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Updated: Jun 10, 2026
13:54
Whole Mount in Situ Hybridization of E8.5 to E11.5 Mouse Embryos
Published on: October 10, 2011
Changes in chromatin structure during processing of wax-embedded tissue sections
Elizabeth Kerr1, Tomoharu Kiyuna, Shelagh Boyle
1Breakthrough Breast Cancer Research Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
Summary
Investigating nuclear organization using immunofluorescence (IF) and fluorescence in situ hybridisation (FISH) in fixed tissues reveals that processing steps significantly alter nuclear architecture and chromatin texture.
Area of Science:
- Cell Biology
- Molecular Biology
- Genomics
Background:
- Immunofluorescence (IF) and fluorescence in situ hybridisation (FISH) are key techniques for studying nuclear and chromatin organization.
- Current research emphasizes the need to study nuclear organization in situ within native tissue architecture, moving beyond cultured cells.
- Formalin-fixed paraffin-embedded (FFPE) tissues are crucial for analyzing archival clinical samples but require additional processing for IF and FISH.
Purpose of the Study:
- To quantify structural changes in the nucleus and chromatin caused by processing steps required for IF and FISH on FFPE tissues.
- To assess the impact of specific treatments, such as microwave antigen retrieval, on nuclear architecture and chromatin texture.
- To inform the interpretation of nuclear organization data derived from FFPE tissue sections.
Main Methods:
- Analysis of nuclear and chromatin structure in FFPE tissue sections subjected to various processing treatments.
- Quantification of structural alterations using microscopy and potentially image analysis techniques.
- Comparison of structural features before and after specific retrieval methods, including microwaving.
Main Results:
- Processing steps, particularly microwaving for fixation reversal, significantly alter nuclear architecture.
- Chromatin texture undergoes notable changes due to the applied treatments.
- These alterations impact the fidelity of nuclear organization studies using FFPE samples.
Conclusions:
- The processing of FFPE tissues for IF and FISH introduces significant changes to nuclear and chromatin structure.
- Researchers must carefully consider these induced alterations when interpreting nuclear organization data from FFPE samples.
- Understanding these modifications is critical for accurate analysis of nuclear organization in native tissue contexts.
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