Extended Data Fig. 9: Regulation of surrogate light-chain genes as well as Irf4, Bcl2l1, and Ikzf1 in early B-cell development.

a, Schematic diagram of the pro-B to pre-B cell transition, which is controlled by signaling of the pre-BCR consisting of the Igμ chain, the surrogate light chains Igll1 (λ5) and Vpreb and the signaling chains Igα and Igβ. Rag1, Rag2, and Dntt expression and the Irf4 and Irf8 upregulation during the large to small pre-B cell transition are shown. b, Schematic diagram of the locus containing Igll1 and Vpreb1. The intron sizes (blue) are indicated in base pairs (bp) and the distance between the Igll1 and Vpreb1 genes in kb. c, Regulation of Vpreb1, Vpreb2, and Vpreb3 in pro-B and small pre-B cells. The abundance of exonic transcript reads was determined by analysis of total RNA-seq data generated for pro-B and small pre-B cells from mice of the indicated genotypes before (–) and after (+) 5-Ph-IAA treatment. The regulation of Vpreb1 and Vpreb2 by Ikaros (8 h), Aiolos (8 h), and Ikaros plus Aiolos (8 h and 12 h) in pre-B cells is shown in the lower panel. The indicated DESeq2-derived fold changes and mean TPM values with SEM are based on two total RNA-seq experiments. The distantly related Vpreb3 protein³⁷ may play only a minor role, if any, in pre-BCR formation, as Vpreb3 cannot compensate for the pre-BCR loss in Vpre1,Vpreb2 double-mutant mice⁸³. d–f, Chromatin accessibility changes at putative enhancers of Irf4 (d), Bcl2l1 (e), and Ikzf1 (f) upon degradation of the indicated TFs in small pre-B cells. Binding of E2A, Ebf1, Pax5, and Ikaros was determined by CUT&RUN in the respective untreated pre-B cells, while open chromatin was determined by ATAC-seq analysis before (–) and after (+) 5-Ph-IAA treatment. A putative E2A- and Pax5-dependent enhancer is located 28 kb upstream of the Irf4 gene.