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. 2011 Apr 6;100(7):1829–1836. doi: 10.1016/j.bpj.2011.02.024

Figure 3.

Figure 3

Comparison of EGFP molecular flow through a change in chromatin density (high-to-low or low-to-high) in a mitotic versus interphase nucleus. (A) Overlay of free EGFP and H2B-mCherry localization in the plane of the 3.3 μm line drawn in a mitotic nucleus. (B) Intensity profile of the H2B-mCherry stain across the line measured in a mitotic nucleus. (C) The pCF(8) carpet derived for intranuclear diffusion between adjacent chromatin density environments in a mitotic nucleus. The green and red arrows indicate positions where diffusion through a change in chromatin density environment is tested. (D–F) A second example of molecular flow in a mitotic nucleus. (G) A plot of the cross correlation function derived from the pCF(8) carpet in panel C for delayed diffusion through a change in chromatin density from the marked arrow positions: in (column 5 in green) and out (column 17 in red) of the chromosome of a mitotic nucleus. (H) Overlay of free EGFP and H2B-mCherry localization in the plane of the 3.3 μm line drawn in an interphase nucleus. (I) Intensity profile of the H2B-mCherry stain across the line measured in an interphase nucleus. (J) The pCF(8) carpet derived for intranuclear diffusion between adjacent chromatin density environments in an interphase nucleus. The orange and cyan arrows indicate positions where diffusion through a change in chromatin density environment is tested. (K–M) A second example of molecular flow in an interphase nucleus. (N) A plot of a cross correlation function derived from the pCF(8) carpet in panel J for the absence of diffusion through a change in chromatin density from the marked arrow positions: in (column 3 in orange) and out (column 18 in cyan) of a high density chromatin bundle. (O) Decomposition of a region corresponding to flow through a change in chromatin density into 5000 line segments for the mitotic and interphase nuclei analyzed, in panels C and F, respectively. As can be seen in the case of interphase (red curve), column 18 which originally appeared as having zero correlation for flow through a change in chromatin density now shows the presence of intermittent periods of communication.