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Sequence Analysis of the CIS-Regulatory Regions of the Bithorax Complex of Drosophila

(Ultrabithorax/abdominal-A/Abdominal-B/Markov chain/cis regulation)

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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 ≈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 non-protein-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 ≤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.

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Authors and Affiliations

  1. Division of Biology, California Institute of Technology, Pasadena, CA, 91125, USA

    Edward B. Lewis, John D. Knafels, David R. Mathog & Susan E. Celniker

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  1. Edward B. Lewis
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  2. John D. Knafels
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  3. David R. Mathog
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  4. Susan E. Celniker
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Editor information

Editors and Affiliations

  1. Program in Developmental Biology, The Hospital for Sick Children Research Institute, Toronto, Canada

    Howard D. Lipshitz (Senior Scientist and Head, Professor of Molecular and Medical Genetics, Canada Research Chair in Developmental Biology) (Senior Scientist and Head, Professor of Molecular and Medical Genetics, Canada Research Chair in Developmental Biology)

  2. University of Toronto, Toronto, Canada

    Howard D. Lipshitz (Senior Scientist and Head, Professor of Molecular and Medical Genetics, Canada Research Chair in Developmental Biology) (Senior Scientist and Head, Professor of Molecular and Medical Genetics, Canada Research Chair in Developmental Biology)

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Lewis, E.B., Knafels, J.D., Mathog, D.R., Celniker, S.E. (2004). Sequence Analysis of the CIS-Regulatory Regions of the Bithorax Complex of Drosophila . In: Lipshitz, H.D. (eds) Genes, Development and Cancer. Springer, Boston, MA. https://doi.org/10.1007/978-1-4419-8981-9_22

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  • DOI: https://doi.org/10.1007/978-1-4419-8981-9_22

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4613-4746-0

  • Online ISBN: 978-1-4419-8981-9

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