Global organization of the B cell genome by the transcription factor Pax5 [Hi-C]

We used genome-wide in situ Hi-C to show that different immune cell populations display distinct chromatin architecture and that the transcription factor Paired box 5 (Pax5) is critical for the lineage-specific architecture of B cells. Hi-C was undertaken for mouse CD4+ T cells, transitional & marginal zone (Tr/MZ) B cells, granulocytes, LSKs, MEFs, pro-B cells, Pax5-/- pro-B cells, follicular B cells, activated B cells and plasmablasts. Also used was a Pax5-/- pro-B cell line with a Pax5:ER fusion construct allowing Pax5 to be reintroduced to the nucleus. The Pax5:ER cells were either untreated, treated with b-estradiol to reintroduce Pax5, or treated with both b-estradiol and a-amanitin to reintroduce Pax5 but prevent further transcription. Two biological replicates were conducted for each cell type and each treatment condition, except for pro-B cells and Pax5-/- prob-B cells, for which three replicates were performed.