Tau modulates mRNA transcription, alternative polyadenylation profiles of hnRNPs, chromatin remodeling and spliceosome complexes

Abstract Tau protein is a known contributor in several neurodegenerative diseases, including Alzheimer ‘s disease (AD) and frontotemporal dementia (FTD). It is well-established that tau forms pathological aggregates and fibrils in these diseases. Tau has been observed within the nuclei of neurons, but there is a gap in understanding regarding the mechanism by which tau modulates transcription. We are interested in the P301L mutation of tau, which has been associated with FTD and increased tau aggregation. Our study utilized tau-inducible HEK (iHEK) cells to reveal that WT and P301L tau distinctively alter the transcription and alternative polyadenylation (APA) profiles of numerous nuclear precursors mRNAs, which then translate to form proteins involved in chromatin remodeling and splicing. We isolated total mRNA before and after over-expressing tau and then performed Poly(A)-ClickSeq (PAC-Seq) to characterize mRNA expression and APA profiles. We characterized changes in Gene Ontology (GO) pathways using EnrichR and Gene Set Enrichment Analysis (GSEA). We observed that P301L tau up-regulates genes associated with reactive oxygen species responsiveness as well as genes involved in dendrite, microtubule, and nuclear body/speckle formation. The number of genes regulated by WT tau is greater than the mutant form, which indicates that the P301L mutation causes loss-of-function at the transcriptional level. WT tau up-regulates genes contributing to cytoskeleton-dependent intracellular transport, microglial activation, microtubule and nuclear chromatin organization, formation of nuclear bodies and speckles. Interestingly, both WT and P301L tau commonly down-regulate genes responsible for ubiquitin-proteosome system. In addition, WT tau significantly down-regulates several genes implicated in chromatin remodeling and nucleosome organization. Although there are limitations inherent to the model systems used, this study will improve understanding regarding the nuclear impact of tau at the transcriptional and post-transcriptional level. This study also illustrates the potential impact of P301L tau on the human brain genome during early phases of pathogenesis. Author summary While tau biology has been extensively studied and closely linked to several neurodegenerative diseases, our current understanding of tau’s functions in the nucleus is limited. Given the role of tau in disease progression and pathogenesis, elucidating the function of tau activity in transcription and its nuclear accumulation may reveal novel therapeutic targets; therefore, helping identify new upstream pathways that have yet to be investigated. In this study, we used tau-inducible cell lines to uncover new molecular mechanisms by which tau functions in the nucleus. This study systematically investigates the changes in transcriptomic and alternative polyadenylation profiles modulated by WT and mutant P301L tau protein. In this manuscript, we report following new findings (i) tau modulates gene expression of transcripts associated with chromatin remodeling and splicing complexes; (ii) WT and mutant P301L tau regulate, differentially, transcription and alternative polyadenylation (APA) profiles; and (iii) P301L mutation affects the transcription mediated by tau protein. The potential role of tau in mediating transcription and alternative polyadenylation processes is not well studied, representing a novelty in the field. Therefore, this research establishes a new direction for investigating tau nuclear function in both human and mouse brains.