Dynamic changes in chromatin accessibility and nucleosome positioning in the control of antigen receptor rearrangement

Developing lymphocytes diversify their antigen receptor (AgR) loci by V(D)J recombination. Here, we use a low-input version of the MACC (MNase Accessibility) assay to define the chromatin accessibility landscape of primary cells during lymphoid development tracking the changes as different AgR loci become primed for recombination. Distinct chromatin structures define unique features of IgH, Igk and TCRa loci. In particular, we find locus-specific temporal changes in accessibility both across megabase-long AgR loci and locally at the recombination signal sequences (RSSs). These changes appear to be regulated independently. We further identify local dynamic rearrangements of individual nucleosomes at RSSs during B-cell commitment. As predicted by the original “accessibility” hypothesis, these changes correlate with AgR lymphoid lineage and developmental-stage specificity. We suggest that local and global changes in chromatin openness, in concert with nucleosome occupancy and histone modifications, represent additional regulatory layers for governing the temporal order of AgR recombination. Overall design: MNase-seq profiles of hematopoietic stem cells (HSCs); lymphoid-primed multipotent progenitors (LMPPs); common lymphoid “A” type precursors (ALPs or CLPs); B cell–biased lymphoid progenitors (BLPs); B-cell progenitors (pro-B); large B-cell precursors (Lpre-B); and small B-cell precursors (small pre-B). Lung epithelium cells (LungEp) were used as nonlymphoid and recombinationally inactive cells. Wild-type C57BL/6N mice (4-6 weeks old) were used to isolate the above cell populations.