BioEssays

Cover image for Vol. 39 Issue 1

Edited By: Andrew Moore

Online ISSN: 1521-1878

Epigenetics


Epigenetic_mechanisms


Find below our most recent articles on a variety of aspects of epigenetics, from chromatin organisation to the role of epigenetics in cancer. This collection sheds light on, and raises new questions on the role of chemical modifications of DNA and chromatin, and non-coding RNAs, in modulating gene expression in a variety of processes from development to cancer. We hope you enjoy delving into this concentration of most recent thinking, insights and future perspectives in epigenetics.

BioEssays is affiliated with EpiGeneSys, the European Network of Excellence for epigenetics research.Epigenesys_logo

For primer literature related to the contents below, see also the Encyclopedia of Life SciencesELS_Logoentry Epigenetics and Disease.


Take a look at this lecture by EpiGeneSys member Leonie Ringrose on Epigenetics: myths, mysteries and molecule.
A larger version of this video can be found here.




Epigenetic-induced alterations in sex-ratios in response to climate change: An epigenetic trap?

Epigenetic‐induced alterations in sex‐ratios in response to climate change: An epigenetic trap?

Sofia Consuegra*, Carlos M. Rodríguez López*

Methylome by environment interactions can regulate sex determination helping species to rapidly adapt to changing environments. However, under the predicted global warming conditions this adaptive strategy could become an epigenetic trap by creating extreme imbalances in sex ratios, which could affect both natural populations and farmed animal and plant species.

BioEssays 2016, 38, No. 10, 950–958 [Insights & Perspectives]


Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification

Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification

Lakshminarayan M. Iyer, Dapeng Zhang, L. Aravind*

Recent studies have brought to fore the importance of DNA adenine methylation as a potential epigenetic mark across phylogenetically distant eukaryotes. We synthesize the current understanding of the manifold origins, biochemistry, and biology of the addition, removal, and reading of this epigenetic mark.

BioEssays 2016, 38, No. 1, 27–40 [Prospects & Overviews]


N6-methyladenine functions as a potential epigenetic mark in eukaryotes

N6‐methyladenine functions as a potential epigenetic mark in eukaryotes

Qinmiao Sun*, Shoujun Huang, Xiaona Wang, Yuanxiang Zhu, Zhenping Chen, Dahua Chen*

Like 5mC, 6mA functions as a potential epigenetic mark in higher eukaryotes. The expression of target genes can be modulated via dynamic and reversible pattern of DNA methylation in a variety of biological processes.

BioEssays 2015, 37, No. 11, 1155–1162 [Insights & Perspectives]


H2A.Z helps genes remember their history so we can remember ours

H2A.Z helps genes remember their history so we can remember ours

Iva B. Zovkic*, Brandon J. Walters

Poised promoters, maintained by histone H2A.Z incorporation into nucleosomes, allow genes to respond to future stimuli based on the history of prior activity. Based on our recent discovery of H2A.Z function in learning and memory, we speculate that stable H2A.Z incorporation supports long-term memory maintenance by promoting re-activation of memory-promoting genes.

BioEssays 2015, 37, No. 6, 596–601 [Insights & Perspectives]


Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum

Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum

Ferhat Ay*, Evelien M. Bunnik, Nelle Varoquaux, Jean-Philippe Vert, William Stafford Noble, Karine G. Le Roch*

The malaria parasite Plasmodium falciparum actively regulates a large fraction of its genes throughout its replicative cycle inside human red blood cells. Recent studies show epigenetic factors such as changes in histone modifications, nucleosome occupancy and the three-dimensional genome structure play an important role in this precise gene regulation.

BioEssays 2015, 37, No. 2, 182–194 [Prospects & Overviews]


Do age-associated DNA methylation changes increase the risk of malignant transformation?

Do age‐associated DNA methylation changes increase the risk of malignant transformation?

Wolfgang Wagner*, Carola I. Weidner, Qiong Lin

Age-predictors based on specific DNA-methylation (DNAm) changes reflect biological aging. The global changes in DNAm pattern may also trigger aberrant DNAm – so called epimutations – that can initiate tumor formation in the elderly. The figure is adopted from Waddington's “epigenetic landscape” (The Strategy of The Genes. London, Allan & Unwin 1957).

BioEssays 2015, 37, No. 1, 20–24 [Insights & Perspectives]


Now you see it: Genome methylation makes a comeback in Drosophila

Now you see it: Genome methylation makes a comeback in Drosophila

Dario Boffelli*, Sachiko Takayama, David I. K. Martin*

Methylcytosine immunoprecipitation and deep sequencing reveal a strand-asymmetric pattern of cytosine methylation in the fly genome (top). Short regions (middle) contain methylcytosine in non-CpG sequence motifs (bottom). The regions are methylated in only a fraction of fly genomes; specific regions might be methylated in distinct subsets of embryonic nuclei (right).

BioEssays 2014, 36, No. 12, 1138–1144 [Insights & Perspectives]


Early life epigenetic programming and transmission of stress-induced traits in mammals

Early life epigenetic programming and transmission of stress‐induced traits in mammals

Katharina Gapp, Lukas von Ziegler, Ry Yves Tweedie-Cullen, Isabelle M. Mansuy*

Evidence for epigenetic inheritance of acquired traits in mammals is growing. Transgenerational transmission is based on mechanisms involving DNA-methylation, histone post-translational modifications, and non-coding small RNAs in the germline. These epigenetic modifications constitute potential vehicles for effects of early life stress and nutrition on brain and behavior across generations.

BioEssays 2014, 36, No. 5, 491–502 [Prospects & Overviews]



Epigenetic programing of depression during gestation

Epigenetic programing of depression during gestation

Stephanie C. Dulawa*

How does the gestational environment transduce vulnerability to depression to the fetus? The in utero environment alters gene expression through epigenetic mechanisms, which mediate long-term effects on physiology and behavior without changing DNA sequence. I examine recent work suggesting that gestational environment programs depression in adult offspring via epigenetics.

BioEssays 2014, 36, No. 4, 353–358 [Insights & Perspectives]


A paternal environmental legacy: Evidence for epigenetic inheritance through the male germ line

A paternal environmental legacy: Evidence for epigenetic inheritance through the male germ line

Adelheid Soubry*, Cathrine Hoyo, Randy L. Jirtle, Susan K. Murphy

Animal and epidemiologic studies on various environmental exposures suggest that transgenerational epigenetic changes can be induced through the paternal germ line, ultimately affecting health status of the offspring. This essay suggests the existence of epigenetic windows of susceptibility to environmental insults during spermatogenesis or other early developmental processes.

BioEssays 2014, 36, No. 4, 359–371 [Insights & Perspectives]


DNA methylation reprogramming in cancer: Does it act by re-configuring the binding landscape of Polycomb repressive complexes?

DNA methylation reprogramming in cancer: Does it act by re‐configuring the binding landscape of Polycomb repressive complexes?

James P. Reddington, Duncan Sproul, Richard R. Meehan*

DNA methylation patterns are subject to widespread reprogramming during cancer development, the implications of which for the regulation of the cancer genome are not fully understood. Here we discuss how DNA methylation reprogramming could influence transcriptional regulation in cancer cells by modifying the genome-wide targeting of the Polycomb repression system.

BioEssays 2014, 36, No. 2, 134–140 [Insights & Perspectives]


Unmasking risk loci: DNA methylation illuminates the biology of cancer predisposition

Unmasking risk loci: DNA methylation illuminates the biology of cancer predisposition

Dvir Aran, Asaf Hellman*

Tumor samples exhibit genetic and epigenetic variations across individuals. However, cancer-associated risk sequence alleles failed to reveal the link with the mechanism of cancer (left). Implementation of DNA methylation data helps to resolve the effect on drivers of cancer development, and hence to explains the biology of cancer susceptibility (right).

BioEssays 2014, 36, No. 2, 184–190 [Prospects & Overviews]


Integrating DNA methylation dynamics into a framework for understanding epigenetic codes

Integrating DNA methylation dynamics into a framework for understanding epigenetic codes

Keith E. Szulwach*, Peng Jin*

DNA methylation regulates gene expression and influences cellular phenotypes, thereby encoding information on the genome. Recently it has been appreciated that DNA methylation may be dynamically regulated. This essay discusses the integration of DNA methylation into epigenetic codes, summarizing paradigm shifts related to the dynamic encoding of epigenetic information.

BioEssays 2014, 36, No. 1, 107–117 [Prospects & Overviews]


Homosexuality via canalized sexual development: A testing protocol for a new epigenetic model

Homosexuality via canalized sexual development: A testing protocol for a new epigenetic model

William R. Rice*, Urban Friberg, Sergey Gavrilets

We recently advanced a new biological model of homosexuality that is based on transgenerational inheritance of sex-specific epigenetic marks from a parent to an offspring of opposite sex. Here, we describe a general framework to test the model using human stem cells from adult hetero- and homosexual individuals.

BioEssays 2013, 35, No. 9, 764–770 [Insights & Perspectives]


How epigenetic mutations can affect genetic evolution: Model and mechanism

How epigenetic mutations can affect genetic evolution: Model and mechanism

Filippos D. Klironomos, Johannes Berg, Sinéad Collins*

Heritable epigenetic mutations have higher mutation and reversion rates than genetic mutations, but can still be acted on by natural selection. We use a model to show why pure epigenetic variation can speed up adaptation and lead to phenotype-first evolution, even on time scales where genetic evolution also happens.

BioEssays 2013, 35, No. 6, 571–578 [Prospects & Overviews]


Is adult stem cell aging driven by conflicting modes of chromatin remodeling?

Is adult stem cell aging driven by conflicting modes of chromatin remodeling?

Jens Przybilla, Joerg Galle, Thimo Rohlf*

We hypothesize that age-related changes of chromatin structure originate in the limited cellular capability to inherit epigenetic information. Spontaneous loss of histone modification, e.g., during replication gives rise to changes in DNA methylation and accordingly in gene expression, manifesting a conflict between stem cell plasticity and long term gene silencing.

BioEssays 2012, 34, No. 10, 841–848 [Insights & Perspectives]


Epigenetics meets mathematics: Towards a quantitative understanding of chromatin biology

Epigenetics meets mathematics: Towards a quantitative understanding of chromatin biology

Philipp A. Steffen, João P. Fonseca, Leonie Ringrose*

Current models for chromatin mediated gene regulation often describe molecules as binding, modifying or recruiting other molecules, but with little reference to the quantitative differences between them. In this review we explore how quantitative and mathematical approaches can give insights into mechanisms of epigenetic regulation.

BioEssays 2012, 34, No. 10, 901–913 [Prospects & Overviews]


Longevity and the long arm of epigenetics: Acquired parental marks influence lifespan across several generations

Longevity and the long arm of epigenetics: Acquired parental marks influence lifespan across several generations

Shanshan Pang, Sean P. Curran*

A recent study reported that longevity in Caenorhabditits elegans can be inherited over several generations. This is probably achieved through the following epigenetic mechanism: inherited demethylated histones at some central loci, such as miRNA, transcription factors or signaling regulators affect the expression of certain genes leading to the longevity phenotype.

BioEssays 2012, 34, No. 8, 652–654 [Insights & Perspectives]



Please also read the following articles from the Encyclopedia of Molecular Cell Biology and Molecular Medicine:

EMCBMM

Epigenetic Medicine

Molecular Genetics of Genome Imprinting

The Human Epigenome

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