Epigenetic inheritance of acquired traits through DNA methylation

Zhang, Ying; Sirard, Marc‐André

doi:10.1093/af/vfab052

Cited by 14 publications

(12 citation statements)

References 70 publications

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“…We propose Methyl-TWAS as a novel approach to conduct in silico TWAS using long-range CpGs instead of genotype data to improve the accuracy of gene expression imputation and therefore in silico TWAS. Methyl-TWAS can estimate epigenetically regulated/associated expression (eGReX), which includes parts of genetically (GReX) and environmentally regulated expression, trait-altered expression, and tissue-specific expression, since DNA methylation is affected by all these [44][45][46] (Figure 1). Note that traditional TWAS methods such as PrediXcan can only estimate GReX.…”

Section: Discussionmentioning

confidence: 99%

Methyl-TWAS: A powerful method forin silicotranscriptome-wide association studies (TWAS) using long-range DNA methylation

Kim,

Qin,

Park

et al. 2023

Preprint

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In silicotranscriptome-wide association studies (TWAS) are commonly used to test whether expression of specific genes is linked to a complex trait. However, genotype-basedin silicoTWAS such as PrediXcan, exhibit low prediction accuracy for a majority of genes because genotypic data lack tissue- and disease-specificity and are not affected by the environment. Because methylation is tissue-specific and, like gene expression, can be modified by environment or disease status, methylation should predict gene expression with more accuracy than SNPs. Therefore, we propose Methyl-TWAS, the first approach that utilizes long-range methylation markers to impute gene expression forin silicoTWAS through penalized regression. Methyl-TWAS 1) predicts epigenetically regulated/associated expression (eGReX), which incorporates tissue-specific expression and both genetically- (GReX) and environmentally-regulated expression to identify differentially expressed genes (DEGs) that could not be identified by genotype-based methods; and 2) incorporates bothcis-andtrans-CpGs, including various regulatory regions to identify DEGs that would be missed usingcis-methylation only. Methyl-TWAS outperforms PrediXcan and two other methods in imputing gene expression in the nasal epithelium, particularly for immunity-related genes and DEGs in atopic asthma. Methyl-TWAS identified 3,681 (85.2%) of the 4,316 DEGs identified in a previous TWAS of atopic asthma using measured expression, while PrediXcan could not identify any gene. Methyl-TWAS also outperforms PrediXcan for expression imputation as well asin silicoTWAS in white blood cells. Methyl-TWAS is a valuable tool forin silicoTWAS, leveraging a growing body of publicly available genome-wide DNA methylation data for a variety of human tissues.

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Section: Discussionmentioning

confidence: 99%

Methyl-TWAS: A powerful method forin silicotranscriptome-wide association studies (TWAS) using long-range DNA methylation

Kim,

Qin,

Park

et al. 2023

Preprint

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“…These studies have analyzed the genome-wide regulation of DNA methylation on gene expression, found some new important genes related to differential methylation regions and ways that may affect important economic traits of cattle and investigated the changes in methylation patterns under the influence of the environment, development and disease. In addition, in the latest study of DNA methylation inheritance, researchers divided DNA methylation inheritance into intergenerational inheritance and transgenerational inheritance and found that environmental factors may induce heritable phenotypes in cattle in a non-genetic way [137][138][139][140][141][142]. Genetic studies of DNA methylation during mitosis in mammalian cells have shown that DNA methylation acts through the establishment of stable genetic epigenetic memory and is stably propagated during cell division, but DNA methylation may also be dynamic in some key regulatory elements, and the kinetics of methylation turnover can influence gene expression [143].…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Effects of DNA Methylation on Gene Expression and Phenotypic Traits in Cattle: A Review

Zhang

Sheng

et al. 2023

IJMS

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Gene expression in cells is determined by the epigenetic state of chromatin. Therefore, the study of epigenetic changes is very important to understand the regulatory mechanism of genes at the molecular, cellular, tissue and organ levels. DNA methylation is one of the most studied epigenetic modifications, which plays an important role in maintaining genome stability and ensuring normal growth and development. Studies have shown that methylation levels in bovine primordial germ cells, the rearrangement of methylation during embryonic development and abnormal methylation during placental development are all closely related to their reproductive processes. In addition, the application of bovine male sterility and assisted reproductive technology is also related to DNA methylation. This review introduces the principle, development of detection methods and application conditions of DNA methylation, with emphasis on the relationship between DNA methylation dynamics and bovine spermatogenesis, embryonic development, disease resistance and muscle and fat development, in order to provide theoretical basis for the application of DNA methylation in cattle breeding in the future.

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“…This de novo DNA methylation occurs during cellular differentiation or germ cell and zygotic reprogramming [87]. De novo methylation is catalyzed by DNA methyltransferases such as DNMT3a, DNMT3b, and DNMT3L to establish methylation on unmodified DNA [88].…”

Section: Dna Methylationmentioning

confidence: 99%

Epigenetic Inheritance: Intergenerational Effects of Pesticides and Other Endocrine Disruptors on Cancer Development

Nicolella

Assis

2022

IJMS

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Parental environmental experiences affect disease susceptibility in the progeny through epigenetic inheritance. Pesticides are substances or mixtures of chemicals—some of which are persistent environmental pollutants—that are used to control pests. This review explores the evidence linking parental exposure to pesticides and endocrine disruptors to intergenerational and transgenerational susceptibility of cancer in population studies and animal models. We also discuss the impact of pesticides and other endocrine disruptors on the germline epigenome as well as the emerging evidence for how epigenetic information is transmitted between generations. Finally, we discuss the importance of this mode of inheritance in the context of cancer prevention and the challenges ahead.

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Epigenetic inheritance of acquired traits through DNA methylation

Cited by 14 publications

References 70 publications

Methyl-TWAS: A powerful method forin silicotranscriptome-wide association studies (TWAS) using long-range DNA methylation

Methyl-TWAS: A powerful method forin silicotranscriptome-wide association studies (TWAS) using long-range DNA methylation

Effects of DNA Methylation on Gene Expression and Phenotypic Traits in Cattle: A Review

Epigenetic Inheritance: Intergenerational Effects of Pesticides and Other Endocrine Disruptors on Cancer Development

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