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Sequence analysis of the cis-regulatory regions of the bithorax complex of Drosophila

Lewis, Edward B. and Knafels, John D. and Mathog, David R. and Celniker, Susan E. (1995) Sequence analysis of the cis-regulatory regions of the bithorax complex of Drosophila. Proceedings of the National Academy of Sciences of the United States of America, 92 (18). pp. 8403-8407. ISSN 0027-8424. http://resolver.caltech.edu/CaltechAUTHORS:LEWpnas95

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Abstract

The bithorax complex (BX-C) of Drosophila, one of two complexes that act as master regulators of the body plan of the fly, has now been entirely sequenced and comprises approximate to 315,000 bp, only 1.4% of which codes for protein. Analysis of this sequence reveals significantly overrepresented DNA motifs of unknown, as well as known, functions in the nonprotein-coding portion of the sequence. The following types of motifs in that portion are analyzed: (i) concatamers of mono-, di-, and trinucleotides; (ii) tightly clustered hexanucleotides (spaced less than or equal to 5 bases apart); (iii) direct and reverse repeats longer than 20 bp; and (iv) a number of motifs known from biochemical studies to play a role in the regulation of the BX-C. The hexanucleotide AGATAC is remarkably overrepresented and is surmised to play a role in chromosome pairing. The positions of sites of highly overrepresented motifs are plotted for those that occur at more than five sites in the sequence, when <0.5 case is expected. Expected values are based on a third-order Markov chain, which is the optimal order for representing the BXCALL sequence.


Item Type:Article
Additional Information:Copyright © 1995 by the National Academy of Sciences. Contributed by Edward B. Lewis, June 19, 1995. We thank Mary Raney, Victor Hsu, Mallory Zhang, Gretl Hornung, and John Hubenschmidt for assistance in running the computer programs. We thank Welcome Bender, Howard Lipshitz, and Joanne Topol for critical reading of the manuscript. This work was supported by research grants to E.B.L. from the March of Dimes and from the National Institutes of Health (HD06331 and HD30727). The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.
Subject Keywords:Ultrabithorax, abdominal-A, Abdominal-B, Markov chain, cis regulation
Record Number:CaltechAUTHORS:LEWpnas95
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:LEWpnas95
Alternative URL:http://www.pnas.org/cgi/content/abstract/92/18/8403
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:1467
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:21 Jan 2006
Last Modified:26 Dec 2012 08:44

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