TDP-43 is a predominantly nuclear RNA-binding protein that forms inclusion bodies in frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). The mRNA targets of TDP-43 in the human brain and its role in RNA processing are largely unknown. Using individual nucleotide-resolution ultraviolet cross-linking and immunoprecipitation (iCLIP), we found that TDP-43 preferentially bound long clusters of UG-rich sequences in vivo. Analysis of RNA binding by TDP-43 in brains from subjects with FTLD revealed that the greatest increases in binding were to the MALAT1 and NEAT1 noncoding RNAs. We also found that binding of TDP-43 to pre-mRNAs influenced alternative splicing in a similar position-dependent manner to Nova proteins. In addition, we identified unusually long clusters of TDP-43 binding at deep intronic positions downstream of silenced exons. A substantial proportion of alternative mRNA isoforms regulated by TDP-43 encode proteins that regulate neuronal development or have been implicated in neurological diseases, highlighting the importance of TDP-43 for the regulation of splicing in the brain.
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We thank K. Zarnack for advice and comments on the manuscript, F. Baralle, Y. Ayalla and A.D. Ambrogio for HeLa knockdown RNA, and J. Hadfield and the genomic team at CRI for Illumina sequencing. This work was supported by the European Research Council (206726-CLIP), the MRC, Slovenian Research Agency (P2-0209, J2-2197, L2-1112, Z7-3665), Wellcome Trust and MRC Strategic Grant Award (089701/Z/09/Z), Motor Neuron Disease Association, Heaton-Ellis Trust and Psychiatry Research Trust.
The authors declare no competing financial interests.
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Tollervey, J., Curk, T., Rogelj, B. et al. Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. Nat Neurosci 14, 452–458 (2011). https://doi.org/10.1038/nn.2778
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