Extended Data Fig. 5: RAG cryptic targeting activity from DQ52-RSS-UP and DQ52-RSS-DN in J_HΔ lines.

a, HTGTS V(D)J-seq profile of upstream RAG cryptic scanning activity from DQ52-RSS-UP with indicated peak regions at IGCR1 and D_H3-2 locales (grey transparent bars). Top, junctions plotted at 100-bp bin size. Bottom, examples of most robust peak near IGCR1 (I) and D_H3-2 (II) plotted at single-base-pair resolution. Letters next to the peaks show DNA duplex sequences of the targeted cryptic heptamers. See text for more details. b, HTGTS V(D)J-seq of downstream RAG cryptic scanning activity from DQ52-RSS-DN with indicated peak regions in Sγ2b and 3′ CBEs locales and lower frequency peaks in iEμ-Sμ, D_H3-2 and IGCR1 (grey transparent bars). Top, junctions plotted at 100-bp bin size. Bottom, examples of most robust Sγ2b (III) and 3′ CBEs (IV) locale peaks plotted at single-base-pair resolution.c, Low frequency DQ52-RSS-DN junctions upstream of RC detected by DQ52-RSS-DN bait. Top, expanded views of IGCR1 and D_H3-2 locales in b plotted at 20-bp bin size with representative junctions labelled (V–X). Bottom, single-base-pair resolution plot of junctions for V–X. Deletions are mediated by cryptic RSSs in divergent orientation (forward CAC) and inversions are mediated by cryptic RSSs in the same orientation (reverse CAC) as DQ52-RSS-DN. Also illustrated are junctions resulting from joining DQ52 CEs to cryptic CEs¹², mediated by DQ52-RSS-UP and cryptic convergent RSSs. A likely explanation for these low level joins is that loop extrusion brings them into proximity with the RC where their location or transcription impedes extrusion, allowing them to access RC-bound RAG by local diffusion¹², analogous to diffusion-mediated DQ52-to-J_H1 joining.