scholarly journals Epimutations driven by small RNAs arise frequently but have limited duration in a metazoan organism

Author(s):  
Toni Beltran ◽  
Vahid Shahrezaei ◽  
Vaishali Katju ◽  
Peter Sarkies

Epigenetic regulation involves changes in gene expression independent of DNA sequence variation that are inherited through cell division (Holliday, 2006). In addition to a fundamental role in cell differentiation, some epigenetic changes can also be transmitted transgenerationally through meiosis (Heard and Martienssen, 2014). Epigenetic alterations (“epimutations”) could thus contribute to heritable variation within populations and be subject to evolutionary processes such as natural selection and drift (Burggren, 2016). However, this suggestion is controversial, partly because unlike classical mutations involving DNA sequence changes, key parameters such as the rate at which epimutations arise and their persistence are unknown. Here, we perform the first genome-wide study of epimutations in a metazoan organism. We use experimental evolution to characterise the rate, spectrum and stability of epimutations driven by small silencing RNAs in the model nematode C. elegans. We show that epimutations arise spontaneously at a rate ∼25 times greater than DNA sequence changes and typically have short half-lives of 2-3 generations. Nevertheless, some epimutations last at least 10 generations. Epimutations thus may contribute to evolutionary processes over a short timescale but are unlikely to bring about long-term divergence without further DNA sequence changes.

2014 ◽  
Vol 16 (3) ◽  
pp. 395-404 ◽  

Epigenetic modifications control chromatin structure and function, and thus mediate changes in gene expression, ultimately influencing protein levels. Recent research indicates that environmental events can induce epigenetic changes and, by this, contribute to long-term changes in neural circuits and endocrine systems associated with altered risk for stress-related psychiatric disorders such as major depression. In this review, we describe recent approaches investigating epigenetic modifications associated with altered risk for major depression or response to antidepressant drugs, both on the candidate gene levels as well as the genome-wide level. In this review we focus on DNA methylation, as this is the most investigated epigenetic change in depression research.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ravneet Chhabra ◽  
Stephanie Rockfield ◽  
Jennifer Guergues ◽  
Owen W. Nadeau ◽  
Robert Hill ◽  
...  

AbstractMalignant transformation of fallopian tube secretory epithelial cells (FTSECs) is a key contributing event to the development of high-grade serous ovarian carcinoma (HGSOC). Our recent findings implicate oncogenic transformative events in chronic iron-exposed FTSECs, including increased expression of oncogenic mediators, increased telomerase transcripts, and increased growth/migratory potential. Herein, we extend these studies by implementing an integrated transcriptomic and mass spectrometry-based proteomics approach to identify global miRNA and protein alterations, for which we also investigate a subset of these targets to iron-induced functional alterations. Proteomic analysis identified > 4500 proteins, of which 243 targets were differentially expressed. Sixty-five differentially expressed miRNAs were identified, of which 35 were associated with the “top” proteomic molecules (> fourfold change) identified by Ingenuity Pathway Analysis. Twenty of these 35 miRNAs are at the 14q32 locus (encoding a cluster of 54 miRNAs) with potential to be regulated by DNA methylation and histone deacetylation. At 14q32, miR-432-5p and miR-127-3p were ~ 100-fold downregulated whereas miR-138-5p was 16-fold downregulated at 3p21 in chronic iron-exposed FTSECs. Combinatorial treatment with methyltransferase and deacetylation inhibitors reversed expression of these miRNAs, suggesting chronic iron exposure alters miRNA expression via epigenetic alterations. In addition, PAX8, an important target in HGSOC and a potential miRNA target (from IPA) was epigenetically deregulated in iron-exposed FTSECs. However, both PAX8 and ALDH1A2 (another IPA-predicted target) were experimentally identified to be independently regulated by these miRNAs although TERT RNA was partially regulated by miR-138-5p. Interestingly, overexpression of miR-432-5p diminished cell numbers induced by long-term iron exposure in FTSECs. Collectively, our global profiling approaches uncovered patterns of miRNA and proteomic alterations that may be regulated by genome-wide epigenetic alterations and contribute to functional alterations induced by chronic iron exposure in FTSECs. This study may provide a platform to identify future biomarkers for early ovarian cancer detection and new targets for therapy.


2017 ◽  
Author(s):  
Ivo M. Chelo ◽  
Bruno Afonso ◽  
Sara Carvalho ◽  
Ioannis Theologidis ◽  
Christine Goy ◽  
...  

AbstractClassical theory on the origin and evolution of selfing and outcrossing relies on the role of inbreeding depression created by unlinked partially-deleterious recessive alleles to predict that individuals from natural populations predominantly self or outcross. Comparative data indicates, however, that maintenance of partial selfing and outcrossing at intermediate frequencies is common in nature. In part to explain the presence of mixed reproductive modes within populations, several hypotheses regarding the evolution of inbreeding depression have been put forward based on the complex interaction of linkage and identity disequilibrium among fitness loci, together with Hill-Robertson effects. We here ask what is the genetic basis of inbreeding depression so that populations with intermediate selfing rates can eliminate it while maintain potentially adaptive genetic diversity. For this, we use experimental evolution in the nematode C. elegans under partial selfing and compare it to the experimental evolution of populations evolved under exclusive selfing and predominant outcrossing. We find that the ancestral risk of extinction upon enforced inbreeding by selfing is maintained when populations evolve under predominant outcrossing, but reduced when populations evolve under partial or exclusive selfing. Analysis of genome-wide single-nucleotide polymorphism (SNP) during experimental evolution and after enforced inbreeding suggests that, under partial selfing, populations were purged of unlinked deleterious recessive alleles that segregate in the ancestral population, which in turn allowed the expression of unlinked overdominant fitness loci. Taken together, these observations indicate that populations evolving under partial selfing gain the short-term benefits of selfing, in purging deleterious recessive alleles, but also the long-term benefits of outcrossing, in maintaining genetic diversity that may important for future adaptation.


2018 ◽  
Author(s):  
David Berger ◽  
Josefine Stångberg ◽  
Julian Baur ◽  
Richard J. Walters

ABSTRACTAdaptation in new environments depends on the amount and type of genetic variation available for evolution, and the efficacy by which natural selection discriminates among this variation to favour the survival of the fittest. However, whether some environments systematically reveal more genetic variation in fitness, or impose stronger selection pressures than others, is typically not known. Here, we apply enzyme kinetic theory to show that rising global temperatures are predicted to intensify natural selection systematically throughout the genome by increasing the effects of DNA sequence variation on protein stability. We tested this prediction by i) estimating temperature-dependent fitness effects of induced random mutations in seed beetles adapted to ancestral or warm temperature, and ii) calculating 100 paired selection estimates on mutations in benign versus stressful environments from a diverse set of unicellular and multicellular organisms. Environmental stress per se did not increase the mean strength of selection on de novo mutation, suggesting that the cost of adaptation does not generally increase in new environments to which the organism is maladapted. However, elevated temperature increased the mean strength of selection on genome-wide polymorphism, signified by increases in both mutation load and mutational variance at elevated temperature. The theoretical predictions and empirical data suggest that this increase may correspond to a doubling of genome-wide selection for a predicted 2-4°C climate warming scenario in ectothermic organism living at temperatures close to their thermal optimum. These results have important implications for global patterns of genetic diversity and the rate and repeatability of evolution under climate change.Impact StatementNatural environments are constantly changing so organisms must also change to persist. Whether they can do so ultimately depends upon the reservoir of raw genetic material available for evolution, and the efficacy by which natural selection discriminates among this variation to favour the survival of the fittest. Here, the biochemical properties of molecules and proteins that underpin the link between genotype and phenotype can exert a major influence over how the physical environment affects the expression of phenotypes and the fitness consequences of DNA sequence polymorphism. Yet, the constraints set by these molecular features are often neglected within eco-evolutionary theory trying to predict evolution in new environments. Here we combine predictions from existing biophysical models of protein folding and enzyme kinetics with experimental data from ectothermic organisms across the tree of life, to show that rising global temperatures are predicted to increase the mean strength of selection on DNA sequence variation in cold-blooded organisms. We also show that environmental stress per se generally does not increase the mean strength of selection on new mutations, suggesting that genome-wide natural selection is not stronger in new environments to which an organism is maladapted. Theoretical predictions and data suggest that an expected climate warming scenario of a 2-4°C temperature raise within the forthcoming century will result in roughly a doubling of genome-wide selection for organisms living close to their thermal optima. However, our results also point to substantial variability in the temperature-dependence of selection on different proteins within and between organisms, suggesting scope for compensatory adaptation to shape this relationship. These results bear witness to and extend the universal temperature dependence of biological rates and have important implications for global patterns of genetic diversity and the rate and repeatability of genome evolution under environmental change.


BMC Genomics ◽  
2010 ◽  
Vol 11 (1) ◽  
Author(s):  
Nicolas Lenfant ◽  
Jolanta Polanowska ◽  
Sophie Bamps ◽  
Shizue Omi ◽  
Jean-Paul Borg ◽  
...  

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1959
Author(s):  
Rubén Rabaneda-Bueno ◽  
Beatriz Mena-Montes ◽  
Sara Torres-Castro ◽  
Norma Torres-Carrillo ◽  
Nora Magdalena Torres-Carrillo

Alzheimer’s disease (AD) is a disabling neurodegenerative disorder that leads to long-term functional and cognitive impairment and greatly reduces life expectancy. Early genetic studies focused on tracking variations in genome-wide DNA sequences discovered several polymorphisms and novel susceptibility genes associated with AD. However, despite the numerous risk factors already identified, there is still no fully satisfactory explanation for the mechanisms underlying the onset of the disease. Also, as with other complex human diseases, the causes of low heritability are unclear. Epigenetic mechanisms, in which changes in gene expression do not depend on changes in genotype, have attracted considerable attention in recent years and are key to understanding the processes that influence age-related changes and various neurological diseases. With the recent use of massive sequencing techniques, methods for studying epigenome variations in AD have also evolved tremendously, allowing the discovery of differentially expressed disease traits under different conditions and experimental settings. This is important for understanding disease development and for unlocking new potential AD therapies. In this work, we outline the genomic and epigenomic components involved in the initiation and development of AD and identify potentially effective therapeutic targets for disease control.


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