ArticleThe plant genome2020
Machine learning analyses of methylation profiles uncovers tissue-specific gene expression patterns in wheat.
Article in The plant genome, 2020. 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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Who cites it
12 citing papers in PubMed, 26 citations in OpenAlex.
- Understanding epigenetic regulation in nonmodel plants: transcriptomic responses to seed demethylation in leaves and roots of the annual herb Erodium cicutarium (Geraniaceae).G3 (Bethesda, Md.) · 2026Article
- Epigenetic maps of pearl millet reveal a prominent role for CHH methylation in regulating tissue-specific gene expression.aBIOTECH · 2025Article
- Gaining insights into epigenetic memories through artificial intelligence and omics science in plants.Journal of integrative plant biology · 2025Review
- DNA methylation in wheat: current understanding and future potential for enhancing biotic and abiotic stress tolerance.Physiology and molecular biology of plants : an international journal of functional plant biology · 2024Review
- Genome-wide characterization and expression analysis of the CINNAMYL ALCOHOL DEHYDROGENASE gene family in Triticum aestivum.BMC genomics · 2024Article
- Deciphering the molecular basis of tissue-specific gene expression in plants: Can synthetic biology help?Current opinion in plant biology · 2022Review
- Epigenetic stress memory: A new approach to study cold and heat stress responses in plants.Frontiers in plant science · 2022Review
- Predicting Tissue-Specific mRNA and Protein Abundance in Maize: A Machine Learning Approach.Frontiers in artificial intelligence · 2022Article
- Biophysics is reshaping our perception of the epigenome: from DNA-level to high-throughput studies.Biophysical reports · 2021Review
- Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig.BMC genomics · 2021Article
- Developmental Methylome of the Medicinal PlantInternational journal of molecular sciences · 2020Article
- Machine learning analyses of methylation profiles uncovers tissue-specific gene expression patterns in wheat.The plant genome · 2020Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation is a mechanism of epigenetic modification in eukaryotic organisms. Generally, methylation within genes promoter inhibits regulatory protein binding and represses transcription, whereas gene body methylation is associated with actively transcribed genes. However, it remains unclear whether there is interaction between methylation levels across genic regions and which site has the biggest impact on gene regulation. We investigated and used the methylation patterns of the bread wheat cultivar Chinese Spring to uncover differentially expressed genes (DEGs) between roots and leaves, using six machine learning algorithms and a deep neural network. As anticipated, genes with higher expression in leaves were mainly involved in photosynthesis and pigment biosynthesis processes whereas genes that were not differentially expressed between roots and leaves were involved in protein processes and membrane structures. Methylation occurred preponderantly (60%) in the CG context, whereas 35 and 5% of methylation occurred in CHG and CHH contexts, respectively. Methylation levels were highly correlated (r = 0.7 to 0.9) between all genic regions, except within the promoter (r = 0.4 to 0.5). Machine learning models gave a high (0.81) prediction accuracy of DEGs. There was a strong correlation (p-value = 9.20×10
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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.