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Markaki, Y.* ; Gunkel, M.* ; Schermelleh, L.* ; Beichmanis, S.* ; Neumann, J.* ; Heidemann, M. ; Leonhardt, H.* ; Eick, D. ; Cremer, C.* ; Cremer, T.

Functional nuclear organization oft transcription and DNA replication: A topographical marriage between chromatin domains and the interchromatin compartment.

Cold Spring Harb. Symp. Quant. Biol. 75, 475-492 (2011)
DOI PMC
We studied the nuclear topography of RNA transcription and DNA replication in mammalian cell types with super-resolution fluorescence microscopy, which offers a resolution beyond the classical Abbe/Raleigh limit. Three-dimensional structured illumination microscopy (3D-SIM) demonstrated a network of channels and wider lacunas, called the interchromatin compartment (IC). The IC starts at nuclear pores and expands throughout the nuclear space. It is demarcated from the compact interior of higher-order chromatin domains (CDs) by a 100-200-nm thick layer of decondensed chromatin, termed the perichromatin region (PR). Nascent DNA, nascent RNA, RNA polymerase II (RNA Pol II), as well as histone modifications for transcriptionally competent/active chromatin, are highly enriched in the PR, whereas splicing speckles are observed in the interior of the IC. In line with previous electron microscopic evidence, spectral precision distance/position determination microscopy (SPDM) confirmed the presence of RNA Pol II clusters indicative of transcription factories. Still, a substantial part of transcription apparently takes place outside of such factories. Previous electron microscopic evidence has suggested that the functional nuclear organization of DNA replication depends on Brownian movements of chromatin between the CD interior and the PR. As an incentive for future studies, we hypothesize that such movements also take place during transcription, i.e., only the actually transcribed part of a gene may be located within the PR, whereas its major part, including previously or later transcribed sequences, is embedded in a higher-order chromatin configuration in the interior of the CD.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords no keywords
ISSN (print) / ISBN 0091-7451
e-ISSN 1943-4456
Journal Cold Spring Harbor Symposia on Quantitative Biology
Quellenangaben Volume: 75, Issue: , Pages: 475-492 Article Number: , Supplement: ,
Publisher Cold Spring Harbor Laboratory Press
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Clinical Molecular Biology and Tumor Genetics (K.MOLBI)