# Reversing chromatin accessibility differences that distinguish homologous mitotic metaphase chromosomes

## TL;DR

The study finds that differences in chromatin accessibility between homologous chromosomes during mitosis can be reversed by inhibiting topoisomerase IIα, suggesting these differences are due to DNA superhelicity and chromosome condensation.

## Contribution

The study reveals that differential chromatin accessibility in metaphase is caused by DNA superhelicity and can be reversed by topoisomerase IIα inhibition, not by epigenetic marks.

## Key findings

- Inhibition of topoisomerase IIα-DNA cleavage complex reverses differential accessibility (DA) in metaphase chromosomes.
- Differential accessibility is not affected by histone modification or cytosine methylation treatments.
- DA reflects allelic differences in chromosome compaction and DNA superhelicity, not epigenetic marks.

## Abstract

Chromatin-modifying reagents that alter histone associating proteins, DNA conformation or its sequence are well established strategies for studying chromatin structure in interphase (G1, S, G2). Little is known about how these compounds act during metaphase. We assessed the effects of these reagents at genomic loci that show reproducible, non-random differences in accessibility to chromatin that distinguish homologous targets by single copy DNA probe fluorescence in situ hybridization (scFISH). By super-resolution 3-D structured illumination microscopy (3D-SIM) and other criteria, the differences correspond to ‘differential accessibility’ (DA) to these chromosomal regions. At these chromosomal loci, DA of the same homologous chromosome is stable and epigenetic hallmarks of less accessible interphase chromatin are present.

To understand the basis for DA, we investigate the impact of epigenetic modifiers on these allelic differences in chromatin accessibility between metaphase homologs in lymphoblastoid cell lines. Allelic differences in metaphase chromosome accessibility represent a stable chromatin mark on mitotic metaphase chromosomes. Inhibition of the topoisomerase IIα-DNA cleavage complex reversed DA. Inter-homolog probe fluorescence intensity ratios between chromosomes treated with ICRF-193 were significantly lower than untreated controls. 3D-SIM demonstrated that differences in hybridized probe volume and depth between allelic targets were equalized by this treatment. By contrast, DA was impervious to chromosome decondensation treatments targeting histone modifying enzymes, cytosine methylation, as well as in cells with regulatory defects in chromatid cohesion. These data altogether suggest that DA is a reflection of allelic differences in metaphase chromosome compaction, dictated by the localized catenation state of the chromosome, rather than by other epigenetic marks.

Inhibition of the topoisomerase IIα-DNA cleavage complex mitigated DA by decreasing DNA superhelicity and axial metaphase chromosome condensation. This has potential implications for the mechanism of preservation of cellular phenotypes that enables the same chromatin structure to be correctly reestablished in progeny cells of the same tissue or individual.

The online version of this article (doi:10.1186/s13039-015-0159-y) contains supplementary material, which is available to authorized users.