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Fig. 5 | Epigenetics & Chromatin

Fig. 5

From: Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters

Fig. 5

Scheme and topography of two contiguous 6-kb segments targeting a DHS[+] and adjacent DHS[−] site. A Scheme of probe 1 (green; DHS[+] in BJ1, DHS[−] in A549) and probe 2 (red; DHS[−] both in BJ1 and in A549 cells) in relation to their DHS profiles (black; browser shots adopted from http://encodeproject.org/). BD SIM light-optical sections from 3D acquisitions of different BJ1 nuclei and representative inset magnifications delineating DAPI-stained DNA after intensity classification (shown as gray gradations and as color heat maps) and segmented probe signals (probe 1 green; probe 2 red). Signal positions are shown as outlines in the color heat maps (red signals outlined in black for better visibility). Magnifications reveal the localization of both red and green signals in compartments of low chromatin compaction. Note variability of signal conformation: B elongated signal pair; C signal pair with extended red signal lined by two separate green signals suggestive for ongoing replication; D two compact separate signal pairs <0.5 µm apart suggest two chromatids after replication. A second signal pair (see Additional files 12, 13, 14) is seen in a different section of each nucleus. E, F Same probe setup in A549 cells shows the preferential topology of targeted sites (both DHS[−]) toward the compacted core of a chromatin domain cluster. Scale bar 2 µm, inset 0.5 µm

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