RAG1, RAG2, and H3K4me3 ChIP-seq data are shown for (A)
Rag1,
(B)
Cd8a,
(C)
Ets2,
(F)
Notch1, and (G)
Bcl11b in WT mouse thymocytes. The 12-cRSSs and 23-cRSSs are indicated by open and filled triangles, respectively. Small arrows represent PCR primers used to assay for RAG-dependent deletions or inversions, and thick lines represent gene bodies. (D and E) The intrinsic recombination activity of selected cRSSs was assayed using a plasmid substrate, diagrammed above each panel. Arrows, PCR primers for recombination assay; position 1, reference cRSS (either the Lmo2 12-cRSS or a modified Ttg1 23-cRSS, open triangle); position 2, test 12- or 23-cRSS (red open triangle); position 3, appropriate consensus partner RSS (filled black triangle). Recombination activity (mean +SEM) of each test cRSS is shown relative to that of the reference cRSS. RAG-mediated deletions at the mouse (H)
Notch1 and (I)
Bcl11b loci were detected using a nested PCR assay. The frequency of deletions (mean ±SEM) is shown for WT, Rag1−/−, Atm−/−, H2ax−/, Mdc1−/−, and P53−/− thymocytes. Each point represents data generated from one mouse. Unpaired t-test, *p ≤ 0.05, *** p ≤ 0.001, ns = not significant. See also Figure S4 and Table S3.