GSE124605
Ago2 PAR-CLIP analysis of Abelson kinase transformed murine B cell progenitors
Knockout of the ubiquitously expressed microRNA-17~92 cluster in mice produces a lethal developmental defect and blocked B lymphopoiesis. We validated the equally widely expressed Bcl2l11 gene as joint target of miR-17~92 cluster members. Bcl2l11 encodes the pro-apoptotic protein BIM, central to life-death decisions in most mammalian cells. To study the contribution of miR-17~92:Bim interaction to miR-17~92 overall function, we set up a system of conditional mutagenesis of the Bim 3'UTR in mice. Ago2 Photoactivatable-Ribonucleoside Cross-linking and Immunoprecipitation (AGO2 PAR-CLIP) allowed us to assess whether the seed match mutations introduced into the Bim 3'UTR in vivo indeed precluded interaction with the miRNAs of the 17~92 cluster. This analysis was done in Abelson Virus transformed B cell progenitors which we generated from wild type and Bim3'UTRmut/mut E14.5 fetal livers, knowing that these cells express both BIM and miR-17~92, can be expanded to large numbers and incorporate 4-thiouridine sufficiently well. Focusing on 21 nt windows around the 9 putative miR-17~92 seed matches in the Bim 3'UTR and excluding reads lacking T-to-C transitions, we we verified that the introduced mutationsare functional, and we discovered differential seed match coverage in the wild type, with one miR-19 seed match co-dominating with two miR-92 seed matches, while in the mutant 3'UTR miR-17~92 binding was completely abolished. These results demonstrate functionality and efficiency of our genetically engineered mouse model for in vivo conditional seed-match inactivation.  These results demonstrate functionality and efficiency of our genetically engineered mouse model for in vivo conditional seed-match inactivation. Overall design: Identification of miRNA binding sites by Ago2 PAR-CLIP using 4-Thiouridine treatment in n=2 wild type Abelson transformed B cells  vs. n=2 Bim3'UTRmut/mut Abelson transformed B cells, cultivated in vitro.