ArticleBMC genomics2015
Genome-wide high-resolution mapping of DNA methylation identifies epigenetic variation across embryo and endosperm in Maize (Zea may).
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 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
45 citing papers in PubMed, 73 citations in OpenAlex.
- Integrated physiological and transcriptomic measurements reveal changes in the accumulation and partitioning of storage reserves after prevention of pollination in maize.BMC plant biology · 2026Article
- Response of DNA methylation and gene expression to light treatments in Norway spruce [Picea abies (L.) Karst.].BMC genomics · 2026Article
- Epigenetic control of seed development and dormancy in cereals.Plant signaling & behavior · 2025Review
- Article
- Profiling of Barley, Wheat, and RyeInternational journal of molecular sciences · 2023Article
- Article
- Adaptation ofInternational journal of molecular sciences · 2022Article
- Global genomic methylation related to the degree of parasitism in cattle.Scientific reports · 2022Article
- Epigenome guided crop improvement: current progress and future opportunities.Emerging topics in life sciences · 2022Review
- Article
- Establishment and maintenance of DNA methylation in nematode feeding sites.Frontiers in plant science · 2022Article
- Can Forest Trees Cope with Climate Change?-Effects of DNA Methylation on Gene Expression and Adaptation to Environmental Change.International journal of molecular sciences · 2021Review
- Genome-wide high-resolution mapping of DNA methylation reveals epigenetic variation in the offspring of sexual and asexual propagation in Robinia pseudoacacia.Plant cell reports · 2021Article
- Evolution of CG Methylation Maintenance Machinery in Plants.Epigenomes · 2021Review
- Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Gene Expression in Parthenogenic Maize Proembryos.Plants (Basel, Switzerland) · 2021Article
- INT-Hi-C reveals distinct chromatin architecture in endosperm and leaf tissues of Arabidopsis.Nucleic acids research · 2021Article
- Reprogramming of Histone H3 Lysine Methylation During Plant Sexual Reproduction.Frontiers in plant science · 2021Review
- DNA methylation changes in clonally propagated oil palm.Plant cell reports · 2020Article
- Epigenomic landscape and epigenetic regulation in maize.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEpigenetic modifications play important roles in plant and animal development. DNA methylation impacts the transposable element (TE) silencing, gene imprinting and expression regulation.
resultsThrough a genome-wide analysis, DNA methylation peaks were characterized and mapped in maize embryo and endosperm genome, respectively. Distinct methylation level was observed across maize embryo and endosperm. The maize embryo genome contained more DNA methylation than endosperm. Totally, 985,478 CG islands (CGIs) were identified and most of them were unmethylated. More CGI shores were methylated than CGIs in maize suggested that DNA methylation level was not positively correlated with CpG density. The promoter sequence and transcriptional termination region (TTR) were more methylated than the gene body (intron and exon) region based on peak number and methylated depth. Result showed that 99% TEs were methylated in maize embryo, but a large portion of them (34.8%) were not methylated in endosperm. Maize embryo and endosperm exhibit distinct pattern/level of methylation. The most differentially methylated region between embryo and endosperm are CGI shores. Our results indicated that DNA methylation is associated with both gene silencing and gene activation in maize. Many genes involved in embryogenesis and seed development were found differentially methylated in embryo and endosperm. We found 41.5% imprinting genes were similarly methylated and 58.5% imprinting genes were differentially methylated between embryo and endosperm. Methylation level was associated with allelic silencing of only a small number of imprinting genes. The expression of maize DEMETER-like (DME-like) gene and MBD101 gene (MBD4 homolog) were higher in endosperm than in embryo. These two genes may be associated with distinct methylation levels across maize embryo and endosperm.
conclusionsThrough MeDIP-seq we systematically analyzed the methylomes of maize embryo and endosperm and results indicated that the global methylation status of embryo was more than that of the endosperm. Differences could be observed at the total number of methylation peaks, DMRs and specific methylated genes which were tightly associated with development of embryo and endosperm. Our results also revealed that many DNA methylation regions didn't affect transcription of the corresponding genes.
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.