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Fig. 5 | BMC Genomics

Fig. 5

From: Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

Fig. 5

3D DNA FISH validations of PE-4Cseq data. a 3D DNA FISH strategy used. Green and red triangles represent query probes along the chromatin fiber separated at fixed distances. The white triangle represents the deletion probe. Red/green probes can also be located bordering the deletion probe. The Df chromosome is distinguished by the absence of the deletion probe, as shown in the nuclear representations of Df/+  Bl6 D and +129/+Bl6 genotypes. b Projection of a 3D DNA FISH image for control BACset4 using Df/+  Bl6 D MEFs. Red and green probes are the query probes, while white probe is the deletion probe. Hybridization images are zoomed inside white rectangles. Note the absence of the deletion probe for one of the chromosomes, classified as Df with our algorithm (dashed rectangle). c Representative 3D DNA FISH image projections for +129/+Bl6 and Df/+  Bl6 D nuclei for BACset2 probes. Probe colors are as described in b. Df chromosome probes are shown inside the white dashed rectangle, and WT probes shown in rectangle. d Query probe distance distributions for BACset2 (brown underline in Fig. 5e) for both +129/+Bl6 chromosomes (left panel) and Df (right panel). The black line indicates the model fit to the probability mass function (PMF). Notice the increase in typical spatial separations as well as a broader distribution in Df, in agreement with the observed decrease in contact probabilities in PE-4Cseq. e Rainbow plot of the zoomed in region near the deletion in Df chromosome. Enrichment and depletion of long-range interactions are color coded as in Fig. 3. The black arrows represent viewpoint positions; dashed box of the chromosome bar is the deletion region; the three distinct colored boxes are the three query probe pairs, also identified by numbers; the dashed rectangle inside the deletion region is the deletion probe. The dashed triangles represent query probe interaction changes as detected from FISH experiments, with enrichment in red and depletion in blue with associated proportional changes in interaction reported as percentages. Notice the agreement between enrichment (red) and depletion (blue) between PE-4Cseq and DNA FISH interactions

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