scholarly journals Transposable Elements: Targets for Early Nutritional Effects on Epigenetic Gene Regulation

2003 ◽  
Vol 23 (15) ◽  
pp. 5293-5300 ◽  
Author(s):  
Robert A. Waterland ◽  
Randy L. Jirtle
Keyword(s):  
Dna Methylation ◽  
Gene Regulation ◽  
Transposable Element ◽  
Methylation Status ◽  
Dietary Supplementation ◽  
Vitamin B ◽  
Transposable Element Insertion ◽  
Insertion Sites ◽  
Nutritional Effects ◽  
Epigenetic Gene Regulation

ABSTRACT Early nutrition affects adult metabolism in humans and other mammals, potentially via persistent alterations in DNA methylation. With viable yellow agouti (Avy ) mice, which harbor a transposable element in the agouti gene, we tested the hypothesis that the metastable methylation status of specific transposable element insertion sites renders them epigenetically labile to early methyl donor nutrition. Our results show that dietary methyl supplementation of a/a dams with extra folic acid, vitamin B12, choline, and betaine alter the phenotype of their Avy/a offspring via increased CpG methylation at the Avy locus and that the epigenetic metastability which confers this lability is due to the Avy transposable element. These findings suggest that dietary supplementation, long presumed to be purely beneficial, may have unintended deleterious influences on the establishment of epigenetic gene regulation in humans.

scholarly journals Allopolyploidy has a moderate impact on restructuring at three contrasting transposable element insertion sites in resynthesizedBrassica napusallotetraploids

2013 ◽  
Vol 198 (2) ◽  
pp. 593-604 ◽  
Author(s):  
Véronique Sarilar ◽  
Paulina Martinez Palacios ◽  
Agnès Rousselet ◽  
Céline Ridel ◽  
Matthieu Falque ◽  
...  
Keyword(s):  
Transposable Element ◽  
Transposable Element Insertion ◽  
Element Insertion ◽  
Insertion Sites

scholarly journals DNA Methylation Changes and Its Associated Genes in Mulberry (Morus alba L.) Yu-711 Response to Drought Stress Using MethylRAD Sequencing

Plants ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 190
Author(s):  
Michael Ackah ◽  
Liangliang Guo ◽  
Shaocong Li ◽  
Xin Jin ◽  
Charles Asakiya ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Gene Regulation ◽  
Drought Stress ◽  
Methylation Status ◽  
Enrichment Analysis ◽  
Plant Genome ◽  
Pcr Analysis ◽  
Kegg Pathways ◽  
Wide Range ◽  
And Control

Drought stress remains one of the most detrimental environmental cues affecting plant growth and survival. In this work, the DNA methylome changes in mulberry leaves under drought stress (EG) and control (CK) and their impact on gene regulation were investigated by MethylRAD sequencing. The results show 138,464 (37.37%) and 56,241 (28.81%) methylation at the CG and CWG sites (W = A or T), respectively, in the mulberry genome between drought stress and control. The distribution of the methylome was prevalent in the intergenic, exonic, intronic and downstream regions of the mulberry plant genome. In addition, we discovered 170 DMGs (129 in CG sites and 41 in CWG sites) and 581 DMS (413 in CG sites and 168 in CWG sites). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicates that phenylpropanoid biosynthesis, spliceosome, amino acid biosynthesis, carbon metabolism, RNA transport, plant hormone, signal transduction pathways, and quorum sensing play a crucial role in mulberry response to drought stress. Furthermore, the qRT-PCR analysis indicates that the selected 23 genes enriched in the KEGG pathways are differentially expressed, and 86.96% of the genes share downregulated methylation and 13.04% share upregulation methylation status, indicating the complex link between DNA methylation and gene regulation. This study serves as fundamentals in discovering the epigenomic status and the pathways that will significantly enhance mulberry breeding for adaptation to a wide range of environments.

Exploring and exploiting epigenetic variation in cropsThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 856-868 ◽  
Author(s):  
Graham J King ◽  
Stephen Amoah ◽  
Smita Kurup
Keyword(s):  
Dna Methylation ◽  
Gene Regulation ◽  
Genetic Improvement ◽  
Developmental Stages ◽  
De Novo ◽  
Methylation Status ◽  
Intervention Strategy ◽  
Morphological Plasticity ◽  
Epigenetic Mark ◽  
Epigenetic Variation

This review addresses the mechanisms by which epigenetic variation modulates plant gene regulation and phenotype. In particular we explore the scope for harnessing such processes within the context of crop genetic improvement. We focus on the role of DNA methylation as an epigenetic mark that contributes to epiallelic diversity and modulation of gene regulation. We outline the prevalence and distribution of epigenetic marks in relation to eukaryote developmental processes, and in particular identify where this may be relevant to crop traits both in terms of specific developmental stages and in relation to physiological responses to environmental change. Recent whole genome surveys have identified specific characteristics of the distribution of DNA methylation within plant genomes. Together with greater understanding of the mode of action of different maintenance and de novo methyltransferases, this provides an opportunity to modulate DNA methylation status at specific loci as an intervention strategy in crop genetic improvement. We discuss alternative approaches that may be suitable for harnessing such induced epiallelic variation. Most of the discussion is associated with Brassica crops, which demonstrate considerable morphological plasticity, segmental chromosomal duplication, and polyploidy.

scholarly journals Association of air pollution and homocysteine with global DNA methylation: A population-based study from North India

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260860
Author(s):  
Suniti Yadav ◽  
Imnameren Longkumer ◽  
Priyanka Rani Garg ◽  
Shipra Joshi ◽  
Sunanda Rajkumari ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Air Pollution ◽  
Methylation Status ◽  
Population Based ◽  
North India ◽  
Nutritional Deficiencies ◽  
Global Dna Methylation ◽  
Vitamin B ◽  
Global Methylation ◽  
B Vitamin

Background Anthropogenic air pollution has been implicated in aberrant changes of DNA methylation and homocysteine increase (>15μM/L). Folate (<3 ng/mL) and vitamin B12 (<220 pg/mL) deficiencies also reduce global DNA methylation via homocysteine increase. Although B-vitamin supplements can attenuate epigenetic effects of air pollution but such understanding in population-specific studies are lacking. Hence, the present study aims to understand the role of air pollution, homocysteine, and nutritional deficiencies on methylation. Methods We examined cross-sectionally, homocysteine, folate, vitamin B12 (chemiluminescence) and global DNA methylation (colorimetric ELISA Assay) among 274 and 270 individuals from low- and high- polluted areas, respectively, from a single Mendelian population. Global DNA methylation results were obtained on 254 and 258 samples from low- and high- polluted areas, respectively. Results Significant decline in median global DNA methylation was seen as a result of air pollution [high-0.84 (0.37–1.97) vs. low-0.96 (0.45–2.75), p = 0.01]. High homocysteine in combination with air pollution significantly reduced global DNA methylation [high-0.71 (0.34–1.90) vs. low-0.93 (0.45–3.00), p = 0.003]. Folate deficient individuals in high polluted areas [high-0.70 (0.37–1.29) vs. low-1.21 (0.45–3.65)] showed significantly reduced global methylation levels (p = 0.007). In low polluted areas, despite folate deficiency, if normal vitamin B12 levels were maintained, global DNA methylation levels improved significantly [2.03 (0.60–5.24), p = 0.007]. Conversely, in high polluted areas despite vitamin B12 deficiency, if normal folate status was maintained, global DNA methylation status improved significantly [0.91 (0.36–1.63)] compared to vitamin B12 normal individuals [0.54 (0.26–1.13), p = 0.04]. Conclusions High homocysteine may aggravate the effects of air pollution on DNA methylation. Vitamin B12 in low-polluted and folate in high-polluted areas may be strong determinants for changes in DNA methylation levels. The effect of air pollution on methylation levels may be reduced through inclusion of dietary or supplemented B-vitamins. This may serve as public level approach in natural settings to prevent metabolic adversities at community level.

scholarly journals Aberrant DNA Methylation of ABC Transporters in Cancer

Cells ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 2281
Author(s):  
Katja Zappe ◽  
Margit Cichna-Markl
Keyword(s):  
Dna Methylation ◽  
Gene Regulation ◽  
Multidrug Resistance ◽  
Cancer Therapy ◽  
Abc Transporters ◽  
Current Knowledge ◽  
Methylation Status ◽  
Limited Effectiveness ◽  
Cancer Types ◽  
Aberrant Dna Methylation

ATP-binding cassette (ABC) transporters play a crucial role in multidrug resistance (MDR) of cancers. They function as efflux pumps, resulting in limited effectiveness or even failure of therapy. Increasing evidence suggests that ABC transporters are also involved in tumor initiation, progression, and metastasis. Tumors frequently show multiple genetic and epigenetic abnormalities, including changes in histone modification and DNA methylation. Alterations in the DNA methylation status of ABC transporters have been reported for a variety of cancer types. In this review, we outline the current knowledge of DNA methylation of ABC transporters in cancer. We give a brief introduction to structure, function, and gene regulation of ABC transporters that have already been investigated for their DNA methylation status in cancer. After giving an overview of the applied methodologies and the CpGs analyzed, we summarize and discuss the findings on aberrant DNA methylation of ABC transporters by cancer types. We conclude our review with the discussion of the potential to target aberrant DNA methylation of ABC transporters for cancer therapy.

scholarly journals Large-Scale Mapping of Transposable Element Insertion Sites Using Digital Encoding of Sample Identity

Genetics ◽  
2013 ◽  
Vol 196 (3) ◽  
pp. 615-623 ◽  
Author(s):  
Daryl M. Gohl ◽  
Limor Freifeld ◽  
Marion Silies ◽  
Jennifer J. Hwa ◽  
Mark Horowitz ◽  
...  
Keyword(s):  
Transposable Element ◽  
Large Scale ◽  
Transposable Element Insertion ◽  
Element Insertion ◽  
Digital Encoding ◽  
Insertion Sites ◽  
Sample Identity

scholarly journals Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods

2020 ◽  
Author(s):  
S. Lewis ◽  
L. Ross ◽  
S.A. Bain ◽  
E. Pahita ◽  
S.A. Smith ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Gene Regulation ◽  
Transposable Elements ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Cytosine Methylation ◽  
Epigenetic Modification ◽  
Small Subset ◽  
Epigenetic Gene Regulation ◽  
Methylation Patterns

AbstractCytosine methylation is an ancient epigenetic modification yet its function and extent within genomes is highly variable across eukaryotes. In mammals, methylation controls transposable elements and regulates the promoters of genes. In insects, DNA methylation is generally restricted to a small subset of transcribed genes, with both intergenic regions and transposable elements (TEs) depleted of methylation. The evolutionary origin and the function of these methylation patterns are poorly understood. Here we characterise the evolution of DNA methylation across the arthropod phylum. While the common ancestor of the arthropods had low levels of TE methylation and did not methylate promoters, both of these functions have evolved independently in centipedes and mealybugs. In contrast, methylation of the exons of a subset of transcribed genes is ancestral and widely conserved across the phylum, but has been lost in specific lineages. Remarkably the same set of genes are likely to be methylated in all species that retained exon-enriched methylation. We show that these genes have characteristic patterns of expression correlating to broad transcription initiation sites and well-positioned nucleosomes, providing new insights into potential mechanisms driving methylation patterns over hundreds of millions of years.Author SummaryAnimals develop from a single cell to form a complex organism with many specialised cells. Almost all of the fantastic variety of cells must have the same sequence of DNA, and yet they have distinct identities that are preserved even when they divide. This remarkable process is achieved by turning different sets of genes on or off in different types of cell using molecular mechanisms known as “epigenetic gene regulation”.Surprisingly, though all animals need epigenetic gene regulation, there is a huge diversity in the mechanisms that they use. Characterising and explaining this diversity is crucial in understanding the functions of epigenetic pathways, many of which have key roles in human disease. We studied how one particular type of epigenetic regulation, known as DNA methylation, has evolved within arthropods. Arthropods are an extraordinarily diverse group of animals ranging from horseshoe crabs to fruit flies. We discovered that the levels of DNA methylation and where it is found within the genome changes rapidly throughout arthropod evolution. Nevertheless, there are some features of DNA methylation that seem to be the same across most arthropods-in particular we found that there is a tendency for a similar set of genes to acquire methylation of DNA in most arthropods, and that this is conserved over 350 million years. We discovered that these genes have distinct features that might explain how methylation gets targeted. Our work provides important new insights into the evolution of DNA methylation and gives some new hints to its essential functions.

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