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Epigenetics Chromatin. 2017 Aug 7;10(1):39. doi: 10.1186/s13072-017-0146-0.

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

Author information

1
LMU Biocenter, Department Biology II, Ludwig Maximilians-Universität (LMU Munich), Grosshadernerstr. 2, 82152, Martinsried, Germany. Marion.cremer@lrz.uni-muenchen.de.
2
BioImaging Group, Department of Statistics, Ludwig Maximilians-Universität (LMU Munich), Munich, Germany.
3
LMU Biocenter, Department Biology II, Ludwig Maximilians-Universität (LMU Munich), Grosshadernerstr. 2, 82152, Martinsried, Germany.
4
Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, 3800, Australia.
5
Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
6
Department of Genome Sciences, University of Washington, Seattle, WA, USA.
7
Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
8
LMU Biocenter, Department Biology II, Ludwig Maximilians-Universität (LMU Munich), Grosshadernerstr. 2, 82152, Martinsried, Germany. Thomas.Cremer@lrz.uni-muenchen.de.

Abstract

BACKGROUND:

The association of active transcription regulatory elements (TREs) with DNAse I hypersensitivity (DHS[+]) and an 'open' local chromatin configuration has long been known. However, the 3D topography of TREs within the nuclear landscape of individual cells in relation to their active or inactive status has remained elusive. Here, we explored the 3D nuclear topography of active and inactive TREs in the context of a recently proposed model for a functionally defined nuclear architecture, where an active and an inactive nuclear compartment (ANC-INC) form two spatially co-aligned and functionally interacting networks.

RESULTS:

Using 3D structured illumination microscopy, we performed 3D FISH with differently labeled DNA probe sets targeting either sites with DHS[+], apparently active TREs, or DHS[-] sites harboring inactive TREs. Using an in-house image analysis tool, DNA targets were quantitatively mapped on chromatin compaction shaped 3D nuclear landscapes. Our analyses present evidence for a radial 3D organization of chromatin domain clusters (CDCs) with layers of increasing chromatin compaction from the periphery to the CDC core. Segments harboring active TREs are significantly enriched at the decondensed periphery of CDCs with loops penetrating into interchromatin compartment channels, constituting the ANC. In contrast, segments lacking active TREs (DHS[-]) are enriched toward the compacted interior of CDCs (INC).

CONCLUSIONS:

Our results add further evidence in support of the ANC-INC network model. The different 3D topographies of DHS[+] and DHS[-] sites suggest positional changes of TREs between the ANC and INC depending on their functional state, which might provide additional protection against an inappropriate activation. Our finding of a structural organization of CDCs based on radially arranged layers of different chromatin compaction levels indicates a complex higher-order chromatin organization beyond a dichotomic classification of chromatin into an 'open,' active and 'closed,' inactive state.

KEYWORDS:

Active and inactive nuclear compartment; Chromatin compaction; Chromatin domain; DNAse I hypersensitive sites; Nuclear architecture; Super-resolution microscopy; Transcription regulatory sequences

PMID:
28784182
PMCID:
PMC5547466
DOI:
10.1186/s13072-017-0146-0
[Indexed for MEDLINE]
Free PMC Article

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