RNA-seq and in situ Hi-C of primary mouse B cell progenitor populations after activation with LPS

During cellular differentiation, chromosome conformation is intricately remodelled to support the lineage-specific transcriptional programs required for initiating and maintaining lineage identity. When these changes occur in relation to cell cycle, division and time is unclear although it has been proposed they would occur during DNA synthesis 5 or after mitosis. Here we elucidate the chromosome conformational changes in B lymphocytes as they differentiate and massively expand from a naïve, quiescent state into antibody secreting plasma cells. Unexpectedly, we find dramatic gene-regulatory chromosome reorganization in late G1 phase prior to the first division, and that this configuration is remarkably stable as the cells massively 10 and rapidly clonally expansion. A second wave of conformational change occurs as cells terminally differentiate into plasma cells, coincident with increased time in G1 phase. In this study we stimulated naive B cells with LPS and harvested activated B cells or plasmablasts at different time points after stimulation. RNA-seq was used to profile gene expression and in situ Hi-C was used to profile DNA-DNA interactions at each time point. Naive resting B-cells were purified from the bone marrow of C57BL/6 mice using flow cytometry sorting. Naive B cells were activated with LPS and harvested 3 hours, 10 hours or 33 hours after the LPS treatment. Expanded activated B cells (CD22+ CD138-) and plasmablasts (CD22- CD138+) were also harvested on day 4 post-stimulation. Two biological replicates from different mice were prepared of each cell population.