Related Experiment Video
Updated: Jun 2, 2026
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
Summary
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.
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.
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