PARCLIP analysis of NONO and SFPQ from U2OS and Hela cells

To identify the RNA targets of the RNA binding proteins NONO and SFPQ in two different cell types, PARCLIP was carried out (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) using a monoclonal antibody that recognises a NONO/SFPQ heterodimer. In this analysis, only the target gene NEAT1 was analysed, to show the binding sites for NONO and SFPQ in this transcript in the two cell lines. HeLa and U2OS cells were cultured and crosslinked according to the PARCLIP protocol. An antibody that pulls down the NONO/SFPQ heterodimer was used to purify these specific complexes. One replicate sample in each case was sequenced and analysed. Analysis of Neat1_2 regions that bind the paraspeckle proteins NONO and SFPQ was performed