Transcription factors ERα and Sox2 have differing multiphasic DNA- and RNA-binding mechanisms

Area of Science:

• Molecular Biology
• Biophysics
• Biochemistry

Background:

• Transcription factors (TFs) are known to bind RNA, but the mechanisms and regulatory roles are not fully understood.
• Investigating TF-nucleic acid interactions is crucial for understanding gene regulation.
• Previous studies have not fully elucidated the kinetics of TF binding to both DNA and RNA.

Purpose of the Study:

• To investigate the binding kinetics (association rate, dissociation rate, and binding affinity) of two human TFs, ERα and Sox2, to both DNA and RNA.
• To elucidate the underlying mechanisms of TF-nucleic acid interactions.
• To explore the role of RNA binding in regulating TF activities.

Main Methods:

• Utilized biophysical assays to measure the on-rate (k_on), off-rate (k_off), and dissociation constant (K_d) for TF-nucleic acid binding.
• Analyzed binding kinetics for ERα and Sox2 with both DNA and RNA.
• Employed kinetic modeling and simulations to interpret observed binding behaviors.

Main Results:

• Both ERα and Sox2 exhibited unexpected multiphasic binding kinetics for nucleic acids.
• Sox2 binding kinetics were explained by sequential monomer association and dissociation.
• ERα displayed novel triphasic association and biphasic dissociation kinetics, not explained by conventional models, suggesting a unique reaction mechanism involving isomerization and feedback.

Conclusions:

• Sox2 and ERα demonstrate complex, multiphasic binding kinetics to both RNA and DNA.
• ERα utilizes a novel reaction mechanism for nucleic acid binding, distinct from conventional models.
• These findings reveal previously unappreciated complexities in TF-nucleic acid interactions and their regulatory potential.