Ribosome profiling of Murine Embryonic Fibroblasts in the context of different Fbxo4 and hnRNPK status.

Background: SCF-Fbxo4 is suspected to regulate activity of RNA binding protein hnRNPK by non-degradive ubiquitylation. Research strategy: To determine the genomic output of SCF-Fbxo4 - hnRNPK interplay, murine embryonic fibroblasts (MEFs) with different status of hnRNPK/Fbxo4 were subjected to Ribosome profiling. Sequencing was performed on total RNA and RNA protected by ribosomes for each condition. Overall design: Applying RNAi strategy hnRNPK was depleted in either wild type MEFs or MEFs Fbxo(-/-). MEFs conditioned in 4 different ways: wt- control (I), Fbxo4 knock-out (II), Fbxo4 knock-out + hnRNPK RNAi knock-down (III) and RNAi hnRNPK knock-down only (IV) were subjected to sequencing of total RNA and Ribosome protected fragment.