Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity

Ecker, Simone; Pancaldi, Véra; Valencia, Alfonso; Beck, Stephan; Paul, Dirk S.

doi:10.1002/bies.201700148

Cited by 76 publications

(73 citation statements)

References 126 publications

(282 reference statements)

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“…Despite historic assumptions that these gene regulatory pathways are highly stable and immutable, there is now an expansive literature describing the impact of a broad range of environmental exposures on epigenetic/epigenomic variation and the consequences of this variation for growth, physiology, neurodevelopment and behaviour. Though life span malleability of the epigenome has been observed, the persistence of early life‐induced epigenetic changes into adulthood is a consistent finding within the study of behavioural and environmental epigenetics and illustrates the complementary properties of stability and plasticity that characterize epigenetic modifications (Ecker, Pancaldi, Valencia, Beck, & Paul, ).…”

Section: Introductionsupporting

confidence: 53%

Interplay between paternal germline and maternal effects in shaping development: The overlooked importance of behavioural ecology

Champagne

2019

Functional Ecology

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Environmental conditions can have a lasting epigenetic impact on development, and there is increasing evidence that these effects can be transmitted across generations. Evidence for parental transmission of epigenetic variation to offspring has been primarily focused on paternal epigenetic influences induced by a male's experience of nutritional, social and toxicological exposures. There is an assumption in the literature that paternal influence on offspring in non‐biparental species is mediated exclusively through epigenetic transmission via the germline. However, integration of concepts from behavioural ecology into the study of parental transmission of environmental effects reveals the importance of mating tactics and maternal–paternal interplay in shaping resource allocation towards offspring in considering the mechanism(s) of epigenetic transmission. This paper describes the current state of knowledge regarding paternal epigenetic germline effects, the interplay between maternal and paternal influences and the importance of considering the complex nature of reproduction when predicting the transmission of phenotype across generations. Further, this paper highlights how incorporating concepts from behavioural ecology into the study of epigenetic transmission can refine predictions of phenotypes that emerge and create a more integrated notion of development and inheritance. It is proposed that theoretical and methodological approaches that consider the impact of reproductive context, which include mating dynamics, fertility, variation in parental life history and assessment of maternal effects, could improve the predictions made within studies of paternal epigenetic effects on offspring development. A free Plain Language Summary can be found within the Supporting Information of this article.

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Section: Introductionsupporting

confidence: 53%

Interplay between paternal germline and maternal effects in shaping development: The overlooked importance of behavioural ecology

Champagne

2019

Functional Ecology

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“…Although a relationship between genome size and phenotypic plasticity is probable, little work has enlightened the nature of this relationship. What is clear is that transcription and gene regulation networks can become more complex with increasing number of nucleotides [20,21]. Variability produced with each replication event can be more accurately approximated.…”

Section: Resultsmentioning

confidence: 99%

Larger viral genome size facilitates emergence of zoonotic diseases

Grewelle

2020

Preprint

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Emergence of new viral diseases is linked to mutation or recombination events.The likelihood of cross-species transmission is related to phenotypic plasticity of a virus and its capacity to produce genetically variable progeny. Herein a model is described connecting the production of genetic variability with increasing genome size. Comparing all known zoonotic viral genome sizes to known non-zoonotic viral genome sizes demonstrates that zoonotic viruses have significantly larger genomes. These results support the notion that large viral genomes are important in producing new zoonotic disease, and suggest that genome size may be a useful surrogate in screening for potential zoonotic viruses.

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“…While the impact of epigenetics on transcription has been moved into the focus of epigenetic research, studies on the consequences of these interrelations and their variability for regulatory dynamics during tissue formation and transformation are still rare [35]. Our studies just provide a Analyzing different states of ISC specification and differentiation, we have not addressed the question about the dynamics of transition states so far [9].…”

Section: Discussionmentioning

confidence: 96%

On the Cooperation between Epigenetics and Transcription Factor Networks in the Specification of Tissue Stem Cells

et al. 2018

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It is generally accepted that epigenetic modifications, such as DNA and histone methylations, affect transcription and that a gene’s transcription feeds back on its epigenetic profile. Depending on the epigenetic modification, positive and negative feedback loops have been described. Here, we study whether such interrelation are mandatory and how transcription factor networks affect it. We apply self-organizing map machine learning to a published data set on the specification and differentiation of murine intestinal stem cells in order to provide an integrative view of gene transcription and DNA, as well as histone methylation during this process. We show that, although gain/loss of H3K4me3 at a gene promoter is generally considered to be associated with its increased/decreased transcriptional activity, such an interrelation is not mandatory, i.e., changes of the modification level do not necessarily affect transcription. Similar considerations hold for H3K27me3. In addition, even strong changes in the transcription of a gene do not necessarily affect its H3K4me3 and H3K27me3 modification profile. We provide a mechanistic explanation of these phenomena that is based on a model of epigenetic regulation of transcription. Thereby, the analyzed data suggest a broad variance in gene specific regulation of histone methylation and support the assumption of an independent regulation of transcription by histone methylation and transcription factor networks. The results provide insights into basic principles of the specification of tissue stem cells and highlight open questions about a mechanistic modeling of this process.

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Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity

Cited by 76 publications

References 126 publications

Interplay between paternal germline and maternal effects in shaping development: The overlooked importance of behavioural ecology

Interplay between paternal germline and maternal effects in shaping development: The overlooked importance of behavioural ecology

Larger viral genome size facilitates emergence of zoonotic diseases

On the Cooperation between Epigenetics and Transcription Factor Networks in the Specification of Tissue Stem Cells

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