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Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs

Nature Neuroscience volume 15, pages 1488–1497 (2012)Cite this article

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Abstract

FUS/TLS (fused in sarcoma/translocated in liposarcoma) and TDP-43 are integrally involved in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. We found that FUS/TLS binds to RNAs from >5,500 genes in mouse and human brain, primarily through a GUGGU-binding motif. We identified a sawtooth-like binding pattern, consistent with co-transcriptional deposition of FUS/TLS. Depletion of FUS/TLS from the adult nervous system altered the levels or splicing of >950 mRNAs, most of which are distinct from RNAs dependent on TDP-43. Abundance of only 45 RNAs was reduced after depletion of either TDP-43 or FUS/TLS from mouse brain, but among these were mRNAs that were transcribed from genes with exceptionally long introns and that encode proteins that are essential for neuronal integrity. Expression levels of a subset of these were lowered after TDP-43 or FUS/TLS depletion in stem cell–derived human neurons and in TDP-43 aggregate–containing motor neurons in sporadic ALS, supporting a common loss-of-function pathway as one component underlying motor neuron death from misregulation of TDP-43 or FUS/TLS.

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Figure 1: FUS/TLS RNA targets in mouse and human brain.
Figure 2: FUS/TLS binding patterns in mouse and human brain.
Figure 3: Changes in the expression of FUS/TLS and TDP-43 targets after depletion (knockdown, KD) of either FUS/TLS or TDP-43 in brain and spinal cord.
Figure 4: FUS/TLS-dependent alternative splicing in mouse brain.
Figure 5: Alterations of TDP-43 and FUS/TLS human targets in neurons derived from ES cells.
Figure 6: Reduction of TDP-43 and FUS/TLS RNA targets in motor neurons from sporadic ALS patients.

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Acknowledgements

The authors would like to thank members of B. Ren's laboratory, especially Z. Ye, S. Kuan, U. Wagner and L. Edsall, for technical help with the Illumina sequencing, M. Ares Jr. for generous support, as well as the members of the Yeo and Cleveland laboratories and the team at Isis Pharmaceuticals for critical comments and suggestions on this project. This work was supported by grants from the US National Institutes of Health (R37NS27036 to D.W.C. and K99NS075216 to M.P.). M.P. is the recipient of a long-term fellowship from the international Human Frontier Science Program Organization. C.L.-T. is the recipient of a Career Development Award from the Muscular Dystrophy Association and the Milton-Safenowitz post-doctoral fellowship from the Amyotrophic Lateral Sclerosis Association. D.W.C. receives salary support from the Ludwig Institute for Cancer Research. S.C.H. is funded by a US National Science Foundation Graduate Research Fellowship. This work was also supported by grant number R01NS075449 from the US National Institute of Neurological Disorders and Stroke, and was partially supported by grants from the US National Institutes of Health (HG004659 and GM084317) and the California Institute for Regenerative Medicine (RB1-01413 and RB3-05009) to G.W.Y. G.W.Y. is a recipient of the Alfred P. Sloan Research Fellowship.

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  1. Clotilde Lagier-Tourenne, Magdalini Polymenidou and Kasey R Hutt: These authors contributed equally to this work.

Authors and Affiliations

  1. Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, California, USA

    Clotilde Lagier-Tourenne, Magdalini Polymenidou, Kevin M Clutario, Shuo-Chien Ling & Don W Cleveland

  2. Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California, USA

    Clotilde Lagier-Tourenne, Magdalini Polymenidou, Kasey R Hutt, Anthony Q Vu, Stephanie C Huelga, Kevin M Clutario, Shuo-Chien Ling, Tiffany Y Liang, Don W Cleveland & Gene W Yeo

  3. Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California, USA

    Kasey R Hutt, Anthony Q Vu, Stephanie C Huelga, Tiffany Y Liang & Gene W Yeo

  4. Department of Neurosciences, University of California at San Diego, La Jolla, California, USA

    Michael Baughn & John Ravits

  5. Isis Pharmaceuticals, Carlsbad, California, USA

    Curt Mazur, Edward Wancewicz, Aneeza S Kim, Andy Watt, Sue Freier & C Frank Bennett

  6. MB Institute of Cell Biology, University of Manitoba, Winnipeg, Canada

    Geoffrey G Hicks

  7. Department of Molecular, RNA Center, Cell and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, California, USA

    John Paul Donohue & Lily Shiue

  8. A*STAR and Department of Biological Sciences, Molecular Engineering Laboratory, National University of Singapore, Singapore

    Gene W Yeo

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Contributions

C.L.-T., M.P., A.Q.V., M.B. and K.M.C. performed the experiments. K.R.H., S.C.H. and T.Y.L. conducted the bioinformatics analysis. S.-C.L. developed the polyclonal FUS/TLS-specific antibody Ab3. J.P.D. and L.S. conducted the preliminary splice-junction microarray analyses. G.G.H. provided the brain samples from the Fus/Tls−/− mice. M.P., C.L.-T., C.M., E.W., A.S.K., A.W., S.F. and C.F.B. conducted the ASO experiments. J.R. provided the ALS patient tissues. C.L.-T., M.P., K.R.H., G.W.Y. and D.W.C. designed the experiments. C.L.-T., M.P., K.R.H., A.Q.V., G.W.Y. and D.W.C. wrote the manuscript.

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Correspondence to Don W Cleveland or Gene W Yeo.

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Lagier-Tourenne, C., Polymenidou, M., Hutt, K. et al. Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs. Nat Neurosci 15, 1488–1497 (2012). https://doi.org/10.1038/nn.3230

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