ArticleGenome research2013
The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 160 papers.
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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.
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Who cites it
160 citing papers in PubMed, 286 citations in OpenAlex.
- Multi-Omics Dissection of Drought Stress Responses in Crops: From Molecular Regulatory Networks to Climate-Resilient Breeding Applications.International journal of molecular sciences · 2026Review
- Genome-wide profiling and functional characterization of N4-acetyldeoxycytosine reveals conserved epigenetic roles in rice and Arabidopsis.BMC genomics · 2026Article
- Habitat-specific alternative splicing shifts and the 5mC methylation landscape of differentially spliced genes inFrontiers in plant science · 2026Article
- Homeostasis of DNA Hemi-Methylation in Arabidopsis through Methylation Maintenance, DNA Replication, and Nucleosome Positioning Mechanisms.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize.Nature genetics · 2025Article
- Genomic and epigenomic insight into giga-chromosome architecture and adaptive evolution of royal lily (Lilium regale).Nature communications · 2025Article
- Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducingGenome research · 2025Article
- Testing the potential of zebularine to induce heritable changes in crop growth and development.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Epigenetic gene regulation in plants and its potential applications in crop improvement.Nature reviews. Molecular cell biology · 2025Review
- MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.Nature communications · 2024Article
- Multiple strategies, including 6mA methylation, affecting plant alternative splicing in allopolyploid peanut.Plant biotechnology journal · 2024Article
- Paramutation at the maize pl1 locus is associated with RdDM activity at distal tandem repeats.PLoS genetics · 2024Article
- Heritable changes of epialleles near genes in maize can be triggered in the absence of CHH methylation.Plant physiology · 2024Article
- The pivotal ripening gene SlDML2 participates in regulating disease resistance in tomato.Plant biotechnology journal · 2023Article
- Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize.Genome biology · 2023Article
- The pattern of alternative splicing and DNA methylation alteration and their interaction in linseed (Linum usitatissimum L.) response to repeated drought stresses.Biological research · 2023Article
- Exploring the crop epigenome: a comparison of DNA methylation profiling techniques.Frontiers in plant science · 2023Review
- Evolutionary fates of gene-body methylation and its divergent association with gene expression in pigeonpea.The plant genome · 2022Article
- Mechanistic basis for maintenance of CHG DNA methylation in plants.Nature communications · 2022Article
- Comparative DNA Methylome of Phytoplasma Associated Retrograde Metamorphosis in Sesame (Biology · 2022Article
100 more citing papers are in PubMed but not listed here.
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Authors and funding
15 authors at 3 institutions in 1 country.
Funding
Abstract
The maize genome, with its large complement of transposons and repeats, is a paradigm for the study of epigenetic mechanisms such as paramutation and imprinting. Here, we present the genome-wide map of cytosine methylation for two maize inbred lines, B73 and Mo17. CG (65%) and CHG (50%) methylation (where H = A, C, or T) is highest in transposons, while CHH (5%) methylation is likely guided by 24-nt, but not 21-nt, small interfering RNAs (siRNAs). Correlations with methylation patterns suggest that CG methylation in exons (8%) may deter insertion of Mutator transposon insertion, while CHG methylation at splice acceptor sites may inhibit RNA splicing. Using the methylation map as a guide, we used low-coverage sequencing to show that parental methylation differences are inherited by recombinant inbred lines. However, frequent methylation switches, guided by siRNA, persist for up to eight generations, suggesting that epigenetic inheritance resembling paramutation is much more common than previously supposed. The methylation map will provide an invaluable resource for epigenetic studies in maize.
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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.