Identification of nucleic acids that supports protein renaturation. Homo sapiens

Many proteins require RNA to remain soluble in cell and tissue lysate. Here we used RNA- and DNA- immunoprecipitation to identify what types of nucleic acids are associated with these proteins after in vitro renaturation. Overall design: RNAse-aggregated proteins were renatured with pre-fragmented genomic DNA or total RNA. After removal of insoluble (re-aggregated) proteins, the soluble fraction was subjected to immunoprecipitation or membrane capture. Each IP was done twice on different material and include IP with IgG or GFP antibodies as controls for the RNA and the DNA, respectively. Membrane capture were performed twice on biological replicates but only once for the negative control. RNA-seq on RNA-immunoprecipitated with antibodies to Abeta, neurofilament heavy chain and Tau in lysate from human neurons. Two biological replicates of each IP were analysed, except for Abeta, where only one sample were available. Significantly associated transcripts were identified by comparing read densities in IP-samples to read densities in samples immunoprecipitated with non-specific IgG antibodies.