The differential impact of HNRNPA1 isoforms on gene expression and their relevance to dsRNA-mediated innate immune response

Heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1) is a highly abundant RNA binding protein alternatively spliced in two main isoforms named, hnRNP A1 and hnRNP A1B. While being ubiquitously expressed, both isoforms have different cellular localizations and are differentially expressed in tissues during development and aging. To improve our understanding of the cellular function of each isoform, we performed RNA sequencing in cells exclusively expressing hnRNP A1 or hnRNP A1B. As expected, some genes were commonly regulated, however >300 genes were differentially regulated by the two isoforms. Functional annotation indicated an enrichment for genes implicate in cellular defense, especially for innate immunity and dsRNA response. Here, we demonstrate that in basal conditions, hnRNP A1, but not hnRNP A1B, represses interferon stimulated genes including the family of dsRNA sensors oligoadenylate synthases (OASs). Thus, the dsRNA-mediated interferon antiviral response can be potentiated by the loss of hnRNP A1-mediated repression. Overall design: RNA-seq library preparation and sequencing Total RNA was extracted from CB3, CB3 A1 and CB3 A1B cells (in triplicate) using TRIzol™ Reagent (Invitrogen) according to the manufacturer's instructions. RNA extracts were purified and concentrated using the RNeasy MinElute cleanup kit (Qiagen) following the manufacturer's instructions. Library preparation and sequencing were performed by the Genome Québec Expertise and Service Center. RNA integrity numbers (RIN), measured on a Bioanalyzer (Agilent), were equal or above 9.7 for all/most samples. For two samples, the Bioanalyzer failed to calculate a RIN number, but manual inspection of the graphs confirmed quality similar to the other samples. An rRNA-depleted stranded (HMR) library was prepared and sequenced via 100 bp paired-end reads on the Illumina NovaSeq 6000 system.