Revealing Cell-Type Specific Differences in Protein Occupancy on RNA

In our previous work we profiled protein occupancy on polyadenylated RNA in HEK293 cells (Baltz et al. 2012). To globally assess differences in protein-RNA contacts in different cell types and their impact on RNA metabolism, we performed protein occupancy profiling in MCF7 cells (Fig. 4.1a, b). MCF7 cells are estrogen receptor positive mammary epithelial adenocarcinoma cells, which are widely used as a cell culture based breast cancer model (Charafe-Jauffret et al. 2006; Lacroix and Leclercq 2004; Levenson and Jordan 1997; Soule et al. 1973).