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Related Concept Videos

Chromosome Replication02:31

Chromosome Replication

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Before a cell can divide, it must accurately replicate all of its chromosomes, including the DNA and its associated histone and non-histone proteins.  This process begins at numerous origins of replication during the S phase of the cell cycle in each of a cell’s chromosomes simultaneously. Certain nucleotides can act as origins of replication, but these sequences are not well defined - especially in complex, multi-cellular, eukaryotic species. The length of DNA that spans an origin...
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In eukaryotic cells, DNA replication is highly conserved and tightly regulated. Multiple linear chromosomes must be duplicated with high fidelity before cell division, so there are many proteins that fulfill specialized roles in the replication process. Replication occurs in three phases: initiation, elongation, and termination, and ends with two complete sets of chromosomes in the nucleus.
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The Replisome03:01

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DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
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Lagging Strand Synthesis01:59

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During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.
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Duplication of Chromatin Structure02:05

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The process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
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DNA replication involves the separation of the two strands of the double helix, with each strand serving as a template from which the new complementary strand is copied.  After replication, each double-stranded DNA includes one parental or “old” strand and one “new” strand. This is known as semiconservative replication. The resulting DNA molecules have the same sequence and are divided equally into the two daughter cells.
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Updated: Jun 1, 2025

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
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Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method

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A tale of two strands: Decoding chromatin replication through strand-specific sequencing.

Zhiming Li1, Zhiguo Zhang2

  • 1Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; West China School of Public Health and West China Fourth Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China.

Molecular Cell
|January 17, 2025
PubMed
Summary
This summary is machine-generated.

Strand-specific sequencing methods like eSPAN and OK-seq are crucial for distinguishing DNA strands during replication. These tools reveal insights into DNA replication, histone transfer, and epigenetic inheritance in eukaryotes.

Keywords:
DNA damage repairDNA replicationepigenetic inheritancegenome maintenancenucleosome assemblyparental histone transferstrand-specific sequencing

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Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
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G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
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Area of Science:

  • Molecular Biology
  • Genetics
  • Epigenetics

Background:

  • DNA replication involves asymmetric synthesis of leading and lagging strands by distinct DNA polymerases (Pol ε and Pol δ).
  • Distinguishing between nascent DNA strands in vivo is essential for understanding replication dynamics and epigenetic inheritance.

Purpose of the Study:

  • To review foundational principles of strand-specific sequencing methodologies.
  • To summarize mechanistic insights gained from applying these techniques in eukaryotic cells.
  • To discuss current limitations and future directions for chromatin replication research.

Main Methods:

  • Review of strand-specific sequencing strategies, including enrichment and sequencing of protein-associated nascent DNA (eSPAN) and Okazaki fragment sequencing (OK-seq).
  • Analysis of data generated by these methods to study DNA replication and epigenetic phenomena.

Main Results:

  • Application of eSPAN and OK-seq has provided key insights into DNA replication mechanisms.
  • These techniques have illuminated processes such as parental histone transfer and epigenetic inheritance.
  • The review synthesizes findings from various studies utilizing these sequencing strategies.

Conclusions:

  • Strand-specific sequencing is indispensable for dissecting eukaryotic DNA replication and its epigenetic consequences.
  • Current techniques have limitations that necessitate further technological innovation.
  • Advanced methods are needed to fully understand the regulation and dynamics of chromatin replication.