Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments

Area of Science:

• Molecular Biology
• Genomics
• Cancer Research

Background:

• Anti-cancer drugs often target thymidylate biosynthesis, leading to uracil incorporation into DNA.
• The positional preference of this genomic uracil incorporation remains poorly understood.
• Understanding uracil patterns is crucial for elucidating drug mechanisms and resistance.

Purpose of the Study:

• To investigate genome-wide uracil incorporation patterns in human cancer cells (HCT116) after drug treatment.
• To determine if uracil incorporation exhibits positional preferences influenced by anti-cancer drugs.
• To explore the dynamic spatio-temporal nature of genomic uracil.

Main Methods:

• Development and application of a novel U-DNA sequencing method (U-DNA-Seq).
• Integration of U-DNA-Seq with in situ super-resolution imaging (dSTORM microscopy).
• Utilizing a robust analysis pipeline to identify uracil distribution and correlate with chromatin features.

Main Results:

• Identified broad genomic regions with elevated uracil occurrence in both treated and non-treated cells.
• Non-treated cells showed uracil predominantly in late-replicating constitutive heterochromatin.
• Drug treatment induced a significant shift of incorporated uracil towards more active/functional genomic segments.

Conclusions:

• Drug-induced genomic uracil incorporation is not random, showing a distinct positional shift.
• This shift from heterochromatin to active regions upon treatment highlights a novel drug-induced genomic alteration.
• The developed U-DNA-Seq approach combined with imaging offers a powerful tool for studying dynamic genomic uracil patterns.