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Rodríguez-Mejía LC, Romero-Estudillo I, Rivillas-Acevedo LA, French-Pacheco L, Silva-Martínez GA, Alvarado-Caudillo Y, Colín-Castelán D, Rodríguez-Ríos D, Wrobel K, Wrobel K, Lund G, Zaina S. The DNA Methyltransferase Inhibitor RG108 is Converted to Activator Following Conjugation with Short Peptides. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10390-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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N'Diaye A, Byrns B, Cory AT, Nilsen KT, Walkowiak S, Sharpe A, Robinson SJ, Pozniak CJ. Machine learning analyses of methylation profiles uncovers tissue-specific gene expression patterns in wheat. THE PLANT GENOME 2020; 13:e20027. [PMID: 33016606 DOI: 10.1002/tpg2.20027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/24/2020] [Accepted: 04/12/2020] [Indexed: 06/11/2023]
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 = 9.20×10-10 ) between all features and gene expression, suggesting that methylation across all genic regions contribute to gene regulation. However, the methylation of the promoter, the CDS and the exon in CG context was the most impactful. Our study provides more insights into the interplay between DNA methylation and gene expression and paves the way for identifying tissue-specific genes using methylation profiles.
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Affiliation(s)
- Amidou N'Diaye
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Brook Byrns
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Aron T Cory
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Kirby T Nilsen
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Sean Walkowiak
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
| | - Andrew Sharpe
- Global Institute for Food Security, Saskatoon, SK, Canada, S7N 0W9
| | - Stephen J Robinson
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
| | - Curtis J Pozniak
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5A8
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Cruz-Carrillo G, Montalvo-Martínez L, Cárdenas-Tueme M, Bernal-Vega S, Maldonado-Ruiz R, Reséndez-Pérez D, Rodríguez-Ríos D, Lund G, Garza-Ocañas L, Camacho-Morales A. Fetal Programming by Methyl Donors Modulates Central Inflammation and Prevents Food Addiction-Like Behavior in Rats. Front Neurosci 2020; 14:452. [PMID: 32581665 PMCID: PMC7283929 DOI: 10.3389/fnins.2020.00452] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/14/2020] [Indexed: 12/16/2022] Open
Abstract
Fetal programming by hypercaloric intake leads to food addiction-like behavior and brain pro-inflammatory gene expression in offspring. The role of methylome modulation during programming on central immune activation and addiction-like behavior has not been characterized. We employed a nutritional programming model exposing female Wistar rats to chow diet, cafeteria (CAF), or CAF-methyl donor’s diet from pre-pregnancy to weaning. Addiction-like behavior in offspring was characterized by the operant training response using Skinner boxes. Food intake in offspring was determined after fasting–refeeding schedule and subcutaneous injection of ghrelin. Genome-wide DNA methylation in the nucleus accumbens (NAc) shell was performed by fluorescence polarization, and brain immune activation was evaluated using real-time PCR for pro-inflammatory cytokines (IL-1β, TNF-1α, and IL-6). Molecular effects of methyl modulators [S-adenosylmethionine (SAM) or 5-azatidine (5-AZA)] on pro-inflammatory cytokine expression and phagocytosis were identified in the cultures of immortalized SIM-A9 microglia cells following palmitic acid (100 μM) or LPS (100 nM) stimulation for 6 or 24 h. Our results show that fetal programming by CAF exposure increases the number of offspring subjects and reinforcers under the operant training response schedule, which correlates with an increase in the NAc shell global methylation. Notably, methyl donor’s diet selectively decreases lever-pressing responses for reinforcers and unexpectedly decreases the NAc shell global methylation. Also, programmed offspring by CAF diet shows a selective IL-6 gene expression in the NAc shell, which is reverted to control values by methyl diet exposure. In vitro analysis identified that LPS and palmitic acid activate IL-1β, TNF-1α, and IL-6 gene expression, which is repressed by the methyl donor SAM. Finally, methylation actively represses phagocytosis activity of SIM-A9 microglia cells induced by LPS and palmitic acid stimulation. Our in vivo and in vitro data suggest that fetal programming by methyl donors actively decreases addiction-like behavior to palatable food in the offspring, which correlates with a decrease in NAc shell methylome, expression of pro-inflammatory cytokine genes, and activity of phagocytic microglia. These results support the role of fetal programming in brain methylome on immune activation and food addiction-like behavior in the offspring.
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Affiliation(s)
- Gabriela Cruz-Carrillo
- Department of Biochemistry, College of Medicine, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico.,Neurometabolism Unit, Center for Research and Development in Health Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Larisa Montalvo-Martínez
- Department of Biochemistry, College of Medicine, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico.,Neurometabolism Unit, Center for Research and Development in Health Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Marcela Cárdenas-Tueme
- Department of Cell Biology and Genetics, College of Biological Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Sofia Bernal-Vega
- Department of Cell Biology and Genetics, College of Biological Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Roger Maldonado-Ruiz
- Department of Biochemistry, College of Medicine, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico.,Neurometabolism Unit, Center for Research and Development in Health Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Diana Reséndez-Pérez
- Department of Cell Biology and Genetics, College of Biological Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | | | - Gertrud Lund
- Department of Genetic Engineering, CINVESTAV Irapuato Unit, Irapuato, Mexico
| | - Lourdes Garza-Ocañas
- Department of Pharmacology and Toxicology, College of Medicine, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Alberto Camacho-Morales
- Department of Biochemistry, College of Medicine, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico.,Neurometabolism Unit, Center for Research and Development in Health Sciences, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
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Methyl Donor Micronutrients that Modify DNA Methylation and Cancer Outcome. Nutrients 2019; 11:nu11030608. [PMID: 30871166 PMCID: PMC6471069 DOI: 10.3390/nu11030608] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/17/2022] Open
Abstract
DNA methylation is an epigenetic mechanism that is essential for regulating gene transcription. However, aberrant DNA methylation, which is a nearly universal finding in cancer, can result in disturbed gene expression. DNA methylation is modified by environmental factors such as diet that may modify cancer risk and tumor behavior. Abnormal DNA methylation has been observed in several cancers such as colon, stomach, cervical, prostate, and breast cancers. These alterations in DNA methylation may play a critical role in cancer development and progression. Dietary nutrient intake and bioactive food components are essential environmental factors that may influence DNA methylation either by directly inhibiting enzymes that catalyze DNA methylation or by changing the availability of substrates required for those enzymatic reactions such as the availability and utilization of methyl groups. In this review, we focused on nutrients that act as methyl donors or methylation co-factors and presented intriguing evidence for the role of these bioactive food components in altering DNA methylation patterns in cancer. Such a role is likely to have a mechanistic impact on the process of carcinogenesis and offer possible therapeutic potentials.
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Baba Y, Karube I, Yoshida W. Global DNA Methylation Level Monitoring by methyl-CpG Binding Domain-Fused Luciferase. ANAL LETT 2018. [DOI: 10.1080/00032719.2018.1494739] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Yuji Baba
- School of Bioscience and Biotechnology, Graduate School of Bionics, Tokyo University of Technology, Tokyo, Japan
| | - Isao Karube
- School of Bioscience and Biotechnology, Graduate School of Bionics, Tokyo University of Technology, Tokyo, Japan
| | - Wataru Yoshida
- School of Bioscience and Biotechnology, Graduate School of Bionics, Tokyo University of Technology, Tokyo, Japan
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Abstract
Owing to the development of new technologies, the epigenome, a second dimensional method for genome analysis has emerged. Epigenetic mechanisms, including DNA methylation, histone modifications and noncoding RNAs, regulate gene expression without changing the genetic sequence. These epigenetic mechanisms normally modulate gene expression, trans-generational effects and inherited expression states in various biological processes. Abnormal epigenetic patterns typically cause pathological conditions, including cancers, age-related diseases, and specific cartilage and bone diseases. Facing the rapidly developing epigenetic field, we reviewed epigenetic mechanisms and their involvement with the skeletal system and their role in skeletal development, homeostasis and degeneration. Finally, we discuss the prospects for the future of epigenetics.
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