U.S. flag

An official website of the United States government

Dot gov

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Https

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

PubAg

Main content area

You searched for: Subject term DNA methylation Remove constraint Subject term: DNA methylation Subject term animals Remove constraint Subject term: animals
Start Over

Search

69  Search Results

« Previous | 1 - 50 of 69 |
Number of results to display per page

Search Results

1. Fine-grained investigation of the relationship between human nutrition and global DNA methylation patterns

Author:
Fabrizia Noro; Annalisa Marotta; Marialaura Bonaccio; Simona Costanzo; Federica Santonastaso; Sabatino Orlandi; Alfonsina Tirozzi; Roberta Parisi; Amalia De Curtis; Mariarosaria Persichillo; Francesco Gianfagna; Augusto Di Castelnuovo; Maria Benedetta Donati; Chiara Cerletti; Giovanni de Gaetano; Licia Iacoviello; Alessandro Gialluisi; Benedetta Izzi; Moli-sani Study Investigators
Source:
European journal of nutrition 2022 v.61 no.3 pp. 1231-1243
ISSN:
1436-6207
Subject:
DNA; DNA methylation; Mediterranean diet; animals; environmental factors; epigenetics; food frequency questionnaires; food intake; human health; human nutrition; niacin; statistics; zinc
Abstract:
... PURPOSE: Nutrition is an important, modifiable, environmental factor affecting human health by modulating epigenetic processes, including DNA methylation (5mC). Numerous studies investigated the association of nutrition with global and gene-specific DNA methylation and evidences on animal models highlighted a role in DNA hydroxymethylation (5hmC) regulation. However, a more comprehensive analysis ...
DOI:
10.1007/s00394-021-02716-8

2. Prolonged exposure of azocyclotin induced inter- and transgenerational endocrine disruption on Danio rerio linked to transcriptomic and DNA methylomic alterations

Author:
Fang Jiao; Yongfang Ma; Tiantian Hu; Kun Qiao; Yao Jiang; Wei Zhu; Quan Jin; Wenjun Gui
Source:
Chemosphere 2022 v.302 pp. 134847
ISSN:
0045-6535
Subject:
DNA; DNA hypomethylation; Danio rerio; acaricides; adults; animals; azocyclotin; body length; body weight; cytosine; egg production; epigenetics; estradiol; gene expression regulation; genes; gonadosomatic index; hepatosomatic index; oocytes; progeny; risk assessment; toxicity; transcriptomics
Abstract:
... The transgenerational effect assessment linked to epigenetic analysis of environmental pollutants on eco (toxico)logical relevant species is regarded as a potential future risk-assessment tool. As an organotin acaricide widely used in China, azocyclotin can lead to endocrine disrupting effect on directly exposed environmental organisms, but whether it has transgenerational negative impact remains ...
DOI:
10.1016/j.chemosphere.2022.134847

3. DNA Methylation and gene expression patterns are widely altered in fetal growth restriction and associated with FGR development

Author:
Seoyeong Lee; Young Nam Kim; DoHwa Im; Su Han Cho; Jiyeon Kim; Jeong-Hyun Kim; Kwoneel Kim
Source:
Animal cells and systems 2021 v.25 no.3 pp. 128-135
ISSN:
2151-2485
Subject:
DNA; DNA methylation; animals; blood; coronary artery disease; epigenetics; fetal development; fetus; gene expression; gene expression regulation; genes; metabolism; noninsulin-dependent diabetes mellitus; stroke; transcriptomics
Abstract:
... Fetal growth restriction (FGR) is the failure of the fetus toachieve its genetically determined growth potential, which increasesrisks for a variety of genetic diseases, such as type 2 diabetes mellitus, coronary artery disease, and stroke, during the lifetime. The dysregulation of DNA methylationis known to interact with environmental fluctuations, affect gene expressions comprehensively, and be ...
DOI:
10.1080/19768354.2021.1925741

4. DNA methylation is not a driver of gene expression reprogramming in young honey bee workers

Author:
Carlos A. M. Cardoso‐Júnior; Boris Yagound; Isobel Ronai; Emily J. Remnant; Klaus Hartfelder; Benjamin P. Oldroyd
Source:
Molecular ecology 2021 v.30 no.19 pp. 4804-4818
ISSN:
0962-1083
Subject:
DNA methylation; DNA methyltransferase; animals; brain; ecology; epigenetics; gene expression; gene expression regulation; genes; social insects
Abstract:
... The presence of DNA methylation marks within genic intervals, also called gene body methylation, is an evolutionarily‐conserved epigenetic hallmark of animal and plant methylomes. In social insects, gene body methylation is thought to contribute to behavioural plasticity, for example between foragers and nurse workers, by modulating gene expression. However, recent studies have suggested that the ...
DOI:
10.1111/mec.16098

5. Epigenetic manipulation of filamentous fungi for biotechnological applications: a systematic review

Author:
Marcio José Poças-Fonseca; Camila Gomes Cabral; João Heitor Colombelli Manfrão-Netto
Source:
Biotechnology letters 2020 v.42 no.6 pp. 885-904
ISSN:
0141-5492
Subject:
Candida albicans; DNA methylation; Saccharomyces cerevisiae; Schizosaccharomyces pombe; animals; cellulases; chromatin; drugs; endophytes; entomopathogens; epigenetics; eukaryotic cells; genes; histones; homeostasis; non-coding RNA; plants (botany); post-translational modification; secondary metabolites; systematic review; virulence; xylanases; yeasts
Abstract:
... The study of the epigenetic regulation of gene function has reached pivotal importance in life sciences in the last decades. The mechanisms and effects of processes such as DNA methylation, histone posttranslational modifications and non-coding RNAs, as well as their impact on chromatin structure and dynamics, are clearly involved in physiology homeostasis in plants, animals and microorganisms. In ...
DOI:
10.1007/s10529-020-02871-8

6. MeCP2: latest insights fundamentally change our understanding of its interactions with chromatin and its functional attributes

Author:
John B. Vincent; Juan Ausió
Source:
BioEssays 2021 v.43 no.3 pp. e2000281
ISSN:
0265-9247
Subject:
DNA; DNA methylation; animals; genome; heterochromatin; histones
Abstract:
... Methyl CpG binding protein 2 (MeCP2) was initially isolated as an exclusive reader of DNA methylated at CpG. This recognition site, was subsequently extended to other DNA methylated residues and it has been the persisting dogma that binding to methylated DNA constitutes its physiologically relevant role. As we review here, two very recent papers fundamentally change our understanding of the intera ...
DOI:
10.1002/bies.202000281

7. Blueberry anthocyanin alleviate perfluorooctanoic acid-induced toxicity in planarian (Dugesia japonica) by regulating oxidative stress biomarkers, ATP contents, DNA methylation and mRNA expression

Author:
Jianyong Zhang; Bin Wang; Bosheng Zhao; Yanqing Li; Xiuyun Zhao; Zuoqing Yuan
Source:
Environmental pollution 2019 v.245 pp. 957-964
ISSN:
0269-7491
Subject:
DNA methylation; Dugesia; adenosine triphosphate; adenosinetriphosphatase; animals; anthocyanins; antioxidants; biomarkers; blueberries; energy metabolism; enzyme activity; gene expression; glutathione peroxidase; glutathione transferase; glutathione-disulfide reductase; malondialdehyde; messenger RNA; oxidative stress; perfluorooctanoic acid; protective effect; toxicity
Abstract:
... Blueberry anthocyanin (BA) have strong health benefits as an active natural antioxidant and perfluorooctanoic acid (PFOA) can result in oxidative stress in animals. In our study, the protective effects of BA against stress induced by PFOA was investigated in the planarian Dugesia japonica using oxidative stress biomarkers, ATP contents, ATPase activity, DNA methylation and mRNA expression. PFOA ex ...
DOI:
10.1016/j.envpol.2018.11.094

8. Epigenomic Remodeling in Huntington’s Disease—Master or Servant?

Author:
Geraldine Zimmer-Bensch
Source:
Epigenomes 2020 v.4 no.3 pp. -
ISSN:
2075-4655
Subject:
DNA methylation; animals; epigenetics; epigenome; exons; gene expression; genetic disorders; glutamine; histones; neurodegenerative diseases; neurons; neurophysiology; pathogenesis; risk; therapeutics
Abstract:
... In light of our aging population, neurodegenerative disorders are becoming a tremendous challenge, that modern societies have to face. They represent incurable, progressive conditions with diverse and complex pathological features, followed by catastrophic occurrences of massive neuronal loss at the later stages of the diseases. Some of these disorders, like Huntington’s disease (HD), rely on defi ...
DOI:
10.3390/epigenomes4030015

9. Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana

Author:
Hainan Zhao; Wenli Zhang; Tao Zhang; Yuan Lin; Yaodong Hu; Chao Fang; Jiming Jiang
Source:
Genome biology 2020 v.21 no.1 pp. 24
ISSN:
1474-760X
Subject:
Arabidopsis thaliana; DNA methylation; animals; chromatin; deoxyribonuclease I; epigenetics; gene expression; genomics; regulatory proteins; regulatory sequences; repressor proteins; transposases; transposons
Abstract:
... BACKGROUND: Regulation of transcription depends on interactions between cis-regulatory elements (CREs) and regulatory proteins. Active CREs are imbedded in open chromatin that are accessible to nucleases. Several techniques, including DNase-seq, which is based on nuclease DNase I, and ATAC-seq, which is based on transposase Tn5, have been widely used to identify genomic regions associated with ope ...
DOI:
10.1186/s13059-020-1927-5
PubMed:
32014062
PubMed Central:
PMC6996174

10. Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis

Author:
Kinga Rutowicz; Maciej Lirski; Benoît Mermaz; Gianluca Teano; Jasmin Schubert; Imen Mestiri; Magdalena A. Kroteń; Tohnyui Ndinyanka Fabrice; Simon Fritz; Stefan Grob; Christoph Ringli; Lusik Cherkezyan; Fredy Barneche; Andrzej Jerzmanowski; Célia Baroux
Source:
Genome biology 2019 v.20 no.1 pp. 157
ISSN:
1474-760X
Subject:
Arabidopsis; DNA methylation; acetylation; animals; callus formation; epigenetics; evolution; flowering date; gene expression; genes; heterochromatin; histones; models; nucleosomes; phenotype; roots; seed dormancy; stomata; transcription (genetics); transcriptome; transposons
Abstract:
... BACKGROUND: Chromatin provides a tunable platform for gene expression control. Besides the well-studied core nucleosome, H1 linker histones are abundant chromatin components with intrinsic potential to influence chromatin function. Well studied in animals, little is known about the evolution of H1 function in other eukaryotic lineages for instance plants. Notably, in the model plant Arabidopsis, w ...
DOI:
10.1186/s13059-019-1767-3
PubMed:
31391082
PubMed Central:
PMC6685187

11. Molecular mechanisms of fumonisin B1-induced toxicities and its applications in the mechanism-based interventions

Author:
Xiaoyi Liu; Lihong Fan; Shutao Yin; Hui Chen; Hongbo Hu
Source:
Toxicon 2019 v.167 pp. 1-5
ISSN:
0041-0101
Subject:
DNA methylation; adverse effects; animals; autophagy; endoplasmic reticulum; fumonisin B1; hepatotoxicity; human health; metabolism; mitogen-activated protein kinase; nephrotoxicity; neurotoxicity; oxidative stress; sphingolipids
Abstract:
... Fumonisin B1 (FB1), the most toxic member of fumonisins, is one of the most common mycotoxins contaminating feed and food. It has been shown to produce pleiotropic toxicities in animals including neurotoxicity, hepatotoxicity and nephrotoxicity, and with highly potential impact on human health. Proposed mechanisms include disruption of sphingolipid metabolism, induction of oxidative stress, activa ...
DOI:
10.1016/j.toxicon.2019.06.009

12. Effects of chronic exposure to benzophenone and diclofenac on DNA methylation levels and reproductive success in a marine copepod

Author:
Anais Guyon; Kirsty F. Smith; Maria P. Charry; Olivier Champeau; Louis A. Tremblay
Source:
Journal of xenobiotics 2018 v.8 no.1 pp. -
ISSN:
2039-4705
Subject:
Copepoda; DNA methylation; UV filters; acute toxicity; animals; benzophenones; breeding; chronic exposure; copper; diclofenac; eggs; females; hatching; reproductive success; toxicity testing; viability; xenobiotics
Abstract:
... The UV-filter benzophenone and the anti-inflammatory diclofenac are commonly detected in the environment. The aim of this study was to assess the multigenerational effects of chronic exposure to low concentrations of these chemicals on toxicity and DNA methylation levels in the copepod Gladioferens pectinatus. Acute toxicity tests were conducted to determine the sensitivity of G. pectinatus to the ...
DOI:
10.4081/xeno.2018.7674
PubMed:
30701062
PubMed Central:
PMC6343104

13. Epigenetics of Social Behaviour

Author:
Frank Seebacher; Jens Krause
Source:
Trends in ecology & evolution 2019 v.34 no.9 pp. 818-830
ISSN:
0169-5347
Subject:
animals; ecology; epigenetics; evolution; gene flow; physiology; social behavior
Abstract:
... Many animals occur in groups, and the ecology and evolution of populations and species are intrinsically linked to group function and social behaviour. Here we summarise recent data showing that the biotic and abiotic environments can have far-reaching consequences for social behaviour via epigenetic mechanisms that modify physiological processes. The environment affects the physiology of individu ...
DOI:
10.1016/j.tree.2019.04.017

14. Plant lamin-like proteins mediate chromatin tethering at the nuclear periphery

Author:
Bo Hu; Nan Wang; Xiuli Bi; Ezgi Süheyla Karaaslan; Anna-Lena Weber; Wangsheng Zhu; Kenneth Wayne Berendzen; Chang Liu
Source:
Genome biology 2019 v.20 no.1 pp. 87
ISSN:
1474-760X
Subject:
Arabidopsis thaliana; DNA; DNA methylation; animals; chromosome painting; cytoplasm; heterochromatin; mutants; nuclear membrane; plants (botany)
Abstract:
... BACKGROUND: The nuclear envelope not only serves as a physical barrier separating nuclear content from the cytoplasm but also plays critical roles in modulating the three-dimensional organization of genomic DNA. For both plants and animals, the nuclear periphery is a functional compartment enriched with heterochromatin. To date, how plants manage to selectively tether chromatin at the nuclear peri ...
DOI:
10.1186/s13059-019-1694-3
PubMed:
31039799
PubMed Central:
PMC6492433

15. Resveratrol up-regulates ATP2A3 gene expression in breast cancer cell lines through epigenetic mechanisms

Author:
Eduardo Izquierdo-Torres; Andrés Hernández-Oliveras; Iván Meneses-Morales; Gabriela Rodríguez; Gabriela Fuentes-García; Ángel Zarain-Herzberg
Source:
international journal of biochemistry & cell biology 2019 v.113 pp. 37-47
ISSN:
1357-2725
Subject:
acetylation; animals; apoptosis; binding proteins; breast neoplasms; calcium; cell lines; chemoprevention; epigenetics; gene expression; gene expression regulation; genes; histones; methylation; models; neoplasm cells; plant estrogens; resveratrol
Abstract:
... Resveratrol (RSV) is a phytoestrogen which has been related to chemoprevention of several types of cancer. In this work, we show up to a 6-fold increased expression of ATP2A3 gene induced by RSV that triggers apoptosis and changes of intracellular Ca2+ management in MCF-7 and MDA-MB-231 breast cancer cell lines. We explored epigenetic mechanisms for that RSV-induced ATP2A3 up-regulation. The resul ...
DOI:
10.1016/j.biocel.2019.05.020

16. Role of methionine on epigenetic modification of DNA methylation and gene expression in animals

Author:
Naifeng Zhang
Source:
Animal nutrition 2018 v.4 no.1 pp. 11-16
ISSN:
2405-6383
Subject:
DNA methylation; S-adenosylmethionine; animal health; animal nutrition; animals; epigenetics; gene expression; genes; hemostasis; metabolism; promoter regions; tissues
Abstract:
... DNA methylation is one of the main epigenetic phenomena affecting gene expression. It is an important mechanism for the development of embryo, growth and health of animals. As a key nutritional factor limiting the synthesis of protein, methionine serves as the precursor of S-adenosylmethionine (SAM) in the hepatic one-carbon metabolism. The dietary fluctuation of methionine content can alter the l ...
DOI:
10.1016/j.aninu.2017.08.009
PubMed:
30167479
PubMed Central:
PMC6112339

17. The role of plant epigenetics in biotic interactions

Author:
Conchita Alonso; Daniela Ramos‐Cruz; Claude Becker
Source:
new phytologist 2019 v.221 no.2 pp. 731-737
ISSN:
0028-646X
Subject:
DNA methylation; animals; antagonists; biocenosis; epigenetics; histones; microorganisms; models; mutualism; phenotypic plasticity; stress response
Abstract:
... Contents Summary 731 I. Biotic interactions in the context of genetic, epigenetic and environmental diversity 731 II. Biotic interactions affect epigenetic configuration 732 III. Plant epigenetic configuration influences biotic interactions 733 IV. Epigenetic memory in the context of biotic interactions 734 V. Conclusions and future research 735 Acknowledgements 735 Author contributions 735 Refere ...
DOI:
10.1111/nph.15408
PubMed:
30156271
PubMed Central:
PMC6726468

18. A comparison and column selection of Hydrophilic Interaction Liquid Chromatography and Reversed-Phase High-Performance Liquid Chromatography for detection of DNA methylation

Author:
Leila Rastegar; Hossein Mighani; Alireza Ghassempour
Source:
Analytical biochemistry 2018 v.557 pp. 123-130
ISSN:
0003-2697
Subject:
DNA; DNA methylation; animals; bacteria; cytosine; detection limit; epigenetics; hydrolysis; hydrophilic interaction chromatography; reversed-phase high performance liquid chromatography; solutes
Abstract:
... 5-methylcytosine (5mC) is an epigenetic mark which has a profound effect on various fundamental processes in cells. In present study, at first Hydrophilic Interaction Liquid Chromatography (HILIC) was compared with Reversed-Phase High-Performance Liquid Chromatography (RP-HPLC) based on their selectivity (α), retention factor (k), and resolution (R) for cytosine (C) and 5mC nucleobases. We tried t ...
DOI:
10.1016/j.ab.2018.07.013

19. Bisphenol A: What lies beneath its induced diabetes and the epigenetic modulation?

Author:
Soheila Rahmani; Nazila Pour Khalili; Fazlullah Khan; Shokoufeh Hassani; Elmira Ghafour-Boroujerdi; Mohammad Abdollahi
Source:
Life sciences 2018 v.214 pp. 136-144
ISSN:
0024-3205
Subject:
DNA methylation; adipocytes; animals; bisphenol A; demethylation; endocrine-disrupting chemicals; epigenetics; estrogenic properties; fatty liver; genes; glucose; histones; homeostasis; insulin; islets of Langerhans; lipids; liver; microRNA; noninsulin-dependent diabetes mellitus; obesity; pollution; skeletal muscle; toxicity
Abstract:
... Nowadays, endocrine disrupting chemical pollution has become one of the major concerns due to the potential role of these chemicals in provoking endocrine disorders especially type 2 diabetes. As a widespread endocrine disrupting chemical, Bisphenol A, with modest estrogenic activity can exert its detrimental effects in the different organs involved in type 2 diabetes such as pancreas, liver, adip ...
DOI:
10.1016/j.lfs.2018.10.044

20. Bisulfite Sequencing with Daphnia Highlights a Role for Epigenetics in Regulating Stress Response to Microcystis through Preferential Differential Methylation of Serine and Threonine Amino Acids

Author:
Asselman Jana; De Coninck Dieter IM; Beert Eline; Janssen Colin R.; Orsini Luisa; Pfrender Michael E.; Decaestecker Ellen; De Schamphelaere Karel AC
Source:
Environmental Science & Technology 2017 v.51 no.2 pp. 924-931
ISSN:
1520-5851
Subject:
epigenetics; alternative splicing; protein synthesis; DNA methylation; animals; ecotoxicology; serine; threonine; stress response; models; risk assessment; codons; toxicity; Microcystis aeruginosa; exons; Daphnia magna
Abstract:
... Little is known about the influence that environmental stressors may have on genome-wide methylation patterns, and to what extent epigenetics may be involved in environmental stress response. Yet, studies of methylation patterns under stress could provide crucial insights on stress response and toxicity pathways. Here, we focus on genome-wide methylation patterns in the microcrustacean Daphnia mag ...
DOI:
10.1021/acs.est.6b03870

21. CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data

Author:
Weilong Guo; Ping Zhu; Matteo Pellegrini; Michael Q Zhang; Xiangfeng Wang; Zhongfu Ni; Inanc Birol
Source:
Bioinformatics 2018 v.34 no.3 pp. 381-387
ISSN:
1460-2059
Subject:
DNA; DNA methylation; animals; bioinformatics; bisulfites; carcinogenesis; computer software; data collection; gene silencing; genes; genetic variation; heterozygosity; neoplasms; plants (botany); sequence analysis; transposons
Abstract:
... DNA methylation is important for gene silencing and imprinting in both plants and animals. Recent advances in bisulfite sequencing allow detection of single nucleotide variations (SNVs) achieving high sensitivity, but accurately identifying heterozygous SNVs from partially C-to-T converted sequences remains challenging. We designed two methods, BayesWC and BinomWC, that substantially improved the ...
DOI:
10.1093/bioinformatics/btx595
PubMed:
28968643
PubMed Central:
PMC6454434

22. Cryphonectria hypovirus 1-Induced Epigenetic Changes in Infected Phytopathogenic Fungus Cryphonectria parasitica

Author:
Lucija Nuskern; Marin Ježić; Zlatko Liber; Jelena Mlinarec; Mirna Ćurković-Perica
Source:
Microbial ecology 2018 v.75 no.3 pp. 790-798
ISSN:
0095-3628
Subject:
Castanea; Cryphonectria hypovirus 1; Cryphonectria parasitica; DNA methylation; animals; biological control; biotic stress; enzymes; epigenetics; forest ecosystems; genome; microbial growth; models; mycoviruses; orchards; plant pathogenic fungi; plants (botany); virulence
Abstract:
... Biotic stress caused by virus infections induces epigenetic changes in infected plants and animals, but this is the first report on methylation pattern changes in a fungus after mycovirus infection. As a model pathosystem for mycovirus-host interactions, we used Cryphonectria hypovirus 1 (CHV1) and its host fungus Cryphonectria parasitica, in which deregulation of methylation cycle enzymes upon vi ...
DOI:
10.1007/s00248-017-1064-1

23. Developmental DNA methyltransferase expression in the fire ant Solenopsis invicta

Author:
Sasha Kay; Daniel Skowronski; Brendan G. Hunt
Source:
Insect science 2018 v.25 no.1 pp. 57-65
ISSN:
1672-9609
Subject:
DNA; DNA methylation; Solenopsis invicta; adults; animals; embryogenesis; females; fire ants; gametogenesis; gene expression regulation; insect development; males; messenger RNA; methyltransferases; plasticity; quantitative polymerase chain reaction; testes
Abstract:
... DNA methylation is accomplished in animals by 2 classes of enzymes known as DNA methyltransferases, DNMT3 and DNMT1, which perform de novo methylation and maintenance methylation, respectively. Several studies of hymenopteran eusocial insects suggest that DNA methylation is capable of influencing developmental plasticity. However, fundamental questions remain about the patterning of DNA methylatio ...
DOI:
10.1111/1744-7917.12413

24. Effect of supplementation with methyl-donor nutrients on neurodevelopment and cognition: considerations for future research

Author:
Sarah E McKee; Teresa M Reyes
Source:
Nutrition reviews 2018 v.76 no.7 pp. 497-511
ISSN:
1753-4887
Subject:
DNA methylation; animals; biomedical research; brain; cognition; diet; fetal development; fetus; gene expression; malnutrition; maternal nutrition; models; nervous system diseases; neurodevelopment; neurons; nutrient deficiencies; nutrients; pregnancy; progeny; risk
Abstract:
... Pregnancy represents a critical period in fetal development, such that the prenatal environment can, in part, establish a lifelong trajectory of health or disease for the offspring. Poor nutrition (macro- or micronutrient deficiencies) can adversely affect brain development and significantly increase offspring risk for metabolic and neurological disease development. The concentration of dietary me ...
DOI:
10.1093/nutrit/nuy007
PubMed:
29701796
PubMed Central:
PMC6887696

25. Entering the Next Dimension: Plant Genomes in 3D

Author:
Mariana Sotelo-Silveira; Ricardo A. Chávez Montes; Jose R. Sotelo-Silveira; Nayelli Marsch-Martínez; Stefan de Folter
Source:
Trends in plant science 2018 v.23 no.7 pp. 598-612
ISSN:
1360-1385
Subject:
Arabidopsis; DNA methylation; animals; chromatin; epigenetics; genes; histones; transcription (genetics)
Abstract:
... After linear sequences of genomes and epigenomic landscape data, the 3D organization of chromatin in the nucleus is the next level to be explored. Different organisms present a general hierarchical organization, with chromosome territories at the top. Chromatin interaction maps, obtained by chromosome conformation capture (3C)-based methodologies, for eight plant species reveal commonalities, but ...
DOI:
10.1016/j.tplants.2018.03.014

26. Epigenetic Effects in Livestock Breeding

Author:
A. F. Yakovlev
Source:
Russian journal of genetics 2018 v.54 no.8 pp. 897-909
ISSN:
1022-7954
Subject:
DNA; DNA methylation; RNA; additives; animals; breeding programs; chromatin; diet; epigenetics; genes; genomics; high-throughput nucleotide sequencing; histones; inheritance (genetics); lipid metabolism; livestock breeding; meiosis; muscle tissues; phenotypic variation; precipitin tests
Abstract:
... Epigenetic effects are considered as a mechanism of the emergence of new inherited traits with their transmission between generations through meiosis. Modern genomic evaluation does not explain the entire phenotypic variance of traits. It is quite obvious that a significant part of the unaccounted dispersion reflects epigenetic effects carried out through DNA methylation, histone and chromatin mod ...
DOI:
10.1134/S1022795418080148

27. ViewBS: a powerful toolkit for visualization of high-throughput bisulfite sequencing data

Author:
Xiaosan Huang; Shaoling Zhang; Kongqing Li; Jyothi Thimmapuram; Shaojun Xie; Jonathan Wren
Source:
Bioinformatics 2018 v.34 no.4 pp. 708-709
ISSN:
1460-2059
Subject:
Arabidopsis thaliana; DNA; DNA methylation; animals; bioinformatics; bisulfites; data collection; heat; plants (botany); sequence analysis
Abstract:
... High throughput bisulfite sequencing (BS-seq) is an important technology to generate single-base DNA methylomes in both plants and animals. In order to accelerate the data analysis of BS-seq data, toolkits for visualization are required. ViewBS, an open-source toolkit, can extract and visualize the DNA methylome data easily and with flexibility. By using Tabix, ViewBS can visualize BS-seq for larg ...
DOI:
10.1093/bioinformatics/btx633
PubMed:
29087450
PubMed Central:
PMC5860610

28. Dynamic DNA methylation reconfiguration during seed development and germination

Author:
Taiji Kawakatsu; Joseph R. Nery; Rosa Castanon; Joseph R. Ecker
Source:
Genome biology 2017 v.18 no.1 pp. 171
ISSN:
1474-760X
Subject:
DNA; DNA methylation; animals; epigenetics; gene expression regulation; genome; germination; heterochromatin; plants (botany); pollen; seed development; seed dormancy; seeds; time series analysis; transposons
Abstract:
... BACKGROUND: Unlike animals, plants can pause their life cycle as dormant seeds. In both plants and animals, DNA methylation is involved in the regulation of gene expression and genome integrity. In animals, reprogramming erases and re-establishes DNA methylation during development. However, knowledge of reprogramming or reconfiguration in plants has been limited to pollen and the central cell. To ...
DOI:
10.1186/s13059-017-1251-x
PubMed:
28911331
PubMed Central:
PMC5599895

29. Epigenomic and functional analyses reveal roles of epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons

Author:
Qingxin Song; Tianzhen Zhang; David M. Stelly; Z. Jeffrey Chen
Source:
Genome biology 2017 v.18 no.1 pp. 99
ISSN:
1474-760X
Subject:
Arabidopsis; DNA methylation; allopolyploidy; animals; cotton; crops; diploidy; domestication; engineering; epigenetics; evolution; flowering date; gene expression; genes; hybrids; loci; meiosis; photoperiod; photoperiodism; seed dormancy; tetraploidy
Abstract:
... BACKGROUND: Polyploidy is a pervasive evolutionary feature of all flowering plants and some animals, leading to genetic and epigenetic changes that affect gene expression and morphology. DNA methylation changes can produce meiotically stable epialleles, which are transmissible through selection and breeding. However, the relationship between DNA methylation and polyploid plant domestication remain ...
DOI:
10.1186/s13059-017-1229-8
PubMed:
28558752
PubMed Central:
PMC5450403

30. Recurrent establishment of de novo centromeres in the pericentromeric region of maize chromosome 3

Author:
Hainan Zhao; Zixian Zeng; Dal-Hoe Koo; Bikram S. Gill; James A. Birchler; Jiming Jiang
Source:
Chromosome research 2017 v.25 no.3-4 pp. 299-311
ISSN:
0967-3849
Subject:
DNA; DNA methylation; Zea mays; animals; centromeres; chromatin; corn; epigenetics; genes; genomics; histones; nucleotide sequences; transcription (genetics)
Abstract:
... Centromeres can arise de novo from non-centromeric regions, which are often called “neocentromeres.” Neocentromere formation provides the best evidence for the concept that centromere function is not determined by the underlying DNA sequences, but controlled by poorly understood epigenetic mechanisms. Numerous neocentromeres have been reported in several plant and animal species. However, it has b ...
DOI:
10.1007/s10577-017-9564-x

31. The Effects of Hormone Treatment on Epigenetic Marks During Organogenesis in Pinus radiata D. Don Embryos

Author:
José L. Rodríguez; Luis Valledor; Rodrigo Hasbún; Pablo Sánchez; Roberto Rodríguez; María J. Cañal
Source:
Journal of plant growth regulation 2016 v.35 no.1 pp. 97-108
ISSN:
0721-7595
Subject:
2,4-D; DNA; DNA methylation; Pinus radiata; acetylation; animals; apical meristems; benzyladenine; cotyledons; epigenetics; gene expression; gene expression regulation; growth retardation; histones; indole butyric acid; organogenesis; plants (botany)
Abstract:
... Adventitious organogenesis from zygotic embryos is one of the most reliable techniques to propagate clonal Pinus radiata individuals. Regulation of gene expression has an important role to generate a correct caulogenic pattern, and genomic DNA methylation is amongst the main studied regulatory mechanisms in animals and plants. The aim of this work is to evaluate the role of DNA methylation and his ...
DOI:
10.1007/s00344-015-9510-0

32. Asymmetric cell division in plants: mechanisms of symmetry breaking and cell fate determination

Author:
Lynn Jo Pillitteri; Xiaoyu Guo; Juan Dong
Source:
Cellular and molecular life sciences 2016 v.73 no.22 pp. 4213-4229
ISSN:
1420-682X
Subject:
DNA methylation; animals; auxins; cell differentiation; cell division; cell polarity; cell wall components; chromatin; epigenetics; plant architecture; plants (botany); stem cells; transcription factors
Abstract:
... Asymmetric cell division is a fundamental mechanism that generates cell diversity while maintaining self-renewing stem cell populations in multicellular organisms. Both intrinsic and extrinsic mechanisms underpin symmetry breaking and differential daughter cell fate determination in animals and plants. The emerging picture suggests that plants deal with the problem of symmetry breaking using uniqu ...
DOI:
10.1007/s00018-016-2290-2
PubMed:
27286799
PubMed Central:
PMC5522748

33. BsRADseq: screening DNA methylation in natural populations of non‐model species

Author:
Emiliano Trucchi; Anna B. Mazzarella; Gregor D. Gilfillan; Maria T. Lorenzo; Peter Schönswetter; Ovidiu Paun
Source:
Molecular ecology 2016 v.25 no.8 pp. 1697-1713
ISSN:
0962-1083
Subject:
Caryophyllaceae; DNA; DNA methylation; Dactylorhiza; Gasterosteidae; animals; bioinformatics; diploidy; epigenetics; genome; habitats; loci; nucleotide sequences; screening; sequence analysis; single nucleotide polymorphism; tetraploidy
Abstract:
... Epigenetic modifications are expected to occur at a much faster rate than genetic mutations, potentially causing isolated populations to stochastically drift apart, or if they are subjected to different selective regimes, to directionally diverge. A high level of genome‐wide epigenetic divergence between individuals occupying distinct habitats is therefore predicted. Here, we introduce bisulfite‐c ...
DOI:
10.1111/mec.13550
PubMed:
26818626
PubMed Central:
PMC4949719

34. CpG methylated ribosomal RNA genes in relation to wing polymorphism in the rice pest Sogatella furcifera

Author:
Shi-Ke Liang; Zi-Qiang Liang; Xiao-Sui Zhou; Jia-Lin Chen; Guang-Hong Li; Fang-Hai Wang
Source:
Journal of Asia-Pacific entomology 2015 v.18 no.3 pp. 471-475
ISSN:
1226-8615
Subject:
DNA; DNA fragmentation; DNA methylation; Sogatella furcifera; adults; animals; cytosine; dimorphism; epigenetics; females; genes; genetic variation; insects; pests; phenotype; ribosomal RNA; rice; suppression subtractive hybridization
Abstract:
... Sogatella furcifera is a major rice pest that exhibits wing dimorphism. The methylation-sensitive representational difference analysis (MS-RDA) is widely used in plants and some animals to identify methylation differences in genomic DNA regions. However the method has been applied to insects very less. The objective of the current research was to monitor differential cytosine methylations at CCGG ...
DOI:
10.1016/j.aspen.2015.06.002

35. Genetic and epigenetic architecture of sex-biased expression in the jewel wasps Nasonia vitripennis and giraulti

Author:
Xu Wang; John H. Werren; Andrew G. Clark
Source:
Proceedings of the National Academy of Sciences of the United States of America 2015 v.112 no.27 pp. E3545
ISSN:
0027-8424
Subject:
DNA; Nasonia vitripennis; adults; animals; enzymes; epigenetics; females; gender differences; gene expression; gene expression regulation; genes; males; methylation; parasitic wasps; sex chromosomes; sex pheromones; sexual dimorphism; testes
Abstract:
... There is extraordinary diversity in sexual dimorphism (SD) among animals, but little is known about its epigenetic basis. To study the epigenetic architecture of SD in a haplodiploid system, we performed RNA-seq and whole-genome bisulfite sequencing of adult females and males from two closely related parasitoid wasps, Nasonia vitripennis and Nasonia giraulti . More than 75% of expressed genes disp ...
DOI:
10.1073/pnas.1510338112
PubMed:
26100871
PubMed Central:
PMC4500217

36. Migration‐related phenotypic divergence is associated with epigenetic modifications in rainbow trout

Author:
Melinda R. Baerwald; Mariah H. Meek; Molly R. Stephens; Raman P. Nagarajan; Alisha M. Goodbla; Katharine M. H. Tomalty; Gary H. Thorgaard; Bernie May; Krista M. Nichols
Source:
Molecular ecology 2016 v.25 no.8 pp. 1785-1800
ISSN:
0962-1083
Subject:
DNA methylation; Oncorhynchus mykiss; animals; circadian rhythm; epigenetics; gene expression regulation; juveniles; life history; migratory behavior; neurodevelopment; phenotypic plasticity; progeny; proteins; reproduction; siblings; smoltification; transcription (genetics)
Abstract:
... Migration is essential for the reproduction and survival of many animals, yet little is understood about its underlying molecular mechanisms. We used the salmonid Oncorhynchus mykiss to gain mechanistic insight into smoltification, which is a morphological, physiological and behavioural transition undertaken by juveniles in preparation for seaward migration. O. mykiss is experimentally tractable a ...
DOI:
10.1111/mec.13231
PubMed:
25958780
PubMed Central:
PMC4641842

37. Arabidopsis VIM Proteins Regulate Epigenetic Silencing by Modulating DNA Methylation and Histone Modification in Cooperation with MET1

Author:
Jeongsik Kim; Jin Hee Kim; Eric J. Richards; Kyung Min Chung; Hye Ryun Woo
Source:
Molecular plant 2014 v.7 no.9 pp. 1470-1485
ISSN:
1674-2052
Subject:
Arabidopsis; DNA; DNA methylation; animals; chromocenters; epigenetics; gene silencing; genes; heterochromatin; histones; mutants; plants (botany); transcription (genetics); transcriptomics
Abstract:
... Methylcytosine-binding proteins containing SRA (SET- and RING-Associated) domain are required for the establishment and/or maintenance of DNA methylation in both plants and animals. We previously proposed that Arabidopsis VIM/ORTH proteins with an SRA domain maintain DNA methylation and epigenetic gene silencing in heterochromatic regions. However, their endogenous targets of epigenetic gene silen ...
DOI:
10.1093/mp/ssu079
PubMed:
25009302
PubMed Central:
PMC4207863

38. Epigenetic and developmental regulation in plant polyploids

Author:
Qingxin Song; Z Jeffrey Chen
Source:
Current opinion in plant biology 2015 v.24 pp. 101-109
ISSN:
1369-5266
Subject:
Brassica napus; DNA methylation; animals; cotton; crops; cytotypes; domestication; epigenetics; gene expression; gene expression regulation; histones; nucleotide sequences; polyploidy; wheat
Abstract:
... Polyploidy or whole-genome duplication occurs in some animals and many flowering plants, including many important crops such as wheat, cotton and oilseed rape. The prevalence of polyploidy in the plant kingdom suggests it as an important evolutionary feature for plant speciation and crop domestication. Studies of natural and synthetic polyploids have revealed rapid and dynamic changes in genomic s ...
DOI:
10.1016/j.pbi.2015.02.007
PubMed:
25765928
PubMed Central:
PMC4395545

39. Epigenetic modulation of DNA methylation by nutrition and its mechanisms in animals

Author:
Naifeng Zhang
Source:
Animal nutrition 2015 v.1 no.3 pp. 144-151
ISSN:
2405-6383
Subject:
DNA; DNA methylation; animals; epigenetics; gene expression regulation; methyltransferases; nutrition; phenotype
Abstract:
... It is well known that phenotype of animals may be modified by the nutritional modulations through epigenetic mechanisms. As a key and central component of epigenetic network, DNA methylation is labile in response to nutritional influences. Alterations in DNA methylation profiles can lead to changes in gene expression, resulting in diverse phenotypes with the potential for decreased growth and heal ...
DOI:
10.1016/j.aninu.2015.09.002
PubMed:
29767106
PubMed Central:
PMC5945948

40. Open and Closed: The Roles of Linker Histones in Plants and Animals

Author:
Ryan S. Over; Scott D. Michaels
Source:
Molecular plant 2014 v.7 no.3 pp. 481-491
ISSN:
1674-2052
Subject:
DNA; animals; cell division; eukaryotic cells; gene expression; genes; histones; neutralization; nucleosomes; plants (botany); post-translational modification
Abstract:
... Histones package DNA in all eukaryotes and play key roles in regulating gene expression. Approximately 150 base pairs of DNA wraps around an octamer of core histones to form the nucleosome, the basic unit of chromatin. Linker histones compact chromatin further by binding to and neutralizing the charge of the DNA between nucleosomes. It is well established that chromatin packing is regulated by a c ...
DOI:
10.1093/mp/sst164
PubMed:
24270504
PubMed Central:
PMC3941478

41. The Splicing Factor PRP31 Is Involved in Transcriptional Gene Silencing and Stress Response in Arabidopsis

Author:
Jin-Lu Du; Su-Wei Zhang; Huan-Wei Huang; Tao Cai; Lin Li; She Chen; Xin-Jian He
Source:
Molecular plant 2015 v.8 no.7 pp. 1053-1068
ISSN:
1674-2052
Subject:
Arabidopsis; DNA; DNA methylation; animals; cold stress; fungi; gene expression; gene silencing; mutants; mutation; proteins; stress response; transcription (genetics); transgenes; transposons
Abstract:
... Although DNA methylation is known to play an important role in the silencing of transposable elements (TEs) and introduced transgenes, the mechanisms that generate DNA methylation-independent transcriptional silencing are poorly understood. Previous studies suggest that RNA-directed DNA methylation (RdDM) is required for the silencing of the RD29A-LUC transgene in the Arabidopsis ros1 mutant backg ...
DOI:
10.1016/j.molp.2015.02.003

42. 5-Methylcytosine Recognition by Arabidopsis thaliana DNA Glycosylases DEMETER and DML3

Author:
Brooks Sonja C.; Fischer Robert L.; Huh Jin Hoe; Eichman Brandt F.
Source:
Biochemistry 2014 v.53 no.15 pp. 2525-2532
ISSN:
1520-4995
Subject:
Arabidopsis thaliana; DNA; DNA methylation; X chromosome; active sites; animals; cytosine; gene expression; genes; glycosylases; models; transposons
Abstract:
... Methylation of cytosine to 5-methylcytosine (5mC) is important for gene expression, gene imprinting, X-chromosome inactivation, and transposon silencing. Active demethylation in animals is believed to proceed by DNA glycosylase removal of deaminated or oxidized 5mC. In plants, 5mC is removed from the genome directly by the DEMETER (DME) family of DNA glycosylases. Arabidopsis thaliana DME excises ...
DOI:
10.1021/bi5002294
PubMed:
24678721
PubMed Central:
PMC4004242

43. Acute dietary zinc deficiency before conception compromises oocyte epigenetic programming and disrupts embryonic development

Author:
X. Tian; F.J. Diaz
Source:
Developmental biology 2013 v.376 no.1 pp. 51-61
ISSN:
0012-1606
Subject:
DNA methylation; animals; blastocyst; cell cycle; chromatin; conception; diet; eggs; embryogenesis; epigenetics; histones; in vitro culture; in vitro fertilization; messenger RNA; nutrient deficiencies; oocytes; ovulation; pregnancy; zinc
Abstract:
... Recent findings show that zinc is an important factor necessary for regulating the meiotic cell cycle and ovulation. However, the role of zinc in promoting oocyte quality and developmental potential is not known. Using an in vivo model of acute dietary zinc deficiency, we show that feeding a zinc deficient diet (ZDD) for 3–5 days before ovulation (preconception) dramatically disrupts oocyte chroma ...
DOI:
10.1016/j.ydbio.2013.01.015
PubMed:
23348678
PubMed Central:
PMC3601821

44. Assessing DNA methylation levels in animals: choosing the right tool for the job

Author:
Christine Couldrey; Vanessa Cave
Source:
Animal genetics 2014 v.45 Suppl s1 no. pp. 15-24
ISSN:
0268-9146
Subject:
DNA methylation; animals; epigenetics
Abstract:
... Selection of agricultural animals for improved performance based on genetics has seen significant progress made over the past few decades. Further improvements are likely by combining genetic selection with epigenetic selection or manipulation. However, before this can be undertaken, an understanding of epigenetic mechanisms is required, and this can be obtained only by precise and accurate analys ...
DOI:
10.1111/age.12186
PubMed:
24990588

45. Epigenetic Memory for Stress Response and Adaptation in Plants

Author:
Tetsu Kinoshita; Motoaki Seki
Source:
Plant & cell physiology 2014 v.55 no.11 pp. 1859-1863
ISSN:
0032-0781
Subject:
DNA methylation; RNA; animals; cell communication; epigenetics; histones; mitosis; stress response; transcription (genetics)
Abstract:
... In contrast to the majority of animal species, plants are sessile organisms and are, therefore, constantly challenged by environmental perturbations. Over the past few decades, our knowledge of how plants perceive environmental stimuli has increased considerably, e.g. the mechanisms for transducing environmental stress stimuli into cellular signaling cascades and gene transcription networks. In ad ...
DOI:
10.1093/pcp/pcu125

46. The Histone Variant H2A.W Defines Heterochromatin and Promotes Chromatin Condensation in Arabidopsis

Author:
Ramesh Yelagandula; Hume Stroud; Sarah Holec; Keda Zhou; Suhua Feng; Xuehua Zhong; Uma M. Muthurajan; Xin Nie; Tomokazu Kawashima; Martin Groth; Karolin Luger; Steven E. Jacobsen; Frédéric Berger
Source:
Cell 2014 v.158 pp. 98-109
ISSN:
0092-8674
Subject:
Animalia; Arabidopsis; DNA methylation; animals; chromosome segregation; gene expression; genome; heterochromatin; histones; plants (botany); transposons
Abstract:
... Histone variants play crucial roles in gene expression, genome integrity, and chromosome segregation. We report that the four H2A variants in Arabidopsis define different genomic features, contributing to overall genomic organization. The histone variant H2A.W marks heterochromatin specifically and acts in synergy with heterochromatic marks H3K9me2 and DNA methylation to maintain transposon silenc ...
DOI:
10.1016/j.cell.2014.06.006
PubMed:
24995981
PubMed Central:
PMC4671829

47. Analysis of rice Snf2 family proteins and their potential roles in epigenetic regulation

Author:
Yongfeng Hu; Ning Zhu; Xuemin Wang; Qingping Yi; Deyan Zhu; Yan Lai; Yu Zhao
Source:
Plant physiology and biochemistry 2013 v.70 pp. 33-42
ISSN:
0981-9428
Subject:
Arabidopsis; DNA; DNA methylation; DNA repair; Oryza sativa; abiotic stress; animals; chromatin; cold; drought; epigenetics; gene expression; genes; histones; homologous recombination; phylogeny; rice; sequence alignment
Abstract:
... Snf2 family proteins are ATP-dependent chromatin remodeling factors that control many aspects of DNA events such as transcription, replication, homologous recombination and DNA repair. In animals several members in this family have been revealed to control gene expression in concert with other epigenetic mechanisms including histone modification, histone variants and DNA methylation. Their functio ...
DOI:
10.1016/j.plaphy.2013.05.001
PubMed:
23770592

48. Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense

Author:
Agnès Yu; Gersende Lepère; Florence Jay; Jingyu Wang; Laure Bapaume; Yu Wang; Anne-Laure Abraham; Jon Penterman; Robert L. Fischer; Olivier Voinnet; Lionel Navarro
Source:
Proceedings of the National Academy of Sciences of the United States of America 2013 v.110 no.6 pp. 2389-2394
ISSN:
0027-8424
Subject:
Arabidopsis; DNA; DNA methylation; Pseudomonas syringae; animals; epigenetics; gene silencing; genes; immune response; innate immunity; leaves; pathogens; promoter regions; transcription (genetics); transcriptional activation; transposons
Abstract:
... DNA methylation is an epigenetic mark that silences transposable elements (TEs) and repeats. Whereas the establishment and maintenance of DNA methylation are relatively well understood, little is known about their dynamics and biological relevance in plant and animal innate immunity. Here, we show that some TEs are demethylated and transcriptionally reactivated during antibacterial defense in Arab ...
DOI:
10.1073/pnas.1211757110
PubMed:
23335630
PubMed Central:
PMC3568381

49. Oxygen, epigenetic signaling, and the evolution of early life

Author:
Albert Jeltsch
Source:
Trends in biochemical sciences 2013 v.38 pp. 172-176
ISSN:
0968-0004
Subject:
Animalia; DNA; DNA methylation; animals; cell differentiation; epigenetics; evolution; histones; lysine; oxygen; oxygenases
Abstract:
... After approximately 3 billion years of unicellular life on Earth, multicellular animals appeared some 600 million years ago, followed by the rapid emergence of most animal phyla during the Cambrian radiation. This evolutionary jump was paralleled by an increase in atmospheric oxygen, which I propose allowed the generation of epigenetic signaling systems that are essential for cellular differentiat ...
DOI:
10.1016/j.tibs.2013.02.001

50. Planarian MBD2/3 is required for adult stem cell pluripotency independently of DNA methylation

Author:
Farah Jaber-Hijazi; Priscilla J.K.P. Lo; Yuliana Mihaylova; Jeremy M. Foster; Jack S. Benner; Belen Tejada Romero; Chen Chen; Sunir Malla; Jordi Solana; Alexey Ruzov; A. Aziz Aboobaker
Source:
Developmental biology 2013 v.384 no.1 pp. 141-153
ISSN:
0012-1606
Subject:
DNA; DNA methylation; adult stem cells; adults; animals; cell differentiation; evolution; genes; homeostasis; proteins; tissue repair
Abstract:
... Planarian adult stem cells (pASCs) or neoblasts represent an ideal system to study the evolution of stem cells and pluripotency as they underpin an unrivaled capacity for regeneration. We wish to understand the control of differentiation and pluripotency in pASCs and to understand how conserved, convergent or divergent these mechanisms are across the Bilateria. Here we show the planarian methyl-Cp ...
DOI:
10.1016/j.ydbio.2013.09.020
PubMed:
24063805
PubMed Central:
PMC3824064