Epigenetics in Human Reproduction and Development

The following sections are included:

• Preface
• Contents

Germ cells bridge generations and are critical for the successful propagation of species. Early in development, a small group of embryonic cells embarks on a long but fascinating journey that will take them through most dramatic changes in their genomic architecture, epigenetic makeup and cellular morphology (Lesch and Page 2012). The germ cell lineage will multiply, protect and prepare a few original copies of the newly created embryonic genome for the ultimate purpose of fertilization. Failure to precisely fulfill these functions at any level of cellular organization leads to deleterious mutations, chromosomal numerical and structural abnormalities, subfertility or infertility of an organism…

Chromatin modifications during oogenesis are essential for the control of gene expression, the establishment of maternal-specific DNA methylation marks and chromosome stability at critical stages of oocyte growth and meiotic maturation. Compelling evidence indicates that establishment of the correct epigenetic landscape during oocyte growth is indispensable to ensure proper chromosome segregation, for silencing of repetitive elements and potentially deleterious transposons and for meiotic centromere stability. During the critical window of post-natal oocyte growth, chromatin modifications are required for the establishment of maternal specific genomic imprinting and global methylation patterns in the oocyte genome. Importantly, large-scale chromatin remodeling in pre-ovulatory oocytes is essential for pericentric heterochromatin formation and the epigenetic control of centromere function in preparation for meiotic chromosome segregation. Functional differentiation of chromatin structure during oogenesis or ‘epigenetic maturation’ is regulated by multiple and hierarchical chromatin modifications established at critical developmental transitions that are regulated at the local (single locus) or global (entire chromosomal domains) levels by an increasing list of chromatin remodeling proteins and histone post-translational modifications. Here, we focus on recent advances in our understanding of epigenetic maturation of the mammalian oocyte genome and the emerging links between chromatin remodeling and transcription in the establishment of maternal DNA methylation and maintenance of chromosome stability during oogenesis.

Homologous recombination (HR) is the exchange of genetic information between similar deoxyribonucleic acid (DNA) molecules. In mammalian meiosis, HR is essential for correct chromosome segregation during gamete formation. Errors of HR lead to aneuploidy, formation of gametes with incorrect number of chromosomes and genetic disorders. Understanding the mechanisms of recombination is important for identifying disease-associated genomic regions and for the study of human genome evolution. With the development of new whole-genome technologies, knowledge of meiotic recombination in germ cells have advanced significantly. The recent discovery of the role of the PR domain containing 9 (PRDM9) protein in the recombination process opens new perspectives in HR research. In this review, I describe the basics of HR; introduce the pedigree, sperm typing and chromatin immunoprecipitation Sequencing (ChIP-seq) approaches that are currently used to study recombination in human germ cells and summarize the properties of recombination “hotspots”, discovered as a result of the understanding of the process involved in double-strand break (DSB) formation. Finally, I discuss the implications of the recombination events for genetic disorders in humans.

The contribution of the male gamete to embryogenesis is more complex than a simple DNA transmission. The sperm nucleus has a very heterogeneous structure containing a haploid genome packaged by basic nucleoproteins that carries various epigenetic information, including DNA methylation, histone modifications, protamines and a large population of transcripts, of which their exact role is not yet well known. This epigenetic landscape may be altered in the sperm of a significant proportion of infertile men. This chapter will discuss what we now know about the relationship between male infertility and epigenetic factors, with a special emphasis on the sperm epigenome.

X-chromosome inactivation is a mammalian epigenetic phenomenon, which occurs during female embryogenesis and has the purpose to equalize expression of X-chromosomal genes between females and males. It is controlled by long noncoding RNAs, most prominently Xist and involves a plethora of epigenetic silencing mechanisms from histone modifications over histone variants to DNA-methylation and conformational changes of the inactive X-chromosome. Although X-inactivation is a classical field of epigenetics, advances of in vitro mouse and human model systems and epigenomic analysis methods increased our knowledge exponentially in the recent years. In this review chapter, I am providing an update on the current state of the X-inactivation field and the questions, which still remain to be answered.

Genomic imprinting is an epigenetic phenomenon that permits a gene to be expressed from a single allele based on the parent-of-origin. While only a small subset of genes is imprinted in the human genome, the correct regulation of these loci is essential for healthy pregnancy. Imprinted loci not only contribute to the development of the fetus, but are required for placental function. This chapter will explore our current understanding of genomic imprinting, its effects on placentation and its contribution to complications of human pregnancy.

Imprinted genes influence prenatal growth, and several studies have demonstrated association between genetic polymorphisms in imprinted regions and birth weight. Association between DNA methylation levels at imprinted loci and birth weights has been also detected. Here, we examine the relationship between haplotypes, DNA methylation and birth weight to determine if DNA methylation acts as a mediator between haplotype and phenotype. Analysis of DNA from infant cord blood at the imprinted H19 locus, in a set of infants of either African American or White ancestry, demonstrated both effects of maternally-inherited haplotypes on birthweight, where one key haplotype was associated with lower birthweight by approximately 210 grams, and also strong effects of DNA methylation levels on birthweight, such that increasing levels of methylation were associated with lower birthweights. Despite the presence of strong cis-associations between the haplotypes and the methylation levels, the genetic and epigenetic effects on birthweight appear to be independent, and the probes involved were not in the imprinting control region.

Folate is an important vitamin that is well known in the prevention of neural tube defects. It is required for the synthesis of nucleotides and S-adenosylmethionine (SAM), a ubiquitous methyl donor. SAM is an important molecule in epigenetic processes that rely on methylation of DNA, histones and other proteins. Decreased production of SAM or high levels of homocysteine and its metabolite S-adenosylhomocysteine, intermediates in the methylation cycle, can inhibit methylation reactions. Common genetic polymorphisms in genes in the folate pathway have been shown to affect the methylation cycle and increase the levels of homocysteine. Maternal nutrition before and during pregnancy has attracted a great deal of interest in recent years due its role in embryonic development and its potential long-term effect on offspring and adult health. One possible mechanism for the disturbances in phenotypes is a change in the epigenetic signature, which can affect expression levels of key genes in a given pathway. Folate intake, including dietary deficiency and excessive supplementation, has also been shown to alter DNA methylation and affect offspring phenotype. In this chapter, we will review one-carbon folate metabolism and describe how disturbances in the pathway, genetic and/or dietary, affect epigenetic processes, developmental outcomes and adult health.

Early life adversity (ELA) frequently associates with maternal depression, anxiety, or trauma during pregnancy and is an important risk factor for the development of psychiatric disease. All of these maternal states manifest deregulation of the hypothalamic-pituitary-adrenal (HPA) axis and can elicit epigenetic changes that are lastingly inscribed into the fetus’s genetic blueprint presetting future interactions with the environment. The HPA axis mediates the stress response and epigenetic programming of HPA-axis regulatory genes offers a versatile mechanism by which ELA gets under the skin. The glucocorticoid receptor (NR3C1) plays an important role in terminating the stress response and can be at the same time epigenetically programmed by stress. Here, we discuss recent evidence on the impact of maternal depression or trauma, but also of mundane stress, on epigenetic programing of NR3C1 and its association with infant HPA-axis activity and neurobehavioral performance. Furthermore, integrate analysis of placental glucocorticoid signaling pathways may enhance insight into stress dynamics in utero. Overall, epigenetic bookmarking of fetal stress systems may have far-reaching implications for mental well-being of generations to come.

One in six couples is diagnosed with infertility. Many infertile couples are turning to assisted reproductive technologies (ART) to facilitate conception and child bearing. While the majority of ART offspring are healthy, there is a concern that ART interventions during major epigenomic reprogramming in oocytes and embryos can have harmful effects on the health of ART-conceived children. This concern has spawned a multitude of ART-related epigenetic-based studies in animals and human. While studies of animal models suggest that there is an association between ART interventions and epigenetic aberrations, these findings may not be fully applicable to humans. This chapter reviews current findings for ART-affected epigenomic perturbations based on human-centric studies.