To investigate genome-wide transcriptomic changes induced by NEAT1 knockdown, we performed whole transcriptome RNA sequencing (RNAseq) on iPSC-derived neurons, with and without KCl-induced depolarization, and before and following ASO-mediated NEAT1 knockdown. We found extensive and significant transcript changes between KCl-treated and mock-depolarized samples, with and without NEAT1 ASOs (Supplementary Fig. 7a), including the expected activation of IEGs such as FOSB, JUNB and PLK2 (Supplementary Fig. 7b and qRT-PCR validation shown in Supplementary Fig. 8). It is notable that the levels of activation of these IEGs was stronger in NEAT1-ASO-treated cells relative to controls, in agreement with our data showing increased neuronal activation after NEAT1 depletion (Fig. 2d). Since only modest expression differences were identified between inactivated NEAT1-knockdown and control neurons (Supplementary Fig. 7a), these regulatory functions of NEAT1 appear restricted to activity-dependent contexts.
