ArticleProceedings of the National Academy of Sciences of the United States of America2023
Non-B-form DNA tends to form in centromeric regions and has undergone changes in polyploid oat subgenomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
34 citing papers in PubMed, 43 citations in OpenAlex.
- Dynamic evolution and hierarchical regulation of rDNA in polyploid oat.The Plant journal : for cell and molecular biology · 2026Article
- Article
- Polarized mitochondrial respiratory chain complexes in synaptic mitochondria induced by plasticity signals.Molecular and cellular biochemistry · 2026Article
- Transposable element dynamics drive rapid evolution of centromere architecture in the Avena genus.Genome biology · 2026Article
- Structure of human lymphoid-specific helicase HELLS in its autoinhibited state.Nucleic acids research · 2026Article
- Centromere evolution in annual and perennial soybeans and its implication for hybridization in cultivated species.Genome biology · 2026Article
- Domestication-Selected Promoter Insertion in WRKY17 Increases Cadmium Sensitivity in Apple.Plant biotechnology journal · 2026Article
- Structure of human lymphoid-specific helicase HELLS in its autoinhibitory state.bioRxiv : the preprint server for biology · 2025Article
- Dynamic evolution of satellite DNAs drastically differentiates the genomes ofGenome research · 2025Article
- Structural composition and evolution of jujube centromere reveal a dominant role for LTR retrotransposon.Horticulture research · 2025Article
- High-resolution genome assembly reveals retrotransposon-mediated centromere dynamics in rye.Genome biology · 2025Article
- Distinct evolutionary trajectories of subgenomic centromeres in polyploid wheat.Genome biology · 2025Article
- Centromeres drive and take a break.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2025Review
- High-quality genome of allotetraploid Avena barbata provides insights into the origin and evolution of B subgenome in Avena.Journal of integrative plant biology · 2025Article
- Centromere-size reduction and chromatin state dynamics following intergenomic hybridization in cotton.PLoS genetics · 2025Article
- Decoding G-Quadruplexes Sequence inPlants (Basel, Switzerland) · 2025Article
- Non-canonical DNA in human and other ape telomere-to-telomere genomes.Nucleic acids research · 2025Article
- Non-canonical DNA in human and other ape telomere-to-telomere genomes.bioRxiv : the preprint server for biology · 2025Article
- Genome assembly of the maize B chromosome provides insight into its epigenetic characteristics and effects on the host genome.Genome biology · 2025Article
- Stable minichromosome and functional neocentromere derived from rye 7R chromosome arm.BMC plant biology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Centromeres are the specialized regions of the chromosomes that direct faithful chromosome segregation during cell division. Despite their functional conservation, centromeres display features of rapidly evolving DNA and wide evolutionary diversity in size and organization. Previous work found that the noncanonical B-form DNA structures are abundant in the centromeres of several eukaryotic species with a possible implication for centromere specification. Thus far, systematic studies into the organization and function of non-B-form DNA in plants remain scarce. Here, we applied the oat system to investigate the role of non-B-form DNA in centromeres. We conducted chromatin immunoprecipitation sequencing using an antibody to the centromere-specific histone H3 variant (CENH3); this accurately positioned oat centromeres with different ploidy levels and identified a series of centromere-specific sequences including minisatellites and retrotransposons. To define genetic characteristics of oat centromeres, we surveyed the repeat sequences and found that dyad symmetries were abundant in oat centromeres and were predicted to form non-B-DNA structures in vivo. These structures including bent DNA, slipped DNA, Z-DNA, G-quadruplexes, and R-loops were prone to form within CENH3-binding regions. Dynamic conformational changes of predicted non-B-DNA occurred during the evolution from diploid to tetraploid to hexaploid oat. Furthermore, we applied the single-molecule technique of AFM and DNA:RNA immunoprecipitation with deep sequencing to validate R-loop enrichment in oat centromeres. Centromeric retrotransposons exhibited strong associations with R-loop formation. Taken together, our study elucidates the fundamental character of non-B-form DNA in the oat genome and reveals its potential role in centromeres.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.