In Eva Jablonka and Lamb’s words, epigenetics is one of the four dimensions of evolution. After decades thinking and acting as if the genome determined  the absolute  fate of any life form in Earth, the relevance of epigenetics for mammalian life, disease and death is now recognized. In fact, assuming similar genomes, lifespan, life style, and risk of diseases, etc. results from a balance between genes and epigenetic traits. The Research Topic aims to  show the differences of epigenetic traits between tissues, their physiological relevance  and potential to target epigenetic mechanisms in human diseases.

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Frontiers in Genetics

Epigenomics and Epigenetics

Frontiers in Cell and Developmental Biology

Epigenetics in Mammalian Tissues

The challenge of understanding epigenetics and reaching a consensus for its role(s) in development is substantial. This is illustrated in the wide range of topics covered by the research topic &#x201c;Epigenetics in Mammalian Tissues.&#x201d; The discovery of new concepts in epigenetics during pregnancy and early development is on-going, together with their potential impact on susceptibility to later disease. A diverse range of examples are included within this issue that cover methodological approaches together with responses of individual tissues and organs ranging from the placenta to the eye.The paper focused on the eye shows evidence of epigenetic factors in diseases affecting organs involved in sense perception. This could be important because in contrast to genetic inheritance of disease, epigenetic factors may be acquired by a variety of circumstances. In the case of the eye, adverse exposure to sunlight can trigger a range of responses that can contribute to the onset of cataracts to glaucoma (<a href="https://doi.org/10.3389/fgene.2017.00144">Alkozi et al.</a>).It is fascinating that cells with the same DNA content may give rise to such diverse tissues, and epigenetic factors are important in this regard. Undoubtedly, development and function of the central nervous system (CNS) is under epigenetic modification, as it is composed of a myriad of phenotypically different cells. For example, whereas the liver is primarily composed of hepatocytes and fibroblasts, the CNS contains neurons and glia with hundreds of diverse neurons. One paper in the special issue focuses on the epigenetic processes taking place in the CNS and how this impacts on the nuclear architecture during development, function, and disease onset (<a href="https://doi.org/10.3389/fgene.2018.00308">Ito and Takizawa</a>).Another paper describes a study (<a href="https://doi.org/10.3389/fcell.2017.00063">He et al.</a>) using a transgenic mouse to model Turner disease, which is a chromosomal disease characterized “by complete or partial X monosomy in some or all cells” (<a href="#B5">Saenger et al., 2001</a>). It compares mice with one single paternally or maternally inherited X chromosome, of which embryos with paternal inheritance have greater risk of miscarriage (<a href="#B3">Hall and Gilchrist, 1990</a>; <a href="#B4">Robinson, 1990</a>). This is probably due to epigenetic factors such as paternally imprinted genes in the placenta or genome-wide differences in chromatin condensation. Differences in the outer zone of the placenta occupied by glycogen cells together with a substantial adaptation of glycogen/glucose storage and metabolism are described. They conclude that changes in glucose metabolism are not directly caused by changes in X-linked genes but are more likely to be a consequence of an altered cellular composition mediated by placental adaptation in early development.The study of the impact of the X chromosome on health and disease is fascinating. One aspect relates to in vitro fertilization, and (<a href="https://doi.org/10.3389/fgene.2017.00042">Min et al.</a>) suggest that epigenetic factors could be involved in the differential expression of X-linked genes in male compared with female in vitro fertilization-derived blastocysts. They also demonstrate epigenetic regulation of X chromosome reactivation with somatic-cell nuclear transfer. Under these conditions, clonal reprogramming of X-chromosome appears incomplete and may differently occur in cells within a single blastocyst.There are a wide range of methods available for examining epigenetics including the assessment of patterns of DNS methylation, histone acetylation, etc. The paper by <a href="https://doi.org/10.3389/fgene.2017.00097">Jeon et al.</a> is technical in nature and describes how it is possible to run parallel assessments of methylation status in hundreds of CpG sites. Their approach is based on bisulfite polymerase chain reaction sequencing (TBPseq). The field has also advanced by exploring how to enhance or depress methylation/acetylation as a therapeutic approach. For example, inhibition of histone acetylation leads to an increase in the expression of genes that enhance cognition and could have potential in treating Alzheimer’s disease (<a href="#B2">Cuadrado-Tejedor et al., 2013</a>; <a href="#B1">Cuadrado-Tejedor et al., 2015</a>).It should also be noted the term epigenetic is not used by all scientists in the same way. One article revisits the concept that epigenetics defines everything that is not genetic, i.e., existing in the DNA sequence, that affects phenotype. On doing so, hormonal regulation, that ultimately impacts on gene expression, could be considered epigenetic. This reasoning makes it necessary to choose a word to define events occurring inside the cell, i.e., those participating after a hormone interacts with a cell surface receptor until a transcription factor is activated or inactivated and gene expression is enhanced or repressed. The word used by <a href="https://doi.org/10.3389/fgene.2017.00179">Navarro et al.</a> has the prefix “cyto” and the suffix “crin,” as there are interacting intracellular cascades with actions at the nuclear level. Specific cytocrin pathways may explain the differential effect of any hormone on mammalian tissues or cells thereby linking epigenetic factors and epigenetic mediators to epigenetic traits. This type of concept could explain the impact of modulating maternal nutrition for which supplementation of the maternal diet with fructose, in rats, modulates the maternal microbiome (<a href="https://doi.org/10.3389/fgene.2018.00203">Astbury et al.</a>) and it was accompanied with reduced gene expression of markers of gut barrier function that could adversely affect its function in later life.In conclusion, our understanding of epigenetic regulation of mammalian tissues is only beginning to become established. Furthermore, as illustrated by the diverse nature of papers included in this edition, the topic has substantial scope for transforming our understanding of development and disease onset.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Editorial: Epigenetics in Mammalian Tissues

Decades of study have shown that epigenetic regulation plays an important role in neural development and function. Several layers of epigenetic mechanisms control functions of the eukaryotic cell nucleus, a well-organized subcellular organelle with distinct compartments: chromatin, its related architectural proteins, and nuclear bodies. As these components function together in the epigenetic regulation of cellular development and functions, they are collectively termed nuclear architecture. In the nervous system, dynamic rearrangement of nuclear architecture correlates with alteration of transcription programs. During maturation and upon depolarization, neurons undergo a reorganization of nuclear architecture that alters gene expression programs. As such changes allow for specialized functions, including learning and memory, nuclear architecture is distinct among cell types. Studying nuclear architecture of neurons may uncover cell-division-independent mechanisms of global and local changes to nuclear architecture. We herein review recent research concerning nuclear architecture in the nervous system and will discuss its importance to the development, maturation, function, and diseases of the nervous system.

Decades of study have shown that epigenetic regulation plays an important role in neural development and function. Several layers of epigenetic mechanisms control functions of the eukaryotic cell nucleus, a well-organized subcellular organelle with distinct compartments: chromatin, its related architectural proteins, and nuclear bodies. As these components function together in the epigenetic regulation of cellular development and functions, they are collectively termed nuclear architecture. In the nervous system, dynamic rearrangement of nuclear architecture correlates with alteration of transcription programs. During maturation and upon depolarization, neurons undergo a reorganization of nuclear architecture that alters gene expression programs. As such changes allow for specialized functions, including learning and memory, nuclear architecture is distinct among cell types. Studying nuclear architecture of neurons may uncover cell-division-independent mechanisms of global and local changes to nuclear architecture. We herein review recent research concerning nuclear architecture in the nervous system and will discuss its importance to the development, maturation, function, and diseases of the nervous system.

Nuclear Architecture in the Nervous System: Development, Function, and Neurodevelopmental Diseases

Studies in pregnant women indicate the maternal microbiome changes during pregnancy so as to benefit the mother and fetus. In contrast, disruption of the maternal microbiota around birth can compromise normal bacterial colonisation of the infant’s gastrointestinal tract. This may then inhibit development of the gut so as to increase susceptibility to inflammation and reduce barrier function. The impact of modulating fructose intake on the maternal microbiome through pregnancy is unknown, therefore we examined the effect of fructose supplementation on the maternal microbiome together with the immediate and next generation effects in the offspring. Wistar rat dams were divided into control and fructose fed groups that received 10% fructose in their drinking water from 8 weeks of age and throughout pregnancy (10–13 weeks). Maternal fecal and blood samples were collected pre-mating (9 weeks) and during early (gestational day 4–7) and late pregnancy (gestational day 19–21). We show supplementation of the maternal diet with fructose appears to significantly modulate the maternal microbiome, with a significant reduction in Lactobacillus and Bacteroides. In offspring maintained on this diet up to pregnancy and term there was a reduction in gene expression of markers of gut barrier function that could adversely affect its function. An exacerbated insulin response to pregnancy, reduced birth weight, but increased fat mass was also observed in these offspring. In conclusion dietary supplementation with fructose modulates the maternal microbiome in ways that could adversely affect fetal growth and later gut development.

Studies in pregnant women indicate the maternal microbiome changes during pregnancy so as to benefit the mother and fetus. In contrast, disruption of the maternal microbiota around birth can compromise normal bacterial colonisation of the infant’s gastrointestinal tract. This may then inhibit development of the gut so as to increase susceptibility to inflammation and reduce barrier function. The impact of modulating fructose intake on the maternal microbiome through pregnancy is unknown, therefore we examined the effect of fructose supplementation on the maternal microbiome together with the immediate and next generation effects in the offspring. Wistar rat dams were divided into control and fructose fed groups that received 10% fructose in their drinking water from 8 weeks of age and throughout pregnancy (10–13 weeks). Maternal fecal and blood samples were collected pre-mating (9 weeks) and during early (gestational day 4–7) and late pregnancy (gestational day 19–21). We show supplementation of the maternal diet with fructose appears to significantly modulate the maternal microbiome, with a significant reduction in Lactobacillus and Bacteroides. In offspring maintained on this diet up to pregnancy and term there was a reduction in gene expression of markers of gut barrier function that could adversely affect its function. An exacerbated insulin response to pregnancy, reduced birth weight, but increased fat mass was also observed in these offspring. In conclusion dietary supplementation with fructose modulates the maternal microbiome in ways that could adversely affect fetal growth and later gut development.

High Fructose Intake During Pregnancy in Rats Influences the Maternal Microbiome and Gut Development in the Offspring

A single word, Epigenetics, underlies one exciting subject in today's Science, with different sides and with interactions with philosophy. The apparent trivial description includes everything in between genotype and phenotype that occurs for a given unique DNA sequence/genome. This Perspective article first presents an historical overview and the reasons for the lack of consensus in the field, which derives from different interpretations of the diverse operative definitions of Epigenetics. In an attempt to reconcile the different views, we propose a novel concept, the “cytocrin system.” Secondly, the article questions the inheritability requirement and makes emphasis in the epigenetic mechanisms, known or to be discovered, that provide hope for combating human diseases. Hopes in cancer are at present in deep need of deciphering mechanisms to support ad hoc therapeutic approaches. Better perspectives are for diseases of the central nervous system, in particular to combat neurodegeneration and/or cognitive deficits in Alzheimer's disease. Neurons are post-mitotic cells and, therefore, epigenetic targets to prevent neurodegeneration should operate in non-dividing diseased cells. Accordingly, epigenetic-based human therapy may not need to count much on transmissible potential.

A single word, Epigenetics, underlies one exciting subject in today's Science, with different sides and with interactions with philosophy. The apparent trivial description includes everything in between genotype and phenotype that occurs for a given unique DNA sequence/genome. This Perspective article first presents an historical overview and the reasons for the lack of consensus in the field, which derives from different interpretations of the diverse operative definitions of Epigenetics. In an attempt to reconcile the different views, we propose a novel concept, the “cytocrin system.” Secondly, the article questions the inheritability requirement and makes emphasis in the epigenetic mechanisms, known or to be discovered, that provide hope for combating human diseases. Hopes in cancer are at present in deep need of deciphering mechanisms to support ad hoc therapeutic approaches. Better perspectives are for diseases of the central nervous system, in particular to combat neurodegeneration and/or cognitive deficits in Alzheimer's disease. Neurons are post-mitotic cells and, therefore, epigenetic targets to prevent neurodegeneration should operate in non-dividing diseased cells. Accordingly, epigenetic-based human therapy may not need to count much on transmissible potential.

The Epigenetic Cytocrin Pathway to the Nucleus. Epigenetic Factors, Epigenetic Mediators, and Epigenetic Traits. A Biochemist Perspective

Sight for mammals is one of the most appreciated senses. In humans there are several factors that contribute to the increment in all kind of eye diseases. This mini-review will focus on some diseases whose prevalence is steadily increasing year after year for non-genetic reasons, namely cataracts, dry eye, and glaucoma. Aging, diet, inflammation, drugs, oxidative stress, seasonal and circadian style-of-live changes are impacting on disease prevalence by epigenetics factors, defined as stable heritable traits that are not explained by changes in DNA sequence. The mini-review will concisely show the data showing epigenetics marks in these diseases and on how knowledge on the epigenetic alterations may guide therapeutic approaches to have a healthy eye.

Sight for mammals is one of the most appreciated senses. In humans there are several factors that contribute to the increment in all kind of eye diseases. This mini-review will focus on some diseases whose prevalence is steadily increasing year after year for non-genetic reasons, namely cataracts, dry eye, and glaucoma. Aging, diet, inflammation, drugs, oxidative stress, seasonal and circadian style-of-live changes are impacting on disease prevalence by epigenetics factors, defined as stable heritable traits that are not explained by changes in DNA sequence. The mini-review will concisely show the data showing epigenetics marks in these diseases and on how knowledge on the epigenetic alterations may guide therapeutic approaches to have a healthy eye.

Epigenetics in the Eye: An Overview of the Most Relevant Ocular Diseases

Methylated-DNA sequencing technologies are producing vast amounts of methylome data from cancer samples, from which cancer-associated differentially methylated CpG sites (cDMCs) are continuously identified and filed. The inclusion of as many cDMCs as possible helps improve the accuracy of cancer diagnosis and sometimes identify cancer subtypes. However, the lack of an established method for the analysis of 100s of cDMCs practically impedes their robust use in clinical medicine. Here, we tested the availability of targeted bisulfite-PCR-sequencing (TBPseq) technology for the assessment of methylation levels of a myriad of CpGs scattered over the genome. In randomly selected 46 cancer cell lines, multiplexed PCR yielded a variety of amplicons harboring 246 CpGs residing at promoters of 97 cancer-associated genes, all of which were sequenced in the same flow cell. Clustering analysis of the TBPseq-assessed methylation levels of target CpGs showed that the lung and liver cancer cell lines correlated relatively strongly with each other while they weakly correlated with colon cancer cells. CpGs at the LIFR gene promoter, which are known to be hypermethylated in colon cancers, indeed were heavily methylated in the tested colon cancer cells. Moreover, the LIFR promoter hypermethylation was found in colon cancer cells only, but not in biliary tract, liver, lung, and stomach cancers cell lines. A meta-analysis with public cancer methylome data verified the colon cancer specificity of LIFR promoter methylation. These results demonstrate that our TBPseq-based methylation assessment could be considered an effective, accurate, and competitive method to simultaneously examine a large number of target cDMCs and patient samples.

Methylated-DNA sequencing technologies are producing vast amounts of methylome data from cancer samples, from which cancer-associated differentially methylated CpG sites (cDMCs) are continuously identified and filed. The inclusion of as many cDMCs as possible helps improve the accuracy of cancer diagnosis and sometimes identify cancer subtypes. However, the lack of an established method for the analysis of 100s of cDMCs practically impedes their robust use in clinical medicine. Here, we tested the availability of targeted bisulfite-PCR-sequencing (TBPseq) technology for the assessment of methylation levels of a myriad of CpGs scattered over the genome. In randomly selected 46 cancer cell lines, multiplexed PCR yielded a variety of amplicons harboring 246 CpGs residing at promoters of 97 cancer-associated genes, all of which were sequenced in the same flow cell. Clustering analysis of the TBPseq-assessed methylation levels of target CpGs showed that the lung and liver cancer cell lines correlated relatively strongly with each other while they weakly correlated with colon cancer cells. CpGs at the LIFR gene promoter, which are known to be hypermethylated in colon cancers, indeed were heavily methylated in the tested colon cancer cells. Moreover, the LIFR promoter hypermethylation was found in colon cancer cells only, but not in biliary tract, liver, lung, and stomach cancers cell lines. A meta-analysis with public cancer methylome data verified the colon cancer specificity of LIFR promoter methylation. These results demonstrate that our TBPseq-based methylation assessment could be considered an effective, accurate, and competitive method to simultaneously examine a large number of target cDMCs and patient samples.

Simultaneous Methylation-Level Assessment of Hundreds of CpG Sites by Targeted Bisulfite PCR Sequencing (TBPseq)

Genetic mouse model (39,XO) for human Turner Syndrome (45,XO) harboring either a single maternally inherited (Xm) or paternally inherited (Xp) chromosome show a pronounced difference in survival rate at term. However, a detailed comparison of XmO and XpO placentas to explain this difference is lacking. We aimed to investigate the morphological and molecular differences between XmO and XpO term mouse placentas. We observed that XpO placentas at term contained a significantly larger area of glycogen cells (GCs) in their outer zone, compared to XmO, XX, and XY placentas. In addition, the outer zone of XpO placentas showed higher expression levels of lactate dehydrogenase (Ldha) than XmO, XX, and XY placentas, suggestive of increased anaerobic glycolysis. In the labyrinth, we detected significantly lower expression level of trophectoderm (TE)-marker keratin 19 (Krt19) in XpO placentas than in XX placentas. The expression of other TE-markers was comparable as well as the area of TE-derived cells between XO and wild-type labyrinths. XpO placentas exhibited specific defects in the amount of GCs and glucose metabolism in the outer zone, suggestive of increased anaerobic glycolysis, as a consequence of having inherited a single Xp chromosome. In conclusion, the XpO genotype results in a more severe placental phenotype at term, with distinct abnormalities regarding glucose metabolism in the outer zone.

Genetic mouse model (39,XO) for human Turner Syndrome (45,XO) harboring either a single maternally inherited (Xm) or paternally inherited (Xp) chromosome show a pronounced difference in survival rate at term. However, a detailed comparison of XmO and XpO placentas to explain this difference is lacking. We aimed to investigate the morphological and molecular differences between XmO and XpO term mouse placentas. We observed that XpO placentas at term contained a significantly larger area of glycogen cells (GCs) in their outer zone, compared to XmO, XX, and XY placentas. In addition, the outer zone of XpO placentas showed higher expression levels of lactate dehydrogenase (Ldha) than XmO, XX, and XY placentas, suggestive of increased anaerobic glycolysis. In the labyrinth, we detected significantly lower expression level of trophectoderm (TE)-marker keratin 19 (Krt19) in XpO placentas than in XX placentas. The expression of other TE-markers was comparable as well as the area of TE-derived cells between XO and wild-type labyrinths. XpO placentas exhibited specific defects in the amount of GCs and glucose metabolism in the outer zone, suggestive of increased anaerobic glycolysis, as a consequence of having inherited a single Xp chromosome. In conclusion, the XpO genotype results in a more severe placental phenotype at term, with distinct abnormalities regarding glucose metabolism in the outer zone.

At Term, XmO and XpO Mouse Placentas Show Differences in Glucose Metabolism in the Trophectoderm-Derived Outer Zone

To better understand X-chromosome reactivation (XCR) during early development, we analyzed transcriptomic data obtained from bovine male and female blastocysts derived by in-vitro fertilization (IVF) or somatic-cell nuclear transfer (SCNT). We found that X-linked genes were upregulated by almost two-fold in female compared with male IVF blastocysts. The upregulation of X-linked genes in female IVFs indicated a transcriptional dimorphism between the sexes, because the mean autosomal gene expression levels were relatively constant, regardless of sex. X-linked genes were expressed equivalently in the inner-cell mass and the trophectoderm parts of female blastocysts, indicating no imprinted inactivation of paternal X in the trophectoderm. All these features of X-linked gene expression observed in IVFs were also detected in SCNT blastocysts, although to a lesser extent. A heatmap of X-linked gene expression revealed that the initial resemblance of X-linked gene expression patterns between male and female donor cells turned sexually divergent in host SCNTs, ultimately resembling the patterns of male and female IVFs. Additionally, we found that sham SCNT blastocysts, which underwent the same nuclear-transfer procedures, but retained their embryonic genome, closely mimicked IVFs for X-linked gene expression, which indicated that the embryo manipulation procedure itself does not interfere with XCR in SCNT blastocysts. Our findings indicated that female SCNTs have less efficient XCR, suggesting that clonal reprogramming of X chromosomes is incomplete and occurs variably among blastocysts, and even among cells in a single blastocyst.

To better understand X-chromosome reactivation (XCR) during early development, we analyzed transcriptomic data obtained from bovine male and female blastocysts derived by in-vitro fertilization (IVF) or somatic-cell nuclear transfer (SCNT). We found that X-linked genes were upregulated by almost two-fold in female compared with male IVF blastocysts. The upregulation of X-linked genes in female IVFs indicated a transcriptional dimorphism between the sexes, because the mean autosomal gene expression levels were relatively constant, regardless of sex. X-linked genes were expressed equivalently in the inner-cell mass and the trophectoderm parts of female blastocysts, indicating no imprinted inactivation of paternal X in the trophectoderm. All these features of X-linked gene expression observed in IVFs were also detected in SCNT blastocysts, although to a lesser extent. A heatmap of X-linked gene expression revealed that the initial resemblance of X-linked gene expression patterns between male and female donor cells turned sexually divergent in host SCNTs, ultimately resembling the patterns of male and female IVFs. Additionally, we found that sham SCNT blastocysts, which underwent the same nuclear-transfer procedures, but retained their embryonic genome, closely mimicked IVFs for X-linked gene expression, which indicated that the embryo manipulation procedure itself does not interfere with XCR in SCNT blastocysts. Our findings indicated that female SCNTs have less efficient XCR, suggesting that clonal reprogramming of X chromosomes is incomplete and occurs variably among blastocysts, and even among cells in a single blastocyst.