Fig 2: Long-term reduction of NOVA1 progressively shortens telomeres. a Terminal restriction fragment length (TRF-Southern blot) analysis of control shRNA or NOVA1 shRNA at two population doublings (PD). b Rescue of shRNA knockdown of NOVA1 with a shRNA mutant cDNA in H1299 cells (stable cell lines were measured a minimum of six times over several passages). hTERT splicing was determined with RT-ddPCR assays. c Western blot of NOVA1 shRNA rescue in H1299 cells (representative image of stable cell lines, measured three times over three passages in culture). d hTERT expression in rescue H1299 cells as determined by RT-PCR of exons 5–9 (representative image; n = 3). e Rescue of shRNA knockdown of NOVA1 with a shRNA mutant cDNA partially restores telomerase activity in H1299 cells (n = 6). Telomerase activity was determined with droplet digital TRAP (ddTRAP with 50 cell equivalents added to the assay). Student’s t test set at *p < 0.05 for significance. f Western blot of V5-tagged NOVA1 expression in Calu6 cells (representative image of stable cell lines). g hTERT splicing profile in Calu6 cells with and without NOVA1 (n = 6). hTERT splicing was determined with RT-ddPCR assays. h Telomerase enzyme activity (ddTRAP with 50 cell equivalents added to the assay) in Calu6 cells with and without NOVA1 (n = 3). Student’s t test set at *p < 0.05 for significance). Data are expressed as means and standard error of the mean where applicable. *p < 0.05. RT: reverse transcription, ddPCR: droplet digital PCR. + indicates presence of shRNA or cDNA construct. − indicates absence of shRNA or cDNA construct (b, d, e). Supplementary data associated with this figure can be found in Supplementary Figure 2

Fig 3: Aberrant NOVA1 states in ALS exhibit gain- and loss-of-function features a Schematic illustrating analysis strategy to identify patterns of altered NOVA1 function in ALS iPSC-derived MNs. b Heatmap of all significant AS events observed in the four ALS datasets. Inclusion level difference for all depicted datasets were clustered using k-means clustering into 8 distinct clusters. Blue denotes inclusion (max: −0.6), red denotes exclusion (max: 0.6). Datasets are clustered using Euclidean distance metric. c Boxplot of inclusion level differences in clusters 0 (sALS vs. Ctrl: purple; fALS vs. Ctrl: pink; sALS vs. Ctrl (AA): orange; C9-ALS vs. Ctrl (AA): green; SPG11-HSP vs. Ctrl: cyan; NOVA1 vs. EGFP overexpression: blue; NOVA1 wt vs. NOVA1 K.O.: yellow). Ideogram on top illustrates the direction of the most prominent observed change in ALS, NOVA1 gain of function (GOF) and NOVA1 loss of function (LOF) (from top to bottom). d Bar blot illustrating significance (negative log10 scale) of CV-B NOVA1 eCLIP-seq binding site enrichment at AS events in the 8 detected AS event clusters at upstream exon, upstream intron, alternative exon, downstream intron, and downstream exon. Statistical significance was calculated with hypergeometric test against all detected AS events in the four ALS datasets as a background. Dashed line represented P value = 0.05. Arrow depicts most significant enrichment in cluster 0. e Bar blot of significance (negative log10 scale) of Ctrl-1-2 NOVA1 eCLIP-seq binding site enrichment at AS events in the 8 detected AS event clusters at upstream exon, upstream intron, alternative exon, downstream intron and downstream exon. Statistical significance was calculated with hypergeometric test against all detected AS events in the four ALS datasets as a background. Dashed line represents P value = 0.05. Arrow depicts most significant enrichment in cluster 0

Fig 4: Binding of NOVA1, NOVA2 and RBFOX2 is associated with AS events that are differentially regulated in ALS. a Schematic illustrating the experimental and analysis workflow n = 2 Ctrl per eCLIP). b Pie charts depicting distribution of gene regions bound by eCLIP-seq peaks in a dataset. The total number of significant peaks is shown below the individual pie charts. c Heatmaps illustrating the percentage of individual peaks (top) and target transcripts (bottom) shared between the indicated eCLIP-seq datasets. d–g Scatter plot presenting k-mer enrichments as Z-scores of d TDP-43 (6-mers), e NOVA1 (4-mers), f NOVA2 (4-mers), and g RBFOX2 (6-mers) in the Ctrl-1-2 (x axis) and the CV-B (y axis) dataset, respectively. k-mers with highest enrichment are colored. h–l Bar graphs illustrating enrichment significance (left graph, −log10(P value))) and fold-enrichment (right graph) of TDP-43 (green), NOVA1 (red), NOVA2 (orange) and RBFOX2 (blue) eCLIP-seq experiments in CV-B (dark shading) and Ctrl-1-2 (light shading) at AS events called in the h sALS vs. Ctrl dataset generated in this study, i fALS vs. Ctrl dataset generated in this study, j sALS vs. Ctrl dataset from AnswerALS, k C9-ALS vs. Ctrl dataset from AnswerALS, and l SPG11-HSP vs Ctrl generated in this study. Dashed vertical lines indicate significance thresholds (P value = 0.05 and fold enrichment=1). Hypergeometric test was used for calculation of significance. All detected events that passed the coverage threshold in the RNA-seq datasets were used as background

Fig 5: NOVA1 mediates AS in human iPSC motor neurons in a position-dependent manner. a Schematic illustrating the experimental workflow. b Western blot of NOVA1 from day 30 iPSC-MN after transduction with lentivirus containing EGFP (n = 3) or NOVA1 (n = 3) ORF expressed under the CAG promoter. GAPDH was used as a loading control. Average fold change of 1.97 (CV-B: 2.2-fold; Ctrl-1-1: 1.6-fold; Ctrl-2-1: 2.1-fold). c Western blot of NOVA1 from day 30 control (n = 5) and NOVA1 K.O. (n = 5) iPSC-MN. GAPDH was used as a loading control. d Venn diagram of significant differential cassette exon alternative splicing events from comparisons of NOVA1 vs. EGFP overexpression (blue) and of NOVA1 wt vs. NOVA1 K.O. (yellow). Significance of overlap was calculated with Fisher's exact test using all events detected in both analyses as background. OR = odds ratio. e, f Bar graphs of significance of differential enrichment of eCLIP-seq binding sites at AS events of TDP-43 (green), NOVA1 (red), NOVA2 (orange) and RBFOX2 (blue) in e NOVA1 vs EGFP overexpression, and f NOVA1 K.O. vs Ctrl. Experiments were performed in two cell lines (CV-B, dark shading; Ctrl-1-2, light shading). Dashed horizontal line at P value = 0.05. Enrichment was calculated using hypergeometric test with all detected events as the background. g Schematic illustrating analysis of positions of interest for NOVA1 binding analysis. h-i Bar graphs of significance of differential enrichment of NOVA1 eCLIP-seq binding sites at excluded (left) and included (right) AS events (upstream exons, upstream introns, alternative exons, downstream introns and downstream exons) in h NOVA1 vs EGFP overexpression, and i NOVA1 K.O. vs Ctrl. Experiments were performed in two cell lines (CV-B, dark shading; Ctrl-1-2, light shading). Dashed vertical line at P value =0.05. Enrichment was calculated using hypergeometric test with all detected events as the background. j Model illustrating physiological modes of action of NOVA1 in human iPSC-derived MN. AE alternative exon, UI upstream intron, DI downstream intron