Break-induced replication plays a prominent role in long-range repeat-mediated deletion

Area of Science:

• Genetics
• Molecular Biology
• Cancer Research

Background:

• Repetitive DNA sequences are implicated in chromosomal rearrangements in cancers.
• Single-strand annealing (SSA) is the conventionally accepted mechanism for homology-directed repair of double-strand breaks (DSBs) between repeats, leading to repeat-mediated deletion (RMD).

Purpose of the Study:

• To investigate the predominant mechanism mediating repeat-mediated deletion (RMD) in mammalian cells.
• To compare the efficiency of break-induced replication (BIR) and SSA in RMD, particularly concerning repeat distance and DSB type.

Main Methods:

• Investigated RMD mechanisms in mammalian cells using assays to differentiate between SSA and BIR.
• Analyzed the impact of repeat distance, oncogene expression, DSB type (single-ended vs. double-ended), H2AX, and sequence divergence on RMD pathways.

Main Results:

• Break-induced replication (BIR) is the predominant mechanism for RMD in mammalian cells, especially for distant repeats (1-2 kb).
• BIR-mediated RMD (BIR/RMD) functions over long distances (~100-200 kb) and is potentiated by oncogene expression.
• BIR/RMD is favored at single-ended DSBs from collapsed replication forks, requires H2AX for long-range repair, and is suppressed by sequence divergence (partially MSH2-dependent).

Conclusions:

• Break-induced replication (BIR) plays a more significant role than SSA in repeat-mediated rearrangements in mammalian cells.
• This discovery reframes the understanding of how repetitive DNA contributes to oncogenesis and chromosomal instability.