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Structural basis for cell type specific DNA binding of C/EBPβ: The case of cell cycle inhibitor p15INK4b promoter

George T Lountos1, Scott Cherry2, Joseph E Tropea2

  • 1Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.

Journal of Structural Biology
|November 7, 2022
PubMed

Insights

CCAAT-enhancer-binding protein beta (C/EBPβ) binding specificity is influenced by DNA sequence variations near its binding sites. These variations affect gene regulation and epigenetic modifications, impacting cellular processes and disease.

Area of Science:

  • Molecular Biology
  • Epigenetics
  • Gene Regulation

Background:

  • CCAAT-enhancer-binding protein beta (C/EBPβ) is a transcription factor regulating cellular processes, with roles in tumorigenesis and viral diseases.
  • Cell-type-specific gene regulation is often determined by the precise DNA sequence of transcription factor binding motifs.
  • C/EBPβ acts as a cofactor in TGFβ signaling for p15INK4b induction in human epithelial cells, involving Smad and FoxO factors.

Purpose of the Study:

  • To investigate how variations in C/EBPβ binding sites influence its specificity and interaction with DNA.
  • To elucidate the structural basis for altered C/EBPβ binding to a non-canonical motif in the p15INK4b promoter.
  • To understand the impact of DNA sequence and epigenetic modifications on C/EBPβ binding and gene regulation.

Main Methods:

  • X-ray crystallography to determine the structure of C/EBPβ bound to the p15INK4b promoter fragment.
  • Analysis of DNA sequence variations and their effect on protein-DNA interactions.
  • Investigation of the role of DNA minor groove width and dinucleotides in C/EBPβ recognition.
  • Assessment of C/EBPβ binding to modified cytosine bases (methylation and hydroxymethylation) in different sequence contexts.

Main Results:

  • A specific C/EBPβ binding site (CTTAA•GAAAG) in the p15INK4b promoter differs from the canonical motif.
  • Structural analysis revealed that GCGC-to-AAGA substitutions enhance C/EBPβ binding specificity and alter epigenetic regulation.
  • CT/GA dinucleotides at the 5' ends of the binding element are crucial for DNA minor groove narrowing and recognition.
  • C/EBPβ accepts all modified cytosines at CpT sites, unlike its response to methylation/hydroxymethylation at the consensus motif.

Conclusions:

  • Local DNA sequence variations significantly modulate C/EBPβ binding specificity and downstream regulatory effects.
  • The structural and epigenetic landscape of C/EBPβ binding sites dictates its functional outcomes in gene regulation.
  • Understanding these sequence-specific interactions is critical for comprehending C/EBPβ's role in normal cellular processes and diseases like cancer.
Keywords:
Binding site specificityC/EBPβ-DNA interactionsDNA methylationDNA sequence motifDNA shape recognitionGenomic occupancy

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