Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43

Abstract

We used cross-linking and immunoprecipitation coupled with high-throughput sequencing to identify binding sites in 6,304 genes as the brain RNA targets for TDP-43, an RNA binding protein that, when mutated, causes amyotrophic lateral sclerosis. Massively parallel sequencing and splicing-sensitive junction arrays revealed that levels of 601 mRNAs were changed (including Fus (Tls), progranulin and other transcripts encoding neurodegenerative disease–associated proteins) and 965 altered splicing events were detected (including in sortilin, the receptor for progranulin) following depletion of TDP-43 from mouse adult brain with antisense oligonucleotides. RNAs whose levels were most depleted by reduction in TDP-43 were derived from genes with very long introns and that encode proteins involved in synaptic activity. Lastly, we found that TDP-43 autoregulates its synthesis, in part by directly binding and enhancing splicing of an intron in the 3′ untranslated region of its own transcript, thereby triggering nonsense-mediated RNA degradation.

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Figure 1: TDP-43 binds distal introns of pre-mRNA transcripts through UG-rich sites in vivo.
Figure 2: In vivo depletion of TDP-43 in mouse brain with ASOs.
Figure 3: Binding of TDP-43 on long transcripts enriched in brain sustains their normal mRNA levels.
Figure 4: TDP-43 mediates alternative splicing regulation of its RNA targets.
Figure 5: Autoregulation of TDP-43 through binding on the 3′ UTR of its own transcript.
Figure 6: TDP-43 regulates expression of FUS/TLS and progranulin.

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Acknowledgements

The authors would like to thank members of B. Ren's laboratory, especially Z. Ye, S. Kuan and L. Edsall for technical help with the Illumina sequencing and U. Wagner for helpful discussions, K. Clutario and J. Boubaker for technical help, as well as all of the members of the Yeo and Cleveland laboratories, M. Ares Jr for generous support, and the neuro-team of ISIS Pharmaceuticals for critical comments and suggestions on this project. M.P. is the recipient of a Human Frontier Science Program Long Term Fellowship. C.L.-T. is the recipient of 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 National Science Foundation Graduate Research Fellowship. This work was supported by grants from the US National Institutes of Health (R37 NS27036 and an American Recovery and Reinvestment Act Challenge grant) to D.W.C and partially by grants from the US National Institutes of Health (HG004659 and GM084317) and the Stem Cell Program at the University of California, San Diego to G.W.Y.

Author information

M.P., C.L.-T., J.M. and T.Y.L. performed the experiments. K.R.H., S.C.H. and T.Y.L. conducted the bioinformatics analysis. S.-C.L. developed the monoclonal TDP-43–specific antibody used for CLIP-seq and the tetracycline-inducible GFP–TDP-43–expressing HeLa cells. S.-C.L. and E.S. generated the transgenic myc–TDP-43 mice. J.P.D. and L.S. conducted the preliminary splice-junction microarray analyses. M.P., C.L.-T., E.W., C.M., Y.S., C.F.B. and H.K. conducted the antisense oligonucleotide experiments. M.P., C.L.-T., K.R.H., G.W.Y. and D.W.C. designed the experiments. M.P., C.L.-T., K.R.H., S.C.H., G.W.Y. and D.W.C. wrote the paper.

Correspondence to Gene W Yeo or Don W Cleveland.

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