Extended Data Fig. 2: Cytokine–activator-induced S-region transcription promotes dynamic loop formation and S-S synapsis during CSR.
From: Fundamental roles of chromatin loop extrusion in antibody class switching
a, Left, additional repeats of GRO-seq profiles shown in Fig. 1c from non-stimulated and anti-CD40–IL-4-stimulated AID−/− mature splenic B cells. Right, magnified view of the GRO-seq profiles on the left to better reveal the transcription level around the iEμ–Cδ locale from non-stimulated and anti-CD40–IL-4-stimulated AID−/− mature splenic B cells. b, c, Additional repeats of 3C-HTGTS profiles shown in Fig. 1d, e from non-stimulated and anti-CD40–IL-4-stimulated AID−/− mature splenic B cells using iEμ–Iμ (b) or 3′ IgHRR(HS4) (c) locale as baits (blue asterisks). Bar graphs on the right of 3C-HTGTS profiling show the relative iEμ–Iμ or 3′ IgHRR(HS4) interaction frequency with Sγ1 and Sε in anti-CD40–IL-4-stimulated mature splenic B cells. Diagrams on the top of the 3C-HTGTS profiling show the digestion and bait strategies used for the 3C-HTGTS experiments. d, e, 3C-HTGTS profiles of interactions within the 3′ IgH locus domain in anti-CD40–IL-4-stimulated AID−/− mature splenic B cells using the first (d) (two biologically independent repeats) and seventh (e) (three biologically independent repeats) 3′ CBE locale as baits (blue asterisks). Diagrams on the right of the 3C-HTGTS profiling show the digestion and bait strategies used for the 3C-HTGTS experiments. f, g, Additional repeats of NIPBL (f) and RAD21 (g) ChIP–seq shown in Fig. 1f, g from non-stimulated and anti-CD40–IL-4-stimulated AID−/− mature splenic B cells. Bar graphs on the right of the ChIP–seq profiling show NIPBL and RAD21 accumulation of indicated regions. All bar graph data (b, c, f, g) are mean ± s.d. from three biologically independent repeats. P values were calculated via an unpaired two-tailed t-test. All other bars and symbols are as indicated in Fig. 1 legend.
