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Nucleic Acids Research 2005 33(5):1435-1444; doi:10.1093/nar/gki281
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Published online 8 March 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Regulated chromatin domain comprising cluster of co-expressed genes in Drosophila melanogaster

Alla I. Kalmykova, Dmitry I. Nurminsky1, Dmirty V. Ryzhov and Yuri Y. Shevelyov*

Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences Moscow 123182, Russia 1Department of Anatomy and Cell Biology, Tufts University School of Medicine Boston, MA 02111, USA

*To whom correspondence should be addressed. Tel: +7 095 1960809; Fax: +7 095 1960221; Email: shevelev{at}img.ras.ru

Received September 7, 2004. Revised January 24, 2005. Accepted February 15, 2005.

Recently, the phenomenon of clustering of co-expressed genes on chromosomes was discovered in eukaryotes. To explore the hypothesis that genes within clusters occupy shared chromatin domains, we performed a detailed analysis of transcription pattern and chromatin structure of a cluster of co-expressed genes. We found that five non-homologous genes (Crtp, Yu, CK2ßtes, Pros28.1B and CG13581) are expressed exclusively in Drosophila melanogaster male germ-line and form a non-interrupted cluster in the 15 kb region of chromosome 2. The cluster is surrounded by genes with broader transcription patterns. Analysis of DNase I sensitivity revealed ‘open’ chromatin conformation in the cluster and adjacent regions in the male germ-line cells, where all studied genes are transcribed. In contrast, in somatic tissues where the cluster genes are silent, the domain of repressed chromatin encompassed four out of five cluster genes and an adjacent non-cluster gene CG13589 that is also silent in analyzed somatic tissues. The fifth cluster gene (CG13581) appears to be excluded from the chromatin domain occupied by the other four genes. Our results suggest that extensive clustering of co-expressed genes in eukaryotic genomes does in general reflect the domain organization of chromatin, although domain borders may not exactly correspond to the margins of gene clusters.

DDBJ/EMBL/GenBank accession nos+

+AF197938, AY078076 and AY078077


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