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Vol 13, Issue 4, 579-588, April 2003

LETTER

Homotypic Regulatory Clusters in Drosophila

Alexander P. Lifanov1, Vsevolod J. Makeev2, Anna G. Nazina3 and Dmitri A. Papatsenko3,4

1Institute of Chemical Physics, Moscow, 117421 Russia; 2Scientific Center "Genetika," Moscow, 113545 Russia; 3Department of Biology, New York University, New York, New York 10003-6688, USA

Cis-regulatory modules (CRMs) are transcription regulatory DNA segments (~1 Kb range) that control the expression of developmental genes in higher eukaryotes. We analyzed clustering of known binding motifs for transcription factors (TFs) in over 60 known CRMs from 20 Drosophila developmental genes, and we present evidence that each type of recognition motif forms significant clusters within the regulatory regions regulated by the corresponding TF. We demonstrate how a search with a single binding motif can be applied to explore gene regulatory networks and to discover coregulated genes in the genome. We also discuss the potential of the clustering method in interpreting the differential response of genes to various levels of transcriptional regulators.

4 Corresponding author.

E-MAIL dap5{at}nyu.edu; FAX (212) 995-4710.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.668403.


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