RNA-sequencing in MCL cell lines after silencing cyclin D1

Mantle cell lymphoma (MCL) is an aggressive B-cell neoplasm characterized by the t(11;14)(q13;q32) translocation leading to cyclin D1 overexpression. Cyclin D1 is a major cell cycle regulator and also has a role in transcription, but the effect of the latter in tumorigenesis remains largely unknown. Here, we investigated the transcriptional role of cyclin D1 in MCL and its impact on the pathogenesis of this neoplasm. Integrating genome-wide expression analysis of cyclin D1-silenced and overexpressing cells with cyclin D1 chromatin binding profiles, we identified a cyclin D1-activated transcriptional program in MCL cells. Overall design: We generated cyclin D1 silenced MCL cell lines (in Granta-519 and JeKo-1) by shRNA. We then performed RNA-sequencing experiments in shCyclinD1 (shCycD1) and control (shCtrl) cells to analyze the cyclin D1-dependent genome-wide expression modulation. Three biological replicates were included in the experiment.