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The evolution of the temporal program of genome replication.

Nicolas Agier1, Stéphane Delmas1, Qing Zhang1

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Genome replication timing evolves via dynamic changes in active replication origins. New origins gain efficiency over time, while lost origins are near strong ones, maintaining spacing.

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Area of Science:

  • Genetics
  • Evolutionary Biology
  • Molecular Biology

Background:

  • Genome replication timing is crucial for cell division and is tightly regulated.
  • Understanding how replication timing programs evolve is essential for comprehending genome stability and evolution.
  • Previous studies have not fully elucidated the evolutionary dynamics of replication origins.

Purpose of the Study:

  • To investigate the evolutionary changes in genome-wide replication timing profiles.
  • To identify the mechanisms driving the evolution of replication origin usage.
  • To model the birth, death, and conservation of active replication origins across an evolutionary range.

Main Methods:

  • Generated genome-wide replication timing profiles for ten Lachancea yeast species.
  • Analyzed the evolutionary turnover of active replication origins.
  • Examined the relationship between origin activity, age, and genomic location.

Main Results:

  • Replication timing programs evolve primarily through the dynamic renewal of active replication origins.
  • Newly gained origins initially show low activity but increase efficiency and fire earlier with age.
  • Lost origins exhibit a wide range of firing strengths and are often located near strong origins.
  • Despite high turnover, active origins maintain regular spacing along chromosomes, preventing large inter-origin gaps.

Conclusions:

  • Replication origin evolution is characterized by continuous birth and death of origins, with a notable aging process for new origins.
  • The regular spacing of active origins suggests an optimization mechanism to ensure efficient genome-wide replication.
  • A model for the evolutionary dynamics of replication origins is proposed, highlighting renewal and spacing constraints.