Background: RNA processing dysfunction has been implicated in the pathology of the neurodegenerative disease amyotrophic lateral sclerosis (ALS), not only due to causative TDP-43 disease mutations (TDP-ALS), but further the characteristic mislocalisation of crucial RNA-binding protein TDP-43 regardless of genetic background. This implicates the importance of investigating the widespread TDP-43 dysfunction-mediated changes in RNA processing, and the need to identify differential gene expression and alternative splicing changes that may underlie neurodegenerative disease. Methods: Two mouse models of TDP-43 were investigated, each containing a single substitution within the coding region of the Tardbp gene: one mutation in the RNA binding domain (RBD), the other in the low complexity domain hotspot region for ALS-causative mutations. RNA sequencing was used to examine resulting differential gene expression and alternative splicing events, and integrated iCLIP analysis highlighted changes in RNA binding patterns. Results and discussion: We identified severe molecular dysregulation in both models. The RBD mutant displayed dose-dependent preferential exon inclusion, including the retention of cryptic exons. Alongside this was downregulation of long intron-containing genes, typically related to neuronal activity. These features, alongside other RNA processing changes, were similar to those resulting from TDP-43 loss, and thus indicated the RBD mutation to cause TDP-43 loss of function. Contrastingly, we found that the LCD mutation caused greater levels of exon skipping, including novel gain of TDP-43 function in splicing which resulted in mutant-specific ‘skiptic’ transcripts. A subset of these was then demonstrated to be conserved in a TDP-ALS mouse model, and further in human TDP-ALS patient settings. Importantly, this gain of function mouse model developed a neurodegenerative, ALS-like phenotype. This indicated that TDP-43 gain of function, even in the absence of loss of function effects, is sufficient to cause a neurodegenerative disease phenotype
