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Molecular and Cellular Biology, September 2005, p. 8379-8386, Vol. 25, No. 18
0270-7306/05/$08.00+0     doi:10.1128/MCB.25.18.8379-8386.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

The Pattern of Chromosome Folding in Interphase Is Outlined by the Linear Gene Density Profile

Alexander M. Boutanaev,{dagger} Lyudmila M. Mikhaylova, and Dmitry I. Nurminsky*

Department of Anatomy and Cellular Biology, Tufts University School of Medicine, Boston, Massachusetts 02111

Received 29 October 2004/ Returned for modification 21 March 2005/ Accepted 11 July 2005

Spatial organization of chromatin in the interphase nucleus plays a role in gene expression and inheritance. Although it appears not to be random, the principles of this organization are largely unknown. In this work, we show an explicit relationship between the intranuclear localization of various chromosome segments and the pattern of gene distribution along the genome sequence. Using a 7-megabase-long region of the Drosophila melanogaster chromosome 2 as a model, we observed that the six gene-poor chromosome segments identified in the region interact with components of the nuclear matrix to form a compact stable cluster. The six gene-rich segments form a spatially segregated unstable cluster dependent on nonmatrix nuclear proteins. The resulting composite structure formed by clusters of gene-rich and gene-poor regions is reproducible between the nuclei. We suggest that certain aspects of chromosome folding in interphase are predetermined and can be inferred through in silico analysis of chromosome sequence, using gene density profile as a manifestation of "folding code."

* Corresponding author. Mailing address: Department of Anatomy and Cellular Biology, Tufts University School of Medicine, 136 Harrison Avenue, MV 509, Boston, MA 02111. Phone: (617) 636-2473. Fax: (617) 636-6536. E-mail: dmitry.nurminsky{at}tufts.edu.

{dagger} Present address: Institute of Basic Problems in Biology, Pushchino 142292, Russia.

Molecular and Cellular Biology, September 2005, p. 8379-8386, Vol. 25, No. 18
0022-538X/05/$08.00+0     doi:10.1128/MCB.25.18.8379-8386.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.





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