title: Sequence analysis of the cis-regulatory regions of the bithorax complex of Drosophila.
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 approximately 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 < or = 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.
authors.affiliation: Division of Biology, California Institute of Technology, Pasadena 91125, USA.
authors.forename: E B
authors.initials: EB
authors.lastname: Lewis
authors.forename: J D
authors.initials: JD
authors.lastname: Knafels
authors.forename: D R
authors.initials: DR
authors.lastname: Mathog
authors.forename: S E
authors.initials: SE
authors.lastname: Celniker
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D004247:DNA / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics; D004330:Drosophila / Q000235:genetics*; D017344:Genes, Insect; D008969:Molecular Sequence Data; D012045:Regulatory Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA