Epigenetics

Within-genotype epigenetic variation enables broad niche width in a flower living yeast.

by Christina Richards

Schrey, A.W. & C.L. Richards. 2012. Within-genotype epigenetic variation enables broad niche width in a flower living yeast. Molecular Ecology 21: 2559-2561.

Niche theory is one of the central organizing concepts in ecology. Generally, this theory defines a given species... more Niche theory is one of the central organizing concepts in ecology. Generally, this theory defines a given species niche as all of the factors that effect the persistence of the species as well as the impact of the species in a given location. Many studies have argued that phenotypic plasticity enhances niche width because plastic responses allow organisms to express advantageous phenotypes in a broader range of environments. Further, species that exploit habitats with fine-grained variation, or that form metapopulations are expected to develop broad niche widths through phenotypic plasticity. Although a long history of laboratory, greenhouse and reciprocal transplant experiments have provided insight into how plasticity contributes to niche width, recent advances in molecular approaches allow for a mechanistic understanding of plasticity at the molecular level. In particular, variation in epigenetic effects is a potential source of the within-genotype variation that underlies the phenotypic plasticity associated with broad niche widths. Epigenetic mechanisms can alter gene expression and function without altering DNA sequence, and may be stably transmitted across generations. Also, epigenetic mechanisms may be an important component of an individual’s response to the environment. While these ideas are intriguing, few studies have made a clear connection between genome-wide DNA methylation patterns and phenotypic plasticity. In this issue of Molecular Ecology, Herrera et al. (2012) present a study that demonstrates epigenetic changes in genome-wide DNA methylation are causally active in a species’ ability to exploit resources from a broad range of environments and are particularly important in harsh environments.

A functional trait perspective on plant invasion: invasiveness to impacts in a changing world.

by Christina Richards

Drenovsky*, R.E., B.J. Grewell*, C.M. D’Antonio, J.L. Funk, J.J. James, N. Molinari, I.M. Parker & C.L. Richards. 2012. A functional trait perspective on plant invasion: invasiveness to impacts in a changing world. Annals of Botany, doi: 10.1093/aob/mcs100. *shared first authorship.

† Background and Aims Global environmental change will affect non-native plant invasions, with profound potential... more † Background and Aims Global environmental change will affect non-native plant invasions, with profound potential impacts on native plant populations, communities and ecosystems. In this context, we review plant functional traits, particularly those that drive invader abundance (invasiveness) and impacts, as well as the integration of these traits across multiple ecological scales, and as a basis for restoration and management.
† Scope We review the concepts and terminology surrounding functional traits and how functional traits influence processes at the individual level. We explore how phenotypic plasticity may lead to rapid evolution of novel traits facilitating invasiveness in changing environments and then ‘scale up’ to evaluate the relative importance of demographic traits and their links to invasion rates. We then suggest a functional trait framework for assessing per capita effects and, ultimately, impacts of invasive plants on plant communities and ecosystems. Lastly, we focus on the role of functional trait-based approaches in invasive species management and restoration in the context of rapid, global environmental change.
†Conclusions To understand how the abundance and impacts of invasive plants will respond to rapid environmental changes it is essential to link trait-based responses of invaders to changes in community and ecosystem properties. To do so requires a comprehensive effort that considers dynamic environmental controls and a targeted approach to understand key functional traits driving both invader abundance and impacts. If we are to
predict future invasions, manage those at hand and use restoration technology to mitigate invasive species impacts, future research must focus on functional traits that promote invasiveness and invader impacts under changing conditions, and integrate major factors driving invasions from individual to ecosystem levels.

Epigenetic mechanism mediating the impact of child adversity on life-long adverse behavior

by Andrés Ginestet

Although epidemiological data provide evidence that early life experience plays a critical role in human development,... more Although epidemiological data provide evidence that early life experience plays a critical role in human development, the mechanism of how this works remains in question. Recent data from human and animal literature suggest that epigenetic changes, such as DNA methylation, are involved not only in cellular differentiation, but also in the modulation of genome function in response to early life experience affecting gene
function and the phenotype. Such modulations may serve as a mechanism for life-long genome adaptation.
These changes seem to be widely distributed across the genome and to involve central and peripheral systems. Examining the environmental circumstances associated with the onset and reversal of DNA methylation will be critical for understanding risk and resiliency.

Epigenetic mechanism mediating the impact of child adversity on life-long adverse behavior

by Andrés Ginestet

Although epidemiological data provide evidence that early life experience plays a critical role in human development,... more Although epidemiological data provide evidence that early life experience plays a critical role in human development, the mechanism of how this works remains in question. Recent data from human and animal literature suggest that epigenetic changes, such as DNA methylation, are involved not only in cellular differentiation, but also in the modulation of genome function in response to early life experience affecting gene
function and the phenotype. Such modulations may serve as a mechanism for life-long genome adaptation.
These changes seem to be widely distributed across the genome and to involve central and peripheral systems. Examining the environmental circumstances associated with the onset and reversal of DNA methylation will be critical for understanding risk and resiliency.

Reliability Study of Methods for Scoring a Non-Metric Human Osteological Trait

by Shannon Freire

Second Author: Ashley Dunford (UW- Milwaukee)
Published in Field Notes: A Journal of Collegiate Anthropology, Volume 4, Issue 1: May 2012.

To gain meaningful insights from non-metric trait analysis in the field of human osteological study, issues of... more To gain meaningful insights from non-metric trait analysis in the field of human osteological study, issues of reliability and context need to be addressed, especially for the analysis of discrete cranial traits. A preliminary study tested the reliability of different methods of quantifying wormian bones, with the purpose of establishing a consistent method that would enable further applicability for this and other non-metric traits in mortuary analysis. The determination of reliability for both methods was made using Olsson and Janson’s (2001) iota statistic together with Pearson’s product-moment correlation. This study examines the reliability of scoring methods on an interobserver scale, an imperative step for the utility of these techniques for the wider archaeological community, as the majority of current data collection is a collaborative effort. The results of this study support the initial application in a case study involving a Bayesian probability analysis utilizing individuals from the Milwaukee County Institutional Grounds collection.
Key words: wormian bones, reliability, non-metric traits, digitization, interobserver, intraobserver

Epigenetic variation may compensate for decreased genetic variation with introductions: a case study using house sparrows (Passer domesticus) on two continents.

by Christina Richards

Schrey, A.W., C.A.C. Coon, M.T. Grispo, M. Awad, T. Imboma, E.D. McCoy, H.R. Mushinsky, C.L. Richards & L.B. Martin. 2012. Epigenetic variation may compensate for decreased genetic variation with introductions: a case study using house sparrows (Passer domesticus) on two continents. Genetics Research International 2012: Article ID 979751.

Epigenetic mechanisms impact several phenotypic traits and may be important for ecology and evolution. The introduced... more Epigenetic mechanisms impact several phenotypic traits and may be important for ecology and evolution. The introduced house sparrow (Passer domesticus) exhibits extensive phenotypic variation among and within populations. We screened methylation in populations from Kenya and Florida to determine if methylation varied among populations, varied with introduction history (Kenyan invasion <50 years old, Florida invasion ∼150 years old), and could potentially compensate for decrease genetic variation with introductions. While recent literature has speculated on the importance of epigenetic effects for biological invasions, this is the first such study among wild vertebrates. Methylation was more frequent in Nairobi, and outlier loci suggest that populations may be differentiated. Methylation diversity was similar between populations, in spite of known lower genetic diversity in Nairobi, which suggests that epigenetic variation may compensate for decreased genetic diversity as a source of phenotypic variation during introduction. Our results suggest that methylation differences may be common among house sparrows, but research is needed to discern whether methylation impacts phenotypic variation.

The Role of Epigenetics in Evolution: The Extended Synthesis.

by Christina Richards

Schrey, A.W., C.L. Richards, V. Meller, V. Sollars & D.M. Ruden. 2012. The Role of Epigenetics in Evolution: The Extended Synthesis. Genetics Research International 2012, Article ID 286164.

Evolutionary biology is currently experiencing an emergence of several research topics that transcend the boundaries... more Evolutionary biology is currently experiencing an emergence of several research topics that transcend the boundaries of the Modern Synthesis, which was the last major conceptual integration in evolutionary biology. The Modern Synthesis used the concepts of population genetics to integrate Mendelian genetics with evolution by natural selection. Pigliucci identified several major areas of innovation that transcend the Modern Synthesis: epigenetics, evolvability, phenotypic plasticity, evolution on adaptive landscapes, evolutionary developmental biology, and systems biology. Integrating these new ideas with the Modern Synthesis will form a new conceptual framework of evolution, which they termed the Extended Synthesis, as it will extend, rather than refute, the Modern Synthesis. This subject has been the focus of much recent work, and an excellent description is provided in the book Evolution—The Extended Synthesis.

Recent advances in MeCP2 structure and function

by Kristopher Hite

Class IIa HDACs: from important roles in differentiation to possible implications in tumourigenesis

by Cristina Florean

Histone deacetylases (HDACs) are important regulators of gene expression. Specific structural features and distinct... more Histone deacetylases (HDACs) are important regulators of gene expression. Specific structural features and distinct regulative mechanisms rationalize the separation of the 18 different human HDACs into four classes. The class II comprises a heterogeneous group of nuclear and cytosolic HDACs involved in the regulation of several cellular functions, not just limited to transcriptional repression. In particular, HDAC4, 5, 7 and 9 belong to the subclass IIa and share many transcriptional partners, including members of the MEF2 family. Genetic studies in mice have disclosed the fundamental contribution of class IIa HDACs to specific developmental/differentiation pathways. In this review, we discuss about the recent literature, which hints a role of class IIa HDACs in the development, growth and aggressiveness of cancer cells.

Down-regulation of serum/glucocorticoid regulated kinase 1 in colorectal tumours is largely independent of promoter hypermethylation

by Andrew Beggs

Evolutionary significance of epigenetic variation

by Christina Richards

Richards, C.L., K.J.F. Verhoeven & O. Bossdorf. 2012. Evolutionary significance of epigenetic variation. In: Plant Genome Diversity. J.F. Wendel, ed. Springer.

Several chapters in this volume demonstrate how epigenetic work at the molecular level over the last few decades has... more Several chapters in this volume demonstrate how epigenetic work at the molecular level over the last few decades has revolutionized our understanding of genome function and developmental biology. However, epigenetic processes not only further our understanding of variation and regulation at the genomic and cellular levels, they also challenge our understanding of heritable phenotypic variation at the level of whole organisms and even the process of evolution by natural selection. Although many of the epigenetic mechanisms involved in differential gene expression are reset each generation, some epigenetic marks are faithfully transmitted across generations. In addition, we now know that natural variation exists not only at the DNA sequence level but also the epigenetic level. This may be particularly common in plants, and several studies suggest that epigenetic variation alone can cause significant heritable variation in phenotypic traits. Because of these observations, there is currently increasing interest in understanding the role of epigenetic processes in ecology and evolution.

An epigenetic activation role of Piwi and a Piwi-associated piRNA in Drosophila melanogaster

by Hang Yin

Heterochromatin, representing the silenced state of transcription, consists largely of transposon-enriched and highly... more Heterochromatin, representing the silenced state of transcription, consists largely of transposon-enriched and highly repetitive sequences. Implicated in heterochromatin formation and transcriptional silencing in Drosophila are Piwi (P-element induced wimpy testis)1, 2 and repeat-associated small interfering RNAs (rasiRNAs)3, 4, 5. Despite this, the role of Piwi in rasiRNA expression and heterochromatic silencing remains unknown. Here we report the identification and characterization of 12,903 Piwi-interacting RNAs (piRNAs) in Drosophila, showing that rasiRNAs represent a subset of piRNAs. We also show that Piwi promotes euchromatic histone modifications and piRNA transcription in subtelomeric heterochromatin (also known as telomere-associated sequence, or TAS), on the right arm of chromosome 3 (3R-TAS). Piwi binds to 3R-TAS and a piRNA uniquely mapped to 3R-TAS (3R-TAS1 piRNA). In piwi mutants, 3R-TAS loses euchromatic histone modifications yet accumulates heterochromatic histone modifications and Heterochromatin Protein 1a (HP1a). Furthermore, the expression of both the 3R-TAS1 piRNA and a white reporter gene in 3R-TAS becomes suppressed. A P element inserted 128 base pairs downstream of the 3R-TAS1 piRNA coding sequence restores the euchromatic histone modifications of 3R-TAS and the expression of 3R-TAS1 piRNA in piwi mutants, as well as partly rescuing their defects in germline stem-cell maintenance. These observations suggest that Piwi promotes the euchromatic character of 3R-TAS heterochromatin and its transcriptional activity, opposite to the known roles of Piwi and the RNA-mediated interference pathway in epigenetic silencing. This activating function is probably achieved through interaction with at least 3R-TAS1 piRNA and is essential for germline stem-cell maintenance.

A High-Resolution Whole-Genome Map of Key Chromatin Modifications in the Adult Drosophila melanogaster

by Hang Yin

Epigenetic research has been focused on cell-type-specific regulation; less is known about common features of... more Epigenetic research has been focused on cell-type-specific regulation; less is known about common features of epigenetic programming shared by diverse cell types within an organism. Here, we report a modified method for chromatin immunoprecipitation and deep sequencing (ChIP–Seq) and its use to construct a high-resolution map of the Drosophila melanogaster key histone marks, heterochromatin protein 1a (HP1a) and RNA polymerase II (polII). These factors are mapped at 50-bp resolution genome-wide and at 5-bp resolution for regulatory sequences of genes, which reveals fundamental features of chromatin modification landscape shared by major adult Drosophila cell types: the enrichment of both heterochromatic and euchromatic marks in transposons and repetitive sequences, the accumulation of HP1a at transcription start sites with stalled polII, the signatures of histone code and polII level/position around the transcriptional start sites that predict both the mRNA level and functionality of genes, and the enrichment of elongating polII within exons at splicing junctions. These features, likely conserved among diverse epigenomes, reveal general strategies for chromatin modifications.

Descendants of primed Arabidopsis plants exhibit resistance to biotic stress

by Xavier DANIEL

Multigene Methylation Analysis of Wilms' Tumour and Adult Renal Cell Carcinoma

by Mark Morris

Emerging roles of epigenetic mechanisms in the enduring effects of early-life stress and experience on learning and memory

by Jessica Cope

Transgenerational epigenetics or a spectral history of the flesh: A Merleau-Pontian approach to epigenetics

by Darian Meacham

The Timescales of Human Adaptation: the Role of Epigenetic Processes and Policy Implications

by Zaneta Thayer

Human biology includes multiple adaptive mechanisms that allow adjustment to varying timescales of environmental... more Human biology includes multiple adaptive mechanisms that allow adjustment to varying timescales of environmental change. Sensitive or critical periods in early development allow for the transfer of environmental information between generations, which helps an organism track gradual environmental change. There is growing evidence that offspring biology is responsive to experiences encoded in maternal biology and her epigenome as signaled through the transfer of nutrients and hormones across the placenta and via breast milk. Principles of evolutionary and comparative biology lead to the expectation that transient fluctuations in early experience should have greater long-term impacts in small, short-lived species compared with large, long-lived species such as humans. This implies greater buffering of the negative effects of early-life stress in humans, but also a reduced sensitivity to short-term interventions that aim to improve long-term health outcomes. Taking the timescales of adaptation seriously will allow the design of interventions that emulate long-term environmental change and thereby coax the developing human body into committing to a changed long-term strategy, yielding lasting improvements in human health and wellbeing.

Biological memories of past environments: Epigenetic pathways to health disparities

by Zaneta Thayer

Human health tends to mirror gradients in social standing
related to class, ethnicity and race. Past research in... more Human health tends to mirror gradients in social standing
related to class, ethnicity and race. Past research in the social
sciences suggests that environmental experiences related to
social status contribute to these disparities, but the underlying
biological mechanisms are only partially understood. Here, we
review research related to three domains of environmental
exposure that point to epigenetic contributions to health
disparities: nutrition, psychosocial stress and environmental
toxicant exposure. Each exposure has effects that may persist
across the life course and in some instances may be transmitted
to offspring via epigenetic inheritance. Since epigenetic
markings provide a “memory” of past experiences, minimizing
future disparities in health will be partially contingent upon
our ability to address inequality in the current environment.
We suggest that future research in environmental epigenetics
focus on establishing the reversibility of stress-induced
epigenetic modifications, and also on identifying positive
epigenetic effects of environmental enrichment.

Signaling epigenetics: Novel insights on cell signaling and epigenetic regulation

by David Valle García

IUBMB Life. 2011 Oct;63(10):907-21. doi: 10.1002/iub.557. Epub 2011 Sep 7.
Authors: Rodrigo G. Arzate-Mejía, David Valle-García, Félix Recillas-Targa

Cells must be able to respond rapidly and precisely not only to changes in their external environment but also to... more Cells must be able to respond rapidly and precisely not only to changes in their external environment but also to developmental and differentiation cues to determine when to divide, die, or acquire a particular cell fate. Signal transduction pathways are responsible for the integration and interpretation of most of such signals into specific transcriptional states. Those states are achieved by the modulation of chromatin structure that activates or represses transcription at particular loci. Although a large variety of signal transduction pathways have already been described, much less is known about the crosstalk between signal transduction and its consequent changes in chromatin structure and, therefore, gene expression. Here we present some examples of the relationship between chromatin-associated proteins and important signal transduction pathways during critical processes like development, differentiation, and disease. There is a great diversity of epigenetic mechanisms that have unexpected interactions with signaling pathways to establish transcriptional programs. Moreover, there are also particular cases where signaling pathways directly affect important components of the epigenetic machinery. Based on such examples, we further propose future research directions linking cell signaling and epigenetics. It is foreseeable that analyzing the relationship between cell signaling and epigenetics will be a huge area for future development that will help us understand the complex process by which a cell is able to induce transcriptional changes in response to external and internal signals.