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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)
  • Edward B. Lewis
  • John D. Knafels
  • David R. Mathog
  • Susan E. Celniker
Chapter
  • 203 Downloads

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.

Keywords

Genetic Computer Group Perfect Repeat Bithorax Complex Reverse Repeat Pseudorandom Control 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer Science+Business Media New York 2004

Authors and Affiliations

  • Edward B. Lewis
    • 1
  • John D. Knafels
    • 1
  • David R. Mathog
    • 1
  • Susan E. Celniker
    • 1
  1. 1.Division of BiologyCalifornia Institute of TechnologyPasadenaUSA

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