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. Author manuscript; available in PMC: 2021 Feb 18.
Published in final edited form as: Immunity. 2020 Feb 11;52(2):257–274.e11. doi: 10.1016/j.immuni.2020.01.003

Figure 6. Oligopaint 3D FISH corroborates the formation of strain-similar and diabetes-specific hyperconnected 3D cliques.

Figure 6.

H3K27ac-HiChIP contacts in C57BL/6 (black) and NOD (red) at the Bcl11b locus (A), Ets1 locus (E), Idd9.2 locus (I), and Idd6.AM locus (M) with E1 (Enhancer 1, magenta), E2 (Enhancer 2, yellow), and E3 (Enhancer 3, cyan) representing the 3 independent 50kbp genomic regions for which Oligopaint probes were designed. Arrows indicate the linear distance between probes. The probes in the Bcl11b clique spanned a distal enhancer (E1), the noncoding RNA ThymoD (E2), and the Bcl11b gene (E3). The probes in the Ets1 clique spanned the Fli1 gene (E1), the Ets1 gene (E2), and the noncoding RNA Gm27162 (E3). The probes in the Idd9.2 clique spanned a distal enhancer (E1), the Zfp982 (E2) gene, and the Zfp981 gene proximal to Zfp985 gene (E3). The probes in the Idd6.AM clique spanned the Klra19 (E1), Klra7 (E2), and Klra1 (E3) genes. Cumulative distribution plots and box plots of the spatial perimeter formed by the three probes in ~500 cells (see Materials & Methods for exact numbers) per condition per locus at the Bcl11b locus (B), Ets1 locus (F), Idd9.2 locus (J), and Idd6.AM locus (N) (KS: Kolmogorov-Smirnov test & MW: Mann-Whitney test). Models representing the relative spatial perimeter formed by the three probes in C57BL/6 (black) and NOD (red) based on the cumulative distribution and box plots at the Bcl11b locus (C), Ets1 locus (G), Idd9.2 locus (K), and Idd6.AM locus (O). Representative images of the Oligopaint FISH probes in one cell per strain (C57BL/6: black and NOD: red) with magnification of each allele (DAPI: blue, E1: magenta, E2: yellow, E3: cyan, scale bar in whole cell image: 5 μM, & scale bar in magnification of alleles: 1 μM) at the Bcl11b locus (D), Ets1 locus (H), Idd9.2 locus (L), and Idd6.AM locus (P).