CLIPseq of hnRNP A1 from the spinal cords of mice with experimental autoimmune encephalomyelitis

Experimental autoimmune encephalomyelitis (EAE) is a mouse model for multiple sclerosis (MS) a chronic autoimmune disease of the central nervous system. We have observed dysfunction of the RNA binding protein hnRNP A1 in neurons from the brains of patients with MS, and the spinal cords of mice with EAE. Here, we sought to characterize the consequences of EAE-induced dysfunction of hnRNP A1 on the RNAs it binds by using CLIPseq to establish both the normal central nervous system RNA binding profile of hnRNP A1 in the spinal cords of naive mice, and any alterations to the binding profile of hnRNP A1 in the spinal cords of mice with EAE. n=7 female C57Bl/6 mice were treated with MOG(35-55) at 8 weeks of age to induce experimental autoimmune encephalomeylitis (EAE). At 15 days post-clinical disease onset, mice were scored for disease severity and euthanized, along with n=3 age-matched naïve (healthy) control mice. Spinal cords from each animal were subjected to UV crosslinking, then lysed for immunoprecipitation in the presence of RNaseI with either an anti-hnRNP A1 antibody (each animal) or a control non-binding IgG2a (pooled Naive lysates [n=1] and pooled EAE lysates [n=1]). Input samples were also collected for each animal prior to immunoprecipitation. All samples were subjected to RNAseq, with input samples and pooled IgG2a immunoprecipitation samples providing "background" signal to subtract from the anti-hnRNP A1 immunoprecipitated samples.