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Structural basis for specific DNA sequence recognition by the transcription factor NFIL3.
Sizhuo Chen1, Ming Lei1, Ke Liu1
1Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China.
The Journal of Biological Chemistry
|February 21, 2024
Summary
NFIL3, a transcription factor, binds DNA at the TTACGTAA motif. Mutations in NFIL3 disrupt DNA binding, revealing its role in disease pathogenesis and immune cell regulation.
Area of Science:
- Molecular Biology
- Genetics
- Structural Biology
Background:
- CCAAT/enhancer-binding proteins (C/EBPs) are key transcription factors regulating cellular processes.
- NFIL3, a member of the C/EBP family, influences immune cell differentiation, circadian rhythms, and neural regeneration.
- The precise DNA binding mechanism of NFIL3 has remained largely uncharacterized.
Purpose of the Study:
- To elucidate the DNA recognition mechanism of the NFIL3 transcription factor.
- To investigate the structural basis of NFIL3 DNA binding.
- To determine the impact of disease-associated mutations on NFIL3 DNA binding.
Main Methods:
- Isothermal Titration Calorimetry (ITC) for binding affinity measurements.
- X-ray crystallography to determine the structure of the NFIL3 bZIP domain bound to DNA.
- Analysis of disease-associated NFIL3 mutations.
Main Results:
- NFIL3 specifically binds to the TTACGTAA DNA motif.
- Structural analysis revealed NFIL3 dimerizes via its leucine zipper and binds DNA through its basic region, with extended basic regions fitting into DNA major grooves.
- NFIL3 shares DNA binding preference for TTACGTAA with C/EBPα/β.
- Disease-associated mutations in the NFIL3 bZIP domain impair its DNA binding capacity.
Conclusions:
- NFIL3 recognizes and binds the TTACGTAA DNA motif through a specific structural mechanism involving its bZIP domain.
- Shared DNA motif preference between NFIL3 and other C/EBPs suggests conserved regulatory roles.
- Disruption of NFIL3 DNA binding by mutations highlights its critical role in disease pathogenesis.
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