Fig. 3: Long-range DNA loops reveal a complex chromatin complex in PFA ependymomas. | Nature Communications

Fig. 3: Long-range DNA loops reveal a complex chromatin complex in PFA ependymomas.

From: 3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma

Fig. 3: Long-range DNA loops reveal a complex chromatin complex in PFA ependymomas.The alternative text for this image may have been generated using AI.

a Hi-C DNA interaction matrices wherein a ~5 million base pair segment of chromosome 2 is aligned along the diagonals shown for PFA (9EP1, left) and ZFTA (4EP53, middle) tumors and normal cerebellum astrocytes (CAs, right). b Hi-C DNA interactions of a PFA tumor (sample BT214) wherein the same ~5 million base pair segment of chromosome 2 shown in panel (a) is aligned horizontally. Circles and dashed lines highlight long-range DNA interactions. c Genome browser view of the PFA-specific chromatin cluster shown in panels (a) and (b). The included data tracks show DNA interactions in PFA and ZFTA tumors via loops. Tracks for RNA-seq, H3K27ac and Hi-C derived DNA loop were obtained from merging PFA (9EP1,9EP9, 7EP18) or ZFTA (11EP22, 4EP53, 7EP41) samples, respectively. Differential specificity of the PFA loop is confirmed from statistical comparison (adjusted p-val 0.0089) via DiffLoop tool. d–f Genetic (CRISPR-Cas9) time-course inhibition of MAP3K20 in one PFA EPD210FH (d) and ZFTA EP1NS (e) and VBT372 (f) cell lines. Changes in the percentage of GFP positive cells are presented after normalization. GFP percentage was normalized to day 4 post infection and presented as day 0. Normalized data represent mean from n = 2 independent experiments in cell lines EPD210FH, EP1NS and mean ± SD for n = 3 independent experiments for VBT373. g EPD210FH and EP1NS cells are treated with the MAP3K20 inhibitor (M443) for 6 days and cell viability is measured by CellTiterGlo assay and IC50 value is calculated by GraphPAD as respectively, 16, 7 and 37, 5 uM. Error bars represent mean ± SD, n = 3 biological replicates are used for all experiments. h, i Genetic (CRISPR-Cas9) time-course inhibition of ITGA6 in PFA EPD210FH (h) and RELA EP1NS (i) cells using a control sgRNA and two individual sgRNA constructs. All constructs are GFP tagged and GFP positive cells are sorted by FACS. Normalized data represent mean from n = 2 independent experiments in each cell line.

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