scholarly journals Author Correction: The role of epigenetic modifications, long-range contacts, enhancers and topologically associating domains in the regulation of glioma grade-specific genes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ilona E. Grabowicz ◽  
Bartek Wilczyński ◽  
Bożena Kamińska ◽  
Adria‑Jaume Roura ◽  
Bartosz Wojtaś ◽  
...  
Keyword(s):  
Long Range ◽  
Epigenetic Modifications ◽  
Topologically Associating Domains

scholarly journals Topologically associated domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation

2016 ◽  
Author(s):  
Nathan Harmston ◽  
Elizabeth Ing-Simmons ◽  
Ge Tan ◽  
Malcolm Perry ◽  
Matthias Merkenschlager ◽  
...  
Keyword(s):  
Long Range ◽  
Close Correspondence ◽  
Developmental Genes ◽  
Regulatory Interactions ◽  
Topologically Associating Domains ◽  
Topologically Associated Domains ◽  
The Difference ◽  
Conserved Noncoding Elements ◽  
Extreme Conservation

AbstractIn vertebrates and other Metazoa, developmental genes are found surrounded by dense clusters of highly conserved noncoding elements (CNEs). CNEs exhibit extreme levels of sequence conservation of unexplained origin, with many acting as long-range enhancers during development. Clusters of CNEs, termed genomic regulatory blocks (GRBs), define the span of regulatory interactions for many important developmental regulators. The function and genomic distribution of these elements close to important regulatory genes raises the question of how they relate to the 3D conformation of these loci. We show that GRBs, defined using clusters of CNEs, coincide strongly with the patterns of topological organisation in metazoan genomes, predicting the boundaries of topologically associating domains (TADs) at hundreds of loci. The set of TADs that are associated with high levels of non-coding conservation exhibit distinct properties compared to TADs called in chromosomal regions devoid of extreme non-coding conservation. The correspondence between GRBs and TADs suggests that TADs around developmental genes are ancient, slowly evolving genomic structures, many of which have had conserved spans for hundreds of millions of years. This relationship also explains the difference in TAD numbers and sizes between genomes. While the close correspondence between extreme conservation and the boundaries of this subset of TADs does not reveal the mechanism leading to the conservation of these elements, it provides a functional framework for studying the role of TADs in long-range transcriptional regulation.

The Role of Technological Change in the Long-run Global Economy Forecasting

2013 ◽  
pp. 97-116 ◽  
Author(s):  
A. Apokin
Keyword(s):  
Technological Change ◽  
Data Quality ◽  
Long Range ◽  
Global Economy ◽  
World Economy ◽  
Qualitative Approaches ◽  
Long Run ◽  
The World ◽  
National Economies

The author compares several quantitative and qualitative approaches to forecasting to find appropriate methods to incorporate technological change in long-range forecasts of the world economy. A?number of long-run forecasts (with horizons over 10 years) for the world economy and national economies is reviewed to outline advantages and drawbacks for different ways to account for technological change. Various approaches based on their sensitivity to data quality and robustness to model misspecifications are compared and recommendations are offered on the choice of appropriate technique in long-run forecasts of the world economy in the presence of technological change.

scholarly journals Role of Chronic Alcoholism Causing Cancer in Omnivores and Vegetarians through Epigenetic Modifications

2020 ◽  
Vol 07 (03) ◽  
pp. 080-086
Author(s):  
Syed Aaquil Hasan Syed Javid Hasan ◽  
Raisa Arifanie O'Zelian Pawirotaroeno ◽  
Syed Abrar Hasan Syed Javid Hasan ◽  
Elene Abzianidze
Keyword(s):  
Folate Deficiency ◽  
Chronic Alcoholism ◽  
Epigenetic Modifications ◽  
Alcohol Metabolism ◽  
Dna Hypomethylation ◽  
Contributing Factors ◽  
Vitamin Deficiencies ◽  
Adenosyl Methionine ◽  
And Oxidative Stress

AbstractOne of the significant consequences of alcohol consumption is cancer formation via several contributing factors such as action of alcohol metabolites, vitamin deficiencies, and oxidative stress. All these factors have been shown to cause epigenetic modifications via DNA hypomethylation, thus forming a basis for cancer development. Several published reviews and studies were systematically reviewed. Omnivores and vegetarians differ in terms of nutritional intake and deficiencies. As folate deficiency was found to be common among the omnivores, chronic alcoholism could possibly cause damage and eventually cancer in an omnivorous individual via DNA hypomethylation due to folate deficiency. Furthermore, as niacin was found to be deficient among vegetarians, damage in vegetarian chronic alcoholics could be due to increased NADH/NAD+ ratio, thus slowing alcohol metabolism in liver leading to increased alcohol and acetaldehyde which inhibit methyltransferase enzymes, eventually leading to DNA hypomethylation. Hence correcting the concerned deficiency and supplementation with S-adenosyl methionine could prove to be protective in chronic alcohol use.

scholarly journals The role of epigenetic modifications, long-range contacts, enhancers and topologically associating domains in the regulation of glioma grade-specific genes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ilona E. Grabowicz ◽  
Bartek Wilczyński ◽  
Bożena Kamińska ◽  
Adria-Jaume Roura ◽  
Bartosz Wojtaś ◽  
...  
Keyword(s):  
Gene Expression ◽  
Long Range ◽  
Genetic Alterations ◽  
Chromatin Organization ◽  
Open Chromatin ◽  
Low Grade ◽  
Strong Impact ◽  
Cell Matrix ◽  
Topologically Associating Domains ◽  
Genome Wide

AbstractGenome-wide studies have uncovered specific genetic alterations, transcriptomic patterns and epigenetic profiles associated with different glioma types. We have recently created a unique atlas encompassing genome-wide profiles of open chromatin, histone H3K27ac and H3Kme3 modifications, DNA methylation and transcriptomes of 33 glioma samples of different grades. Here, we intersected genome-wide atlas data with topologically associating domains (TADs) and demonstrated that the chromatin organization and epigenetic landscape of enhancers have a strong impact on genes differentially expressed in WHO low grade versus high grade gliomas. We identified TADs enriched in glioma grade-specific genes and/or epigenetic marks. We found the set of transcription factors, including REST, E2F1 and NFKB1, that are most likely to regulate gene expression in multiple TADs, containing specific glioma-related genes. Moreover, many genes associated with the cell–matrix adhesion Gene Ontology group, in particular 14 PROTOCADHERINs, were found to be regulated by long-range contacts with enhancers. Presented results demonstrate the existence of epigenetic differences associated with chromatin organization driving differential gene expression in gliomas of different malignancy.

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.

Sign in / Sign up

Export Citation Format

Share Document