering of FOX2 CLIP-seq reads around regulated splicing events.
Figure 4: RNA map of FOX2-regulated alternative splicing.
Figure 5: FOX2 is important for hESC survival.

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Acknowledgements

The authors would like to acknowledge S. Aigner for technical advice, J. Simon for illustration assistance and R. Keithley and B. Miller for cell culture. G.W.Y. was funded by a Junior Fellowship from the Crick-Jacobs Center for Theoretical and Computational Biology, Salk Institute. F.H.G. is funded by the California Institute of Regenerative Medicine, The Picower Foundation and the Lookout Foundation. Part of this work was supported by US National Institutes of Health grants to X.-D.F. (GM049369 and HG004659) and G.W.Y. (HG004659).

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Author notes

  1. Gene W Yeo & Tiffany Y Liang

    Present address: Present address: Stem Cell Program, Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-5004, USA.,

Authors and Affiliations

  1. Crick-Jacobs Center for Theoretical and Computational Biology, Salk Institute, 10010 North Torrey Pines Road, La Jolla, 92037, California, USA

    Gene W Yeo & Tiffany Y Liang

  2. Laboratory of Genetics, Salk Institute, 10010 North Torrey Pines Road, La Jolla, 92037, California, USA

    Gene W Yeo, Nicole G Coufal, Grace E Peng & Fred H Gage

  3. Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093-5004, Calfornia, USA

    Tiffany Y Liang & Xiang-Dong Fu

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  1. Gene W Yeo
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  5. Xiang-Dong Fu
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Contributions

G.W.Y. directed the project; G.W.Y. and F.H.G. designed the project; G.W.Y., N.G.C. and X.-D.F. analyzed the data and wrote the manuscript; G.W.Y., N.G.C., T.Y.L. and G.E.P. performed the experiments; G.W.Y. and T.Y.L. carried out bioinformatics data analysis.

Corresponding authors

Correspondence to Gene W Yeo, Xiang-Dong Fu or Fred H Gage.

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Supplementary Figures 1–11, Supplementary Tables 1 and 2 and Supplementary Methods (PDF 5186 kb)

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Yeo, G., Coufal, N., Liang, T. et al. An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat Struct Mol Biol 16, 130–137 (2009). https://doi.org/10.1038/nsmb.1545

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