Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification

Area of Science:

• Genetics
• Molecular Biology
• Evolutionary Biology

Background:

• DNA replication errors contribute significantly to genomic evolution, leading to variations from single nucleotide polymorphisms to large-scale copy number variations (CNVs).
• Interstitial inverted triplications are a class of CNVs with potential implications for adaptive phenotypes due to novel inversion junctions and increased copy number.

Purpose of the Study:

• To test a specific replication-based model, Origin-Dependent Inverted-Repeat Amplification (ODIRA), for the generation of interstitial inverted triplications.
• To investigate the feasibility of the proposed replication error mechanism and its downstream effects on chromosome structure.

Main Methods:

• Utilized a combination of in vitro and in vivo experimental approaches.
• Employed the yeast Saccharomyces cerevisiae as a model organism.
• Analyzed replication intermediates and genomic integration events.

Main Results:

• Demonstrated that the proposed replication error, involving the ligation of nascent DNA strands to form "closed" replication forks, can occur in vitro at short, interrupted inverted repeats.
• Showed that hairpin-capped linear duplexes resulting from these errors replicate in vivo to form inverted dimeric plasmids.
• Confirmed that these plasmids can integrate into the genome via homologous recombination, generating inverted triplications.

Conclusions:

• The ODIRA model provides a plausible mechanism for generating interstitial inverted triplications.
• The model also explains the formation of human de novo inverted amplicons with mixed homologous sequences.
• Findings support the ODIRA mechanism and highlight its significance in understanding the origins of CNVs relevant to human health and evolution.