GSE97148
Clonally stable V? allelic choice instructs Ig? repertoire
Although much research has been done to understand how rearrangement of the Ig? locus is regulated during B-cell development, very little is known about the way the variable (V) segments themselves are selected. Using B6/Cast hybrid pre-B cell clones, we show that a limited number of V segments on each allele is stochastically activated as characterized by the appearance of ncRNA and histone modifications. The activation states are clonally distinct, stable across cell division and developmentally important in directing the Ig repertoire upon differentiation. By employing a new approach of allelic ATAC-seq we demonstrate that the Ig? V alleles have differential chromatin accessibility, which may serve as the underlying basis of clonal maintenance at this locus, as well as other instances of monoallelic expression throughout the genome. These findings highlight a new level of immune-system regulation that appears to be geared at optimizing gene diversity. Overall design: ATAC-seq was performed in biological duplicate on mouse pre-B cell clones and pool grown in IL-7 cultures, as well as B220+IgM-CD43-CD25+ bone marrow derived pre-B cells on a C57BL6/Castaneous background. Nuclear enriched total stranded RNA-seq was performed in biological duplicate on the same clones, and B220+IgM-CD43-CD25+ bone marrow derived pre-B cells. Kappa_VJ-seq was performed on  mouse pre-B cell clones and pool where IL7 was removed from culture for 12-48 hours.