Engineering intrinsically disordered regions for guiding genome navigation.

Area of Science:

• Molecular Biology
• Genomics
• Biophysics

Background:

• Intrinsically disordered regions (IDRs) are crucial for the function of many proteins, including transcription factors (TFs).
• The mechanisms by which IDRs within TFs mediate specific genome recognition remain incompletely understood.
• Understanding IDR sequence determinants is key to deciphering TF-genome interactions.

Purpose of the Study:

• To define the principles governing how intrinsically disordered region (IDR) sequences encode for specific genome recognition.
• To investigate the role of hydrophobic amino acid distribution within IDRs for directing transcription factor binding.
• To engineer novel IDRs capable of selective genome targeting.

Main Methods:

• Design and synthesis of 185 de novo intrinsically disordered regions (IDRs).
• Systematic variation of hydrophobic amino acid dispersion and disorder scaffold properties.
• Genome-wide binding analysis in budding yeast to assess target specificity of synthetic IDRs.

Main Results:

• De novo designed IDRs, lacking sequence similarity to native TFs, demonstrated activity in directing genome binding.
• The binding specificity of synthetic IDRs was tunable by altering hydrophobic spread and disorder scaffold.
• A continuum of sequence-directed binding preferences was observed across hundreds of yeast promoters.

Conclusions:

• IDR sequences can encode specific genome recognition principles independent of sequence homology to native factors.
• The spatial distribution of hydrophobic residues within a hydrophilic scaffold is a key determinant of IDR-mediated binding specificity.
• These findings provide a foundation for understanding and engineering selective DNA-binding proteins.