Mapping DNA glycosylase binding across lesion sequence contexts reveals extended sequence and structural recognition...

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• DNA repair mechanisms are crucial for maintaining genomic integrity.
• Base excision repair (BER) pathway glycosylases identify and remove damaged DNA bases.
• The influence of DNA sequence context on glycosylase recognition and repair outcomes is not fully understood.

Purpose of the Study:

• To develop a high-throughput method for quantifying glycosylase binding to various DNA sequences containing lesions.
• To map the recognition landscapes of human uracil-DNA glycosylase (UDG), thymine DNA glycosylase (TDG), and methyl-CpG-binding domain protein 4 (MBD4).
• To link glycosylase recognition specificity to observed mutation patterns in cancer.

Main Methods:

• Developed a high-throughput sequencing approach to measure glycosylase binding across thousands of DNA sequences with specific lesions.
• Focused on the cytosine deamination pathway.
• Utilized structural analyses and molecular dynamics simulations to investigate DNA-shape features influencing recognition.

Main Results:

• Glycosylase binding is highly dependent on DNA sequence context, extending beyond the immediate lesion site.
• Non-additive interactions between neighboring DNA positions significantly affect binding.
• DNA shape features, such as minor groove width, are critical determinants of glycosylase recognition.
• Observed nearest-neighbor preferences correlate with cancer mutational signatures associated with deamination.
• Broader sequence context preferences align with variations in cytosine-thymine balance in human genomes.

Conclusions:

• The developed platform provides a versatile method for decoding glycosylase recognition.
• Glycosylase specificity is shaped by intricate sequence and structural contexts.
• This research links DNA repair specificity to genome-wide mutational patterns, offering insights into cancer development.