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Related Concept Videos

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DNA replication has three main steps: initiation, elongation, and termination. Replication in prokaryotes begins when initiator proteins bind to the single origin of replication (ori) on the cell's circular chromosome. Replication then proceeds around the entire circle of the chromosome in each direction from the two replication forks, resulting in two DNA molecules.
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Genome-wide Determination of Mammalian Replication Timing by DNA Content Measurement
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Multiplexed TrAEL-seq captures DNA replication dynamics in mammalian cells.

Neesha Kara1, Laura Biggins2, Alex Whale1

  • 1Epigenetics programme, Babraham Institute, CB22 3AT Babraham, United Kingdom.

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|March 14, 2026
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Summary
This summary is machine-generated.

This study refines TrAEL-seq (truncated adapter ligation sequencing) for genome-wide DNA replication profiling. The updated method offers high resolution and throughput, enabling detailed analysis of replication dynamics in various cell types.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Cell Biology

Background:

  • DNA replication is a fundamental cellular process essential for cell division and genomic stability.
  • Accurate genome-wide profiling of DNA replication is crucial for understanding various biological phenomena, including development, aging, and disease.
  • Existing methods for DNA replication profiling often have limitations such as requiring synchronized cells or specific chemical treatments.

Purpose of the Study:

  • To present an updated and improved protocol for TrAEL-seq (truncated adapter ligation sequencing).
  • To enhance the throughput and sample quality of TrAEL-seq.
  • To validate the enhanced TrAEL-seq method in multiple mammalian cell lines and dynamic biological systems.

Main Methods:

  • The study details an updated TrAEL-seq protocol.
  • The method involves multiplexing up to six samples for increased throughput.
  • The protocol was validated in various mammalian cell lines, including during oncogene-induced senescence.

Main Results:

  • The updated TrAEL-seq protocol provides high-resolution genome-wide DNA replication profiles comparable to existing methods like OK-seq.
  • The method successfully mapped replication initiation and termination zones.
  • TrAEL-seq revealed insights into replication fork speed, showing slower progression through transcribed regions but overall acceleration in early S-phase.

Conclusions:

  • The enhanced TrAEL-seq method is a robust, high-throughput, and high-resolution technique for profiling DNA replication genome-wide.
  • This method is suitable for analyzing replication dynamics in unsynchronized cells and complex biological systems.
  • The findings suggest that replication fork progression is influenced by transcriptional activity and proximity to initiation zones, with fewer competing forks later in S-phase.