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Generic Features of Tertiary Chromatin Structure as Detected in Natural Chromosomes

Waltraud G. Müller,^1, Dietmar Rieder,^2, Gregor Kreth,³ Christoph Cremer,³ Zlatko Trajanoski,² and James G. McNally^1*

Fluorescence Imaging Group, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, Maryland,¹ Institute for Genomics and Bioinformatics, Christian Doppler Laboratory for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria,² Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany³

Received 12 May 2004/ Returned for modification 21 June 2004/ Accepted 13 August 2004

Knowledge of tertiary chromatin structure in mammalian interphase chromosomes is largely derived from artificial tandem arrays. In these model systems, light microscope images reveal fibers or beaded fibers after high-density targeting of transactivators to insertional domains spanning several megabases. These images of fibers have lent support to chromonema fiber models of tertiary structure. To assess the relevance of these studies to natural mammalian chromatin, we identified two different 400-kb regions on human chromosomes 6 and 22 and then examined light microscope images of interphase tertiary chromatin structure when the regions were transcriptionally active and inactive. When transcriptionally active, these natural chromosomal regions elongated, yielding images characterized by a series of adjacent puncta or "beads", referred to hereafter as beaded images. These elongated structures required transcription for their maintenance. Thus, despite marked differences in the density and the mode of transactivation, the natural and artificial systems showed similarities, suggesting that beaded images are generic features of transcriptionally active tertiary chromatin. We show here, however, that these images do not necessarily favor chromonema fiber models but can also be explained by a radial-loop model or even a simple nucleosome affinity, random-chain model. Thus, light microscope images of tertiary structure cannot distinguish among competing models, although they do impose key constraints: chromatin must be clustered to yield beaded images and then packaged within each cluster to enable decondensation into adjacent clusters.

W.G.M. and D.R. contributed equally to this work.

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