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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.

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 programing of depression during gestation
Stephanie C. Dulawa, BioEssays, Volume 36, Issue 4, April 2014, pages 353-358.
DOI: 10.1002/bies.201300089

animal model, chromatin remodeling, depression, development, methylation, mood disorder, prenatal

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.


A paternal environmental legacy: Evidence for epigenetic inheritance through the male germ line
Adelheid Soubry, Cathrine Hoyo, Randy L. Jirtle and Susan K. Murphy, BioEssays, Volume 36, Issue 4, April 2014, pages 359-371.
DOI: 10.1002/bies.201300113

developmentaly origins of health and disease (DOHaD), environment, epigenetics, imprinted genes, offspring, paternal exposures, spermatogenesis, transgenerational effects

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.


DNA methylation reprogramming in cancer: Does it act by re-configuring the binding landscape of Polycomb repressive complexes?
James P. Reddington, Duncan Sproul and Richard Meehan, BioEssays, Volume 36, Issue 2, February 2014, pages 134-140.
DOI: 10.1002/bies.201300130

cancer epigenetics, DNA methylation, epigenomics, H3K27me3, Polycomb, reprogramming

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.


Unmasking risk loci: DNA methylation illuminates the biology of cancer predisposition
Dvir Aran and Asaf Hellman, BioEssays, Volume 36, Issue 2, February 2014, pages 184-190.
DOI: 10.1002/bies.201300119

cancer, common human disease, disease risk loci, DNA methylation, epigenomics, gene regulation, transcriptional enhancers

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).


Integrating DNA methylation dynamics into a framework for understanding epigenetic codes
Keith E. Szulwach and Peng Jin, BioEssays, Volume 36, Issue 1, January 2014, pages 107-117.
DOI: 10.1002/bies.201300090

chromatin, DNA demethylation, DNA methylation, epigenetics

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.


Homosexuality via canalized sexual development: A testing protocol for a new epigenetic model
William R. Rice, Urban Friberg and Sergey Gavrilets, BioEssays, Volume 35, Issue 9, September 2013, pages 764-770.
DOI: 10.1002/bies.201300033

epigenetics, gonad-trait discordance, homosexuality

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.


How epigenetic mutations can affect genetic evolution: Model and mechanism
Filippos D. Klironomos, Johannes Berg and Sinéad Collins, BioEssays, Volume 35, Issue 6, June 2013, pages 571-578.
DOI: 10.1002/bies.201200169

adaptive walks, epigenetics, methylation, non-genetic inheritance

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.


Is adult stem cell aging driven by conflicting modes of chromatin remodeling?
Jens Przybilla, Joerg Galle and Thimo Rohlf, BioEssays, Volume 34, Issue 10, October 2012, pages 841-848.
DOI: 10.1002/bies.201100190

age-related changes of chromatin structure, DNA-methylation, histone modification, inheritance of epigenetic information, stem cell plasticity

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.


Epigenetics meets mathematics: Towards a quantitative understanding of chromatin biology
Philipp A. Steffen, Joao P. Fonseca and Leonie Ringrose, BioEssays, Volume 34, Issue 10, October 2012, pages 901-913.
DOI: 10.1002/bies.201200076

chromatin, epigenetics, mathematical modelling, quantification, rate constants

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.


Longevity and the long arm of epigenetics: Acquired parental marks influence lifespan across several generations
Shanshan Pang and Sean P. Curran, BioEssays, Volume 34, Issue 8, August 2012, pages 652-654.
DOI: 10.1002/bies.201200046

epigenetics, lifespan, longevity, parental marks

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.


First annual meeting of the EpiGeneSys Network of Excellence: Moving epigenetics towards systems biology
Alysia vandenBerg and Leonie Ringrose, BioEssays, Volume 34, Issue 7, July 2012, pages 620-625.
DOI: 10.1002/bies.201200026

epigenetics, EpiGeneSys, meeting report

This meeting united participants from the fields of experimental epigenetics, mathematics and computational biology, to discuss results and challenges in the endeavour to explore points of synergy between these fields. The design shown here expresses the idea of moving complex biological phenomena (left nucleosome) towards precise mathematical descriptions (right nucleosome).


Genes at work in random bouts
Alexey Golubev, BioEssays, Volume 34, Issue 4, April 2012, pages 311-319.
DOI: 10.1002/bies.201100119

cell cycle, cell differentiation, embryogenesis, gene expression, stochasticity

Stochastically discontinuous gene activity makes cell cycle duration and cell fate decisions varaible, thus providing for stem cells plasticity.


Histone crotonylation specifically marks the haploid male germ cell gene expression program
Emilie Montellier, Sophie Rousseaux, Yingming Zhao and Saadi Khochbin, BioEssays, Volume 34, Issue 3, March 2012, pages 187-193.
DOI: 10.1002/bies.201100141

acetylation, H2A.X, H2A.Z, histone variants, macroH2A

Post-meiotic male-specific gene expression.


The molecular and mathematical basis of Waddington's epigenetic landscape: A framework for post-Darwinian biology?
Sui Huang, BioEssays, Volume 34, Issue 2, February 2012, pages 149-157.
DOI: 10.1002/bies.201100031

attractor, epigenetics, gene regulatory network, Neo-Darwinism, systems biology

The straightforward causality implicit in one genotype leading to only one phenotype must nowadays be expanded to incorporate epigenetics, gene regulatory networks and gene expression noise.


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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