ArticleNature plants2023
Single-molecule targeted accessibility and methylation sequencing of centromeres, telomeres and rDNAs in Arabidopsis.
Article in Nature plants, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 28 citations in OpenAlex.
- Methylcytosine oxidation derivatives are preferentially associated with repetitive chromatin and mark active rDNA inFrontiers in plant science · 2026Article
- Single-molecule views of chromatin accessibility and structure during photomorphogenesis.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Extensive nrDNA Polymorphism inPlants (Basel, Switzerland) · 2025Article
- The regulatory potential of transposable elements in maize.Nature plants · 2025Article
- Integrating Arabidopsis and crop species gene discovery for crop improvement.The Plant cell · 2025Review
- Telomere-to-telomere Phragmites australis reference genome assembly with a B chromosome provides insights into its evolution and polysaccharide biosynthesis.Communications biology · 2025Article
- Profiling the epigenome using long-read sequencing.Nature genetics · 2025Review
- DeepBAM: a high-accuracy single-molecule CpG methylation detection tool for Oxford nanopore sequencing.Briefings in bioinformatics · 2024Article
- Technology to the rescue: how to uncover the role of transposable elements in preimplantation development.Biochemical Society transactions · 2024Review
- Simultaneous profiling of chromatin accessibility and DNA methylation in complete plant genomes using long-read sequencing.Nucleic acids research · 2024Article
- Single-molecule long-read methylation profiling reveals regional DNA methylation regulated by Elongator Complex Subunit 2 in Arabidopsis roots experiencing spaceflight.Biology direct · 2024Article
- Telomere Length Variation in Model Bryophytes.Plants (Basel, Switzerland) · 2024Article
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The short read-length of next-generation sequencing makes it challenging to characterize highly repetitive regions (HRRs) such as centromeres, telomeres and ribosomal DNAs. Based on recent strategies that combined long-read sequencing and exogenous enzymatic labelling of open chromatin, we developed single-molecule targeted accessibility and methylation sequencing (STAM-seq) in plants by further integrating nanopore adaptive sampling to investigate the HRRs in wild-type Arabidopsis and DNA methylation mutants that are defective in CG- or non-CG methylation. We found that CEN180 repeats show higher chromatin accessibility and lower DNA methylation on their forward strand, individual rDNA units show a negative correlation between their DNA methylation and accessibility, and both accessibility and CHH methylation levels are lower at telomere compared to adjacent subtelomeric region. Moreover, DNA methylation-deficient mutants showed increased chromatin accessibility at HRRs, consistent with the role of DNA methylation in maintaining heterochromatic status in plants. STAM-seq can be applied to study accessibility and methylation of repetitive sequences across diverse plant species.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.