Exploring the DNA-recognition potential of homeodomains

UMMS Affiliation

Program in Gene Function and Expression; Department of Biochemistry and Molecular Pharmacology; Program in Bioinformatics and Integrative Biology; Program in Molecular Medicine

Publication Date


Document Type



Homeodomain Proteins


Genetics and Genomics


The recognition potential of most families of DNA-binding domains (DBDs) remains relatively unexplored. Homeodomains (HDs), like many other families of DBDs, display limited diversity in their preferred recognition sequences. To explore the recognition potential of HDs, we utilized a bacterial selection system to isolate HD variants from a randomized library that are compatible with each of the 64 possible 3' triplet sites (i.e. TAANNN). The majority of these selections yielded sets of HDs with overrepresented residues at specific recognition positions, implying the selection of specific binders. The DNA-binding specificity of 151 representative HD variants was subsequently characterized, identifying HDs that preferentially recognize 44 of these target sites. Many of these variants contain novel combinations of specificity determinants that are uncommon or absent in extant HDs. These novel determinants, when grafted into different HD backbones, produce a corresponding alteration in specificity. This information was used to create more explicit HD recognition models, which can inform the prediction of transcriptional regulatory networks for extant HDs or the engineering of HDs with novel DNA-recognition potential. The diversity of recovered HD recognition sequences raises important questions about the fitness barrier that restricts the evolution of alternate recognition modalities in natural systems.

DOI of Published Version



Genome Res. 2012 Apr 26. [Epub ahead of print] doi 10.1101/gr.139014.112

Journal/Book/Conference Title

Genome research

Related Resources

Link to article in PubMed

PubMed ID