scholarly journals Epigenetic mechanisms in Tendon Ageing

2020 ◽  
Vol 135 (1) ◽  
pp. 90-107
Author(s):  
Kiran Riasat ◽  
David Bardell ◽  
Katarzyna Goljanek-Whysall ◽  
Peter D Clegg ◽  
Mandy J Peffers
Keyword(s):  
Tendon Injury ◽  
Chromatin Accessibility ◽  
Epigenetic Mechanisms ◽  
Relative Importance ◽  
Protective Mechanisms ◽  
Multiple Datasets ◽  
Genome Wide ◽  
Holistic Understanding ◽  
Homeostatic Mechanisms

Abstract Introduction Tendon is a composite material with a well-ordered hierarchical structure exhibiting viscoelastic properties designed to transfer force. It is recognized that the incidence of tendon injury increases with age, suggesting a deterioration in homeostatic mechanisms or reparative processes. This review summarizes epigenetic mechanisms identified in ageing healthy tendon. Sources of data We searched multiple databases to produce a systematic review on the role of epigenetic mechanisms in tendon ageing. Areas of agreement Epigenetic mechanisms are important in predisposing ageing tendon to injury. Areas of controversy The relative importance of epigenetic mechanisms are unknown in terms of promoting healthy ageing. It is also unknown whether these changes represent protective mechanisms to function or predispose to pathology. Growing point Epigenetic markers in ageing tendon, which are under-researched including genome-wide chromatin accessibility, should be investigated. Areas timely for developing research Metanalysis through integration of multiple datasets and platforms will enable a holistic understanding of the epigenome in ageing and its relevance to disease.

scholarly journals Epigenetic mechanisms in sexual differentiation of the brain and behaviour

2016 ◽  
Vol 371 (1688) ◽  
pp. 20150114 ◽  
Author(s):  
Nancy G. Forger
Keyword(s):  
Gene Expression ◽  
Sex Differences ◽  
Sexual Differentiation ◽  
Wide Distribution ◽  
Epigenetic Modifications ◽  
Epigenetic Mechanism ◽  
Epigenetic Mechanisms ◽  
Genome Wide ◽  
The Brain

Circumstantial evidence alone argues that the establishment and maintenance of sex differences in the brain depend on epigenetic modifications of chromatin structure. More direct evidence has recently been obtained from two types of studies: those manipulating a particular epigenetic mechanism, and those examining the genome-wide distribution of specific epigenetic marks. The manipulation of histone acetylation or DNA methylation disrupts the development of several neural sex differences in rodents. Taken together, however, the evidence suggests there is unlikely to be a simple formula for masculine or feminine development of the brain and behaviour; instead, underlying epigenetic mechanisms may vary by brain region or even by dependent variable within a region. Whole-genome studies related to sex differences in the brain have only very recently been reported, but suggest that males and females may use different combinations of epigenetic modifications to control gene expression, even in cases where gene expression does not differ between the sexes. Finally, recent findings are discussed that are likely to direct future studies on the role of epigenetic mechanisms in sexual differentiation of the brain and behaviour.

scholarly journals DNA methylation regulates transcriptional homeostasis of algal endosymbiosis in the coral modelAiptasia

2017 ◽  
Author(s):  
Yong Li ◽  
Yi Jin Liew ◽  
Guoxin Cui ◽  
Maha J Cziesielski ◽  
Noura Zahran ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Molecular Mechanisms ◽  
Model System ◽  
Epigenetic Mechanism ◽  
Symbiotic Relationship ◽  
Epigenetic Mechanisms ◽  
Genome Wide ◽  
Spurious Transcription ◽  
Coral Reef Ecosystems

The symbiotic relationship between cnidarians and dinoflagellates is the cornerstone of coral reef ecosystems. Although research is focusing on the molecular mechanisms underlying this symbiosis, the role of epigenetic mechanisms, which have been implicated in transcriptional regulation and acclimation to environmental change, is unknown. To assess the role of DNA methylation in the cnidarian-dinoflagellate symbiosis, we analyzed genome-wide CpG methylation, histone associations, and transcriptomic states of symbiotic and aposymbiotic anemones in the model systemAiptasia. We find methylated genes are marked by histone H3K36me3 and show significant reduction of spurious transcription and transcriptional noise, revealing a role of DNA methylation in the maintenance of transcriptional homeostasis. Changes in DNA methylation and expression show enrichment for symbiosis-related processes such as immunity, apoptosis, phagocytosis recognition and phagosome formation, and unveil intricate interactions between the underlying pathways. Our results demonstrate that DNA methylation provides an epigenetic mechanism of transcriptional homeostasis during symbiosis.

scholarly journals Intergenerational epigenetic inheritance in reef-building corals

2018 ◽  
Author(s):  
Yi Jin Liew ◽  
Emily J. Howells ◽  
Xin Wang ◽  
Craig T. Michell ◽  
John A. Burt ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Intergenerational Transmission ◽  
Epigenetic Inheritance ◽  
Cpg Methylation ◽  
Epigenetic Mechanisms ◽  
Transgenerational Inheritance ◽  
Genome Wide ◽  
Methylation Patterns ◽  
Hypermethylated Genes

MainThe notion that intergenerational or transgenerational inheritance operates solely through genetic means is slowly being eroded: epigenetic mechanisms have been shown to induce heritable changes in gene activity in plants1,2and metazoans1,3. Inheritance of DNA methylation provides a potential pathway for environmentally induced phenotypes to contribute to evolution of species and populations1–4. However, in basal metazoans, it is unknown whether inheritance of CpG methylation patterns occurs across the genome (as in plants) or as rare exceptions (as in mammals)4. Here, we demonstrate genome-wide intergenerational transmission of CpG methylation patterns from parents to sperm and larvae in a reef-building coral. We also show variation in hypermethylated genes in corals from distinct environments, indicative of responses to variations in temperature and salinity. These findings support a role of DNA methylation in the transgenerational inheritance of traits in corals, which may extend to enhancing their capacity to adapt to climate change.

scholarly journals Leveraging genome-wide datasets to quantify the functional role of the anti-Shine–Dalgarno sequence in regulating translation efficiency

Open Biology ◽  
2017 ◽  
Vol 7 (1) ◽  
pp. 160239 ◽  
Author(s):  
Adam J. Hockenberry ◽  
Adam R. Pah ◽  
Michael C. Jewett ◽  
Luís A. N. Amaral
Keyword(s):  
Start Codon ◽  
Translation Efficiency ◽  
Multiple Datasets ◽  
Mrna Structure ◽  
Genome Wide ◽  
Sequence Complementarity ◽  
Endogenous Genes ◽  
Shine Dalgarno Sequence ◽  
The Relationship

Studies dating back to the 1970s established that sequence complementarity between the anti-Shine–Dalgarno (aSD) sequence on prokaryotic ribosomes and the 5′ untranslated region of mRNAs helps to facilitate translation initiation. The optimal location of aSD sequence binding relative to the start codon, the full extents of the aSD sequence and the functional form of the relationship between aSD sequence complementarity and translation efficiency have not been fully resolved. Here, we investigate these relationships by leveraging the sequence diversity of endogenous genes and recently available genome-wide estimates of translation efficiency. We show that—after accounting for predicted mRNA structure—aSD sequence complementarity increases the translation of endogenous mRNAs by roughly 50%. Further, we observe that this relationship is nonlinear, with translation efficiency maximized for mRNAs with intermediate levels of aSD sequence complementarity. The mechanistic insights that we observe are highly robust: we find nearly identical results in multiple datasets spanning three distantly related bacteria. Further, we verify our main conclusions by re-analysing a controlled experimental dataset.

scholarly journals Pathogen Infection and MORC Proteins Affect Chromatin Accessibility of Transposable Elements and Expression of Their Proximal Genes in Arabidopsis

2016 ◽  
Vol 29 (9) ◽  
pp. 674-687 ◽  
Author(s):  
Yogendra Bordiya ◽  
Yi Zheng ◽  
Ji-Chul Nam ◽  
April C. Bonnard ◽  
Hyong Woo Choi ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Pseudomonas Syringae ◽  
Plant Immunity ◽  
Chromatin Accessibility ◽  
Biotic And Abiotic Stress ◽  
Defense Genes ◽  
Genome Wide ◽  
Hypersensitive Sites ◽  
Stress Related Genes

To assess the role of MORC1 in epigenetics in relation to plant immunity, genome-wide chromatin accessibility was compared between mock- or Pseudomonas syringae pv. tomato–inoculated wild type (WT) Arabidopsis, the morc1/2 double mutant, or both. Most changes in chromatin accessibility, scored by DNase I hypersensitive sites (DHSs), were located in the promoters of genes and transposable elements (TEs). Comparisons between morc1/2 and WT receiving the same treatment revealed differential DHSs (dDHSs) predominantly associated with heterochromatic TEs. By contrast, comparisons between mock- and P. syringae pv. tomato–inoculated plants from the same genotype showed dDHSs associated with biotic and abiotic stress-related genes; a smaller but significant population was in TEs. Moreover, many defense genes, including PR-1, PR-2, and PR-5, were proximal to P. syringae pv. tomato–induced, TE-associated dDHSs. A random subset of these defense genes showed moderately delayed or reduced expression or both in P. syringae pv. tomato–infected morc1/2 as compared with WT. MORC1 was physically bound to chromatin in a P. syringae pv. tomato infection-responsive manner at sites dispersed throughout the genome. Notably, silencing of TE-associated dDHSs proximal to these infection-induced, MORC1-interacting sites led to significant suppression of P. syringae pv. tomato–induced transcription of adjacent defense genes, including PR-1. These results provide evidence that MORC1 is associated with TEs and suggest that a subset of these TEs may help regulate their proximal defense genes.

scholarly journals SOX11 is a lineage-dependency factor and master epigenetic regulator in neuroblastoma

2020 ◽  
Author(s):  
Bieke Decaesteker ◽  
Amber Louwagie ◽  
Siebe Loontiens ◽  
Fanny De Vloed ◽  
Juliette Roels ◽  
...  
Keyword(s):  
Target Genes ◽  
Epigenetic Modification ◽  
Chromatin Accessibility ◽  
Copy Number Alterations ◽  
Specific Expression ◽  
Genome Wide ◽  
Mutation Burden ◽  
Epigenetic Regulator ◽  
Pioneer Factor

ABSTRACTThe pediatric extra-cranial tumor neuroblastoma (NB) is characterised by a low mutation burden while copy number alterations are present in most high-risk cases. We identified SOX11 as a strong lineage dependency transcription factor in adrenergic NB based on recurrent chromosome 2p focal gains and amplifications, its specific expression in the normal sympatho-adrenal lineage and adrenergic NBs and its regulation by multiple adrenergic specific cis-interacting (super-)enhancers. Adrenergic NBs are strongly dependent on high SOX11 expression levels for growth and proliferation. Through genome-wide DNA-binding and transcriptome analysis, we identified and validated functional SOX11 target genes, several of which implicated in chromatin remodeling and epigenetic modification. SOX11 controls chromatin accessibility predominantly affecting distal adrenergic lineage-specific enhancers marked by binding sites of the adrenergic core regulatory circuitry. During normal sympathoblast differentiation we find expression of SOX11 prior to members of the adrenergic core regulatory circuitry. Given the broad control of SOX11 of multiple epigenetic regulatory complexes and its presumed pioneer factor function, we propose that adrenergic NB cells have co-opted the normal role of SOX11 as a crucial regulator of chromatin accessibility and cell identity.

Population Control (Review Article)

1961 ◽  
Vol 1 (3) ◽  
pp. 89-98
Author(s):  
Karol J. Krotki
Keyword(s):  
Population Control ◽  
Review Article ◽  
Small Enterprise ◽  
Opportunity Costs ◽  
Relative Importance ◽  
Factual Information ◽  
Undue Influence ◽  
Clear Cut ◽  
Economic Considerations

Discussions about the role of small enterprise in economic development tend to remain inconclusive partly because of the difficulty of assessing the relative importance of economic and non-economic objectives and partly because of the dearth of factual information on which to base an economic calculus. It is probably true, moreover, that, because of a lack of general agreement as to the economic case for or against small enterprise, non-economic considerations, including some merely romantic attitudes toward smallness and bigness, tend to exert an undue influence on public policies. There may, of course, be no clear-cut economic case. And noneconomic considerations should and will inevitably weigh significantly in policy decisions. If, however, some of the economic questions could be settled by more and better knowledge, these decisions could more accurately reflect the opportunity costs of pursuing non-economic objectives.

Alcohol Use Disorder

2018 ◽  
Author(s):  
Igor Ponomarev
Keyword(s):  
Alcohol Use ◽  
Alcohol Use Disorder ◽  
Critical Discussion ◽  
Epigenetic Mechanisms ◽  
Future Directions ◽  
Clinically Significant ◽  
Early Life Exposures ◽  
The Brain ◽  
Epigenetic Research

Alcohol use disorder (AUD) is characterized by clinically significant impairments in health and social function. Epigenetic mechanisms of gene regulation may provide an attractive explanation for how early life exposures to alcohol contribute to the development of AUD and exert lifelong effects on the brain. This chapter provides a critical discussion of the role of epigenetic mechanisms in AUD etiology and the potential of epigenetic research to improve diagnosis, evaluate risks for alcohol-induced pathologies, and promote development of novel therapies for the prevention and treatment of AUD. Challenges of the current epigenetic approaches and future directions are also discussed.

scholarly journals Role of propagule pressure in colonization success: disentangling the relative importance of demographic, genetic and habitat effects

2013 ◽  
Vol 26 (8) ◽  
pp. 1691-1699 ◽  
Author(s):  
R. A. Hufbauer ◽  
A. Rutschmann ◽  
B. Serrate ◽  
H. Vermeil de Conchard ◽  
B. Facon
Keyword(s):  
Propagule Pressure ◽  
Relative Importance ◽  
Colonization Success
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