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Related Concept Videos

Restarting Stalled Replication Forks02:37

Restarting Stalled Replication Forks

DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart, a...
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Polytene Chromosomes

Polytene chromosomes are giant interphase chromosomes with several DNA strands placed side by side. They were discovered in the year 1881 by Balbiani in salivary glands, intestine, muscles, malpighian tubules, and hypoderm of larvae Chironomus plumosus. Hence, these are also called "Salivary gland chromosomes." These are found in insects of the order Diptera and Collembola; in certain organs of mammals; and synergids, antipodes of flowering plants. Polytene chromosomes are also regularly...
The Replisome03:01

The Replisome

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Replication in Eukaryotes01:29

Replication in Eukaryotes

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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Replication in Eukaryotes02:31

Replication in Eukaryotes

Overview
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...

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Updated: Jun 2, 2026

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
08:53

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

Published on: May 2, 2025

Sequence-directed R-loop formation coupled with DNA methylation reprogramming during polyploidization of

Kaibiao Zhang1,2, Lisha Shen1, Yishuang Sun1

  • 1State Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.

The Plant Journal : for Cell and Molecular Biology
|June 1, 2026
PubMed
Summary
This summary is machine-generated.

R-loops, crucial DNA:RNA structures, are sequence-driven and conserved during plant polyploidization. Their dynamics are linked to genetic variation and epigenetic changes, influencing genome evolution.

Keywords:
BrachypodiumDNA methylationPolyploidizationR‐loopssequence variations

Related Experiment Videos

Last Updated: Jun 2, 2026

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
08:53

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

Published on: May 2, 2025

Area of Science:

  • Genetics
  • Molecular Biology
  • Plant Science

Background:

  • R-loops (DNA:RNA hybrid and single-stranded DNA) have vital roles in eukaryotes.
  • Their function in hybridization and polyploidization evolution is not well understood.

Purpose of the Study:

  • To investigate R-loop profiles in the allotetraploid Brachypodium hybridum and its diploid progenitors.
  • To understand the role of R-loops in genome evolution following polyploidization.

Main Methods:

  • Comparative analysis of R-loop profiles across diploid and allotetraploid Brachypodium species.
  • Assessment of R-loop association with sequence features, RNA abundance, chromatin accessibility, genetic variation, and DNA methylation.

Main Results:

  • R-loops are conserved in syntenic regions and are sequence-dependent, persisting through genomic rearrangements.
  • R-loop formation is linked to small sequence variations (SNPs, indels) and not strongly influenced by RNA levels or chromatin accessibility.
  • DNA methylation levels (CG, CHG, CHH) globally increased or decreased with upregulated or downregulated R-loops, respectively.

Conclusions:

  • R-loop dynamics during polyploidization are primarily directed by DNA sequences.
  • R-loop formation is coupled with genetic variation and epigenetic reprogramming (DNA methylation).
  • These findings offer new insights into the role of R-loops in shaping plant genome structure during evolution.