Cell
Volume 163, Issue 1, 24 September 2015, Pages 246-255
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A High-Resolution Imaging Approach to Investigate Chromatin Architecture in Complex Tissues

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Highlights

  • ChromATin allows for 3D analysis of chromatin architecture in complex tissues

  • Low-temperature FISH allows for array tomography localization of nucleic acids

  • Cell-type-specific increase in chromatin compaction is seen in Mecp2-null neurons

  • Spatial reorganization of the H4K20me3 modification accompanies chromatin compaction

Summary

We present ChromATin, a quantitative high-resolution imaging approach for investigating chromatin organization in complex tissues. This method combines analysis of epigenetic modifications by immunostaining, localization of specific DNA sequences by FISH, and high-resolution segregation of nuclear compartments using array tomography (AT) imaging. We then apply this approach to examine how the genome is organized in the mammalian brain using female Rett syndrome mice, which are a mosaic of normal and Mecp2-null cells. Side-by-side comparisons within the same field reveal distinct heterochromatin territories in wild-type neurons that are altered in Mecp2-null nuclei. Mutant neurons exhibit increased chromatin compaction and a striking redistribution of the H4K20me3 histone modification into pericentromeric heterochromatin, a territory occupied normally by MeCP2. These events are not observed in every neuronal cell type, highlighting ChromATin as a powerful in situ method for examining cell-type-specific differences in chromatin architecture in complex tissues.

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