Title: The ALS-linked gene TDP-43 regulates IFNb expression through a novel mechanism of 3' UTR-mediated promoter cis-regulation
Description: The TAR DNA-binding protein (TDP-43) is a heterogeneous nuclear ribonucleprotein that is involved in multiple stages of RNA processing. Mutations in the TDP-43 gene and mislocalization of TDP-43 protein have been implicated in a growing number of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Here, we show that TDP-43 negatively regulates innate immune gene expression in response to RNA virus sensing. Perturbation of TDP-43 protein expression leads to an increase in antiviral gene expression in a variety of human and mouse cells. Crosslinked RNA immunoprecipitation (CLIP) experiments revealed that TDP-43 binds to type I interferon (IFN) and interferon stimulated gene (ISGs) transcripts. Using massively parallel 3' UTR reporter assays coupled with high throughput sequencing (MPRA-seq), we identified polyadenylation signal sequences in the 3' UTRs of innate immune genes to be specifically regulated by TDP-43. Surprisingly, IFN and ISG mRNA decay rates are faster in TDP-43-perturbed cells. Using a metabolic labeling approach to measure nascent transcript generation, we found that perturbation of TDP-43 expression leads to an increase in antiviral gene transcription rates. Additionally, RNA polymerase II (pol II) chromatin immunoprecipitation (ChIP) confirmed that there is greater pol II occupancy on innate immune genes when TDP-43 is depleted. Although TDP-43 perturbation has no effect on an isolated IFNβ promoter reporter, we found that TDP-43 inhibits IFNβ promoter activity when the IFNβ 3' UTR sequence is inserted downstream of the IFNβ promoter element, suggesting a novel mechanism of 3'UTR-mediated promoter cis-regulation.