Optimal DNA sequence recognition by the Ultrabithorax homeodomain of Drosophila.

The sequence specificity of homeodomain-DNA interaction.

The Drosophila developmental gene, engrailed, encodes a sequence-specific DNA binding activity. Using deletion constructs expressed as fusion proteins in E. coli, we localized this activity to the conserved homeodomain (HD). The binding site consensus, TCAATTAAAT, is found in clusters in the engrailed regulatory region. Weak binding of the En HD to one copy of a synthetic consensus is enhanced ...

A MODEL FOR THE BASIC HELIX- LOOPHELIX MOTIF AND ITS SEQUENCE SPECIFIC RECOGNITION OF DNA

A three dimensional model of the basic Helix-Loop-Helix motif and its sequence specific recognition of DNA is described. The basic-helix I is modeled as a continuous ?-helix because no ?-helix breaking residue is found between the basic region and the first helix. When the basic region of the two peptide monomers are aligned in the successive major groove of the cognate DNA, the hydrophobi...

Discovery, optimization and validation of an optimal DNA-binding sequence for the Six1 homeodomain transcription factor

The Six1 transcription factor is a homeodomain protein involved in controlling gene expression during embryonic development. Six1 establishes gene expression profiles that enable skeletal myogenesis and nephrogenesis, among others. While several homeodomain factors have been extensively characterized with regards to their DNA-binding properties, relatively little is known of the properties of S...

DNA sites . homeodomain protein to nearby and distant Cooperative binding of an Ultrabithorax

A Lexicon for Homeodomain-DNA Recognition

Decoding the cis-regulatory logic of eukaryotic genomes requires knowledge of the DNA-binding specificities of all transcription factors. New work (Berger et al., 2008; Noyes et al., 2008) provides individual specificities for nearly all Drosophila and mouse homeodomains, key DNA-binding domains in many transcription factors. The data underscore the complexity of determining target specificitie...