Perinatal and Developmental Epigenetics

Perinatal and Developmental Epigenetics, Volume 32, a new volume in the Translational Epigenetics series, provides a thorough overview of epigenetics in the early developmental and perinatal stages, illuminating pathways for drug discovery and clinical advances. Here, over 25 international researchers examine recent steps forward in our understanding of epigenetic programming during perinatal and early development. The book opens with an in-depth introduction to known and newly discovered epigenetic marks and how they regulate various cellular processes. Later sections examine various prenatal and perinatal environmental experiences and their ability to derail the normal developmental trajectory via epigenetic reprogramming.

Insights and suggestions for future research illuminate approaches for identifying individual disease susceptibility. Concluding chapters highlight preventative and targeted therapeutic pathways to improve quality of life into adulthood.

• Examines disease onset stemming from epigenetic changes during the perinatal periods
• Features contributions from international experts in the field, including basic biology, disease research and drug discovery
• Offers intervention strategies to mitigate adverse developmental programming to improve health outcomes

• Language: English
• Publisher: Academic Press
• Release date: Dec 2, 2022
• ISBN: 9780128217863

Book preview

Section 1

The ever-growing complexity of epigenetic regulation of gene expression

Outline

Chapter 1. Epigenetic regulation of gene expression: an overview of classical and recently discovered novel players

Chapter 2. Histone modifications in germline development and maintenance

Chapter 3. Epigenetic regulation of cis-regulatory elements and transcription factors during development

Chapter 4. Genomic imprinting and developmental physiology: intrauterine growth and postnatal period

Chapter 5. Role of RNA epigenetics in development

Chapter 1: Epigenetic regulation of gene expression: an overview of classical and recently discovered novel players

Beenish Rahat ¹ , Renuka Sharma ² , Taqveema Ali ² , and Jyotdeep Kaur ²       ¹ National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States      ² Postgraduate Institute of Medical Education and Research, Chandigarh, Punjab, India

Abstract

Cells in a human body are phenotypically heterogenous although genetically homogenous, owing to differential gene expression. Such differences are acquired during development and propagated through rounds of meiosis and mitosis and termed as epigenetic. Epigenetic processes, viz., DNA methylation, genomic imprinting, histone modifications, and noncoding RNAs by altering DNA accessibility and chromatin structure regulate gene expression. All these epigenetic mechanisms play a crucial role during embryonic development via gene regulation through various processes such as genomic imprinting, X-inactivation, chromatin remodeling of embryonic stem cells, and organ and body patterning. Aberrations in these epigenetic mechanisms result in the loss of cellular identity and development of various pathologies. Perinatal insults as well as lifestyle factors in terms of nutritional and environmental challenges are known to alter the epigenetic mechanisms and are associated with an increased susceptibility to several metabolic disorders and cancers. This chapter summarizes the implication of epigenetic mechanisms in both physiological and pathological conditions with special reference to developmental epigenetics.

Keywords

Development; DNA methylation; Genomic imprinting; Histone modifications; Long-noncoding RNAs

Introduction

The inefficiency of nuclear cloning as a result of associated epigenetic abnormalities highlights the crucial role of epigenetic modifications and their reprogramming during embryonic development. ¹ Epigenetic mechanisms are defined as the processes that cause stable heritable alterations in gene expression without altering the deoxyribonucleic acid (DNA) sequence. ²

The mammalian life cycle goes through a unique sequence of steps that changes a fertilized cell zygote into a complex, multicellular adult organism. It includes critical reprogramming in germ cells and the zygote preparing the genome for a new cycle. This is followed by extended phases of cellular differentiation with the help of transcription factors, which promotes strict lineage restriction–based development toward a particular cell type. Such regulations are both encoded in cis and directed by transcription factors as well as in heritable, covalent modifications to DNA and histones known as epigenetic mechanisms that promote cell fate decisions and avoid reversible changes. ³ Various epigenetic mechanisms such as DNA methylation, genomic imprinting, histone modifications, and noncoding RNAs (ncRNAs) work to set up epigenome that propagates gene expression profiles through multiple rounds of meiosis and mitosis. ⁴

Although different cells in a multicellular organism have similar genetic material, differential expression of the genes regulated by multiple epigenetic mechanisms makes these cells functionally heterogenous. Such differential expression is established during early development and maintained through mitosis. Epigenetic modifications can also arise under the influence of environmental changes in mature humans and mice. ⁵

DNA methylation plays an essentially important role during embryonic development regulating crucial developmental processes such as genomic imprinting, X-inactivation, and gene regulation. Advances in the detection sequencing technologies have led to better understanding of the role of DNA methylation and its distribution over different genomic regions such as promoters, exons, and imprinted control regions (ICRs). DNA methylation plays a critical role during epigenetic reprogramming in primordial germ cells (PGCs) and preimplantation developmental stages. ⁴

Genomic imprinting regulates allele-specific expression of imprinted genes in parent-of-origin-specific manner. Different types of epigenetic marks present at the ICRs of these imprinted genes maintain allele-specific expression of these genes. These epigenetic marks are established on the maternal and paternal allele during gamete formation in germline cells and then maintained after fertilization. ⁶ Genomic imprinting regulates normal development of both placenta and the fetus. Abnormal genomic imprinting in placenta not only alters the functioning of the placenta but also affects the normal fetal development. Placenta is known to express various imprinted genes, which are more sensitive to early environmental cues. ⁷

Histone methylation is related to early developmental process and plays a crucial role in differentiation of trophectoderm (TE) and inner cell mass (ICM). Various types of known histone modifications are linked specifically to both gene activation and gene repression. Recent studies on the role of noncoding RNAs (ncRNAs) have emphasized the importance of these RNAs in various cellular processes such as in gene expression during development.

Alteration in these epigenetic mechanisms results in the loss of cellular identity, cellular transformation, or development of several diseases. ⁴ Environmental factors can specifically influence epigenetic modifications, leading to defective cellular differentiation as a consequence developing multiple disorder during pregnancy and neonatal period. Various antenatal as well as postnatal factors, such as pollution, maternal nutrition, neonatal diet, and the composition of microbiota, promote epigenetic alterations changing the adaptation of particular individual to the environment and in addition can also enhance the lifelong health risk and making an individual prone to late-onset diseases such as allergies, autoimmunity, obesity, diabetes, and asthma. ² Some of these epigenetic changes are also inherited transgenerationally. ⁸

DNA methylation

DNA methylation is the most studied and essential epigenetic modifications. It is a postreplication modification that is primarily found at C5 position of cytosine (mC) of the CpG dinucleotides. It undergoes dynamic remodeling including reprogramming and de novo methylation during mammalian development. DNA methylation ⁹ maintains stable gene expression through mitotic cell division by stably propagating the methylation pattern through mitosis, ¹⁰ thus contributing to the stability of gene expression states. In combination with nucleosome-modifying proteins, DNA methylation helps to establish repressed state of chromatin. ¹¹

Although 80% of CpGs are methylated in nonembryonic cells, CpG islands, which includes short sequence domains, are generally unmethylated irrespective of the gene expression. ¹² These CpG islands are associated with active promoters and genes. ¹³ Transcriptional expression of such genes is regulated by transcription factor Sp1 and various CpG-binding proteins. ¹⁴ Methylation of such CpG islands during development results in long-term repression of the corresponding genes. ¹⁵

DNMTs and DNA-binding proteins

DNA methylation is regulated during development by DNMT1 (maintenance methyltransferase) and Dnmt3a and Dnmt3b (de novo methyltransferases). Recent studies based on DNMTs have emphasized the importance of DNA methylation during development. Studies have shown activation of transposable elements and derepression of ectopic gene expression in absence of DNA methylation. ¹⁶ Dnmt1 ¹⁷ is an oocyte-specific isoform that plays a role in maintenance of maternal imprints. Dnmt3a and Dnmt3b are involved in global de novo methylation after implantation ¹⁸ and in combination with Dnmt3L, which has no methyltransferases activity; these de novo methyltransferases establish methylation imprints in the female germline. ¹⁹

DNA methylation represses gene expression by forming nonaccessible boundaries and blocking the binding of transcription regulatory proteins. ²⁰ It inhibits binding of CTCF (CCCTC-binding factor) that is a chromatin boundary element–binding protein, which blocks association between an enhancer and its promoter ²¹ and, thus, allows interaction between a promoter and an enhancer across the inert boundary site. Certain proteins known as methyl-CpG-binding proteins have specific affinity for methylated CpG sites. Such proteins such as MeCP2, ²² MBD1–MBD4 (methyl-CpG-binding domain proteins), ²³ and Kaiso ²⁴ act as mediators of transcriptional repression. MeCP2 further interacts with corepressor complex containing HDACs to facilitate gene repression. ²⁵ Defects in the methyl-binding proteins are related to certain disorders. Rett syndrome, a neurological disorder, is caused by a missense mutations, leading to decreased binding of MECP2 to methylated DNA. ²⁶ Null mutation in Mecp2 also results in abnormal brain structure and function. ²⁷ The mutations associated with the DNMTs and methyl-binding proteins have been related with multiple disorders as listed in Table 1.1.

Importance of epigenetic reprogramming during development

In general, DNA methylation patterns are stable across different tissues throughout life; however, during implantation and in germ cells, paternal and maternal genomes undergoes rapid demethylation. ⁹ DNA methylation regulates long-term silencing of the gene expression, during development; however, at the midblastula transition extensive gene expression is associated with promoter demethylation. ¹⁶ During mammalian development, the amount of DNA methylation changes in a systematic pattern. Immediately after fertilization, the male genome is actively stripped of DNA methylation, ³⁸ while demethylation of maternal genome occurs passively and subsequently in further cleavage divisions. ³⁹ Implantation is generally followed by a wave of genome-wide de novo methylation increasing the amount of DNA methylation in gastrulating embryo, which then decreases with differentiation in specific tissues. ¹⁶

Table 1.1

DNMT1 ensures epigenetic inheritance by playing a role in maintaining DNA methylation by recognizing nascent strand of DNA opposite to a previously methylated position. In mammalian genomes, with the exception of CpG islands specifically present at the promoter regions of many housekeeping and developmentally regulated genes, the CpG islands especially the ones at intragenic regions are methylated during development. ⁴⁰ Aberrant methylation at these sites is prevented by enzymes such as TET and thymidine DNA glycosylase. Exclusion of DNMT1 from promoter region CpG islands and transcription start sites (TSS) is ensured by binding of specific transcription factor to ensure the hypomethylated status. This has been confirmed by observed demethylation upon incorporation of SP1-binding site into an endogenously methylated locus. ⁴¹ H3K4 methyltransferases and nucleosome exclusion provides additional protection from DNA methylation. De novo methylation is also prevented by formation of R-loops of single-stranded DNA due to active transcription at these sites. However, certain promoters are stably silenced by repressive transcription, which recruit a variety of proteins working together to silence the promoter. These proteins include de novo DNA methyltransferases, heterochromatin protein 1, and H3K9 methyltransferases. ⁹

DNA methyltransferase 3B (DNMT3B) is involved in silencing of germline gene promoters and is mainly mediated by DNA methyltransferase 3B (DNMT3B), which acts downstream of transcriptional repressors (E2F transcription factor 6). DNMT3A and DNMT3B target certain low CpG promoters for their de novo methylation in association with histone deacetylases and methyltransferases. Cooperation between nucleosome remodeler (lymphoid-specific helicase) and epigenetic silencers forms a heterochromatin assembly at these promoters. ⁴² Furthermore, H3K9 dimethyltransferase G9A is also recruited along with DNMT3A or DNMT3B ⁴³ accelerating repression. ⁴⁴ H3K9 methylation is believed to trigger the formation of heterochromatin followed by stable silencing by DNA methylation. ⁴⁵

DNA methylation plays an important role in repression of transposable elements such as long terminal repeat (LTR), long interspersed nuclear elements (LINEs), and short interspersed nuclear elements (SINEs). ⁴⁶ The promoter regions of these elements are constitutively hypermethylated to block their function. In embryonic stem cells (ESCs), activities of both DNMT1 and DNMT3 are required to maintain stable DNA methylation at these transposable elements. Tripartite motif-containing protein 28 (TRIM28) and H3K9 methyltransferase SETDB1 play an essential role in silencing of LTRs. ⁴⁷ , ⁴⁸ The expression of transposable elements silencing factors is restricted to early embryogenesis and ESCs. In adults, the repression of transposable elements is mediated by methyl-CpG-binding protein 2 (MECP2) and histone deacetylases (HDACs). ⁴⁹ , ⁵⁰

Role of DNA methylation in embryonic stem cells

Although DNA methylation has no role establishment and maintenance of pluripotency, it plays an essential role in regulating commitment of ESCs, which is highlighted by loss of DNA methylation. In absence of DNA methyltransferases, ESCs show no observable aneuploidy, ⁵¹ while in the absence of DNA methylation, these loose the potential to differentiate and are unable to repress pluripotency factors and upregulate germ layer-associated markers. ⁵²

In mouse embryonic stem cells, transcriptional repression of trophectodermal transcription factor gene E74-like factor 5 (Elf5) by hypermethylation maintains extraembryonic potential and trophectodermal lineage commitment of these cells. Only a small portion of cells have extraembryonic potential. DNA methylation regulates extraembryonic commitment. ⁵² Absence of DNMT1 leads to upregulation and demethylation of ELF5 in hematopoietic stem cells (HSCs). ⁵³

DNA methylation determines the lineage specificity toward myeloid vs. lymphoid lineages when they exit from self-renewal to become restricted progenitors. Absence of DNMT1 blocks the self-renewal of HSCs, while the commitment toward myeloid lineage is favored in DNMT1 hypomorphic HSCs. Methylation of Elf5 in ESCs and that of Oct4 and Nanog in trophectodermal stem cells regulate the extraembryonic or embryonic fate of these cells. ⁵⁴ Loss of either maintenance or de novo methyltransferase leads to markedly disparate rates of global methylation. DNMT1 loss leads to loss of methylation, which stabilizes to ∼20%, while loss of DNMT3A or DNMT3A results in the loss of all the methylation with ongoing divisions. ⁵²

Pathological impact of altered DNA methylation

Mammalian development cannot tolerate any substantial amount of epigenetic abnormality as evident from the global deregulation of gene expression in the clones that are able to survive. This gene deregulation and the resulting phenotypes are observed in clones of all species. ⁵⁵ The reprogramming errors impact majorly on the mammalian development. Recent studies have demonstrated the role of epigenetic abnormalities in the development of cancer. Global hypomethylation accompanied with hypermethylation of CpG islands is a general feature of cancerous cells. ⁵⁶ Epigenetic deregulation leads to several alterations such as aberrant expression of oncogenes and tumor suppressor genes and disables DNA repair machinery and chromosomal instability. ⁵⁷ Altered promoter methylation of oncogenes such as c-myc ⁵⁸ and tumor suppressor genes ⁵⁹ leads to the development preeclampsia and choriocarcinoma.

Genomic imprinting

In mammals, a set of genes are expressed specifically from either maternal or paternal copy of the gene in a unique parent-of-origin-specific manner. These are known as imprinted genes. Initial period of the life ranging from conception to the second anniversary is especially important for genomic imprinting. Epigenetic alterations and nutritional factors play a vital role during this time period in determining the developmental progress and future susceptibility to various diseases. ⁶⁰ In genomic imprinting, one of the two homologous chromosomal sets is marked reversibly during development blocking the expression of the particular set. This phenomenon was discovered in mammals in 1980s. ⁷ These genes are generally present in clusters of three or four genes spanning 1MB and encode for both protein-coding and noncoding RNAs. ⁶ Some imprinted genes are not present within these clusters and are called as microimprinted loci. ⁶¹

Epigenetic mechanisms of gene regulation for imprinted genes

Imprinted genes are regulated via two different mechanisms: (1) the insulator model (e.g., H19/Igf2 locus), where allele-specific expression is facilitated by insulator protein CTCF, and (2) ncRNA model (e.g., Igf2r/Airn and Kcnq1/Kcnq1ot1), ⁶² where the expression of ncRNA that has promoter located within the ICR of imprinting locus regulates the allele-specific expression of imprinted genes. ⁶³ There are approximately 150 known imprinted genes in mice and are highly conserved among mammals. ⁶² This conservative nature of imprinted genes helps in mouse and human research. Deregulation or specific mutation of parental allele causes rare congenital disorders. ⁶⁴

Establishing epigenetic marks on imprinted genes

Various epigenetic marks are present differentially between the two alleles regulating imprinted gene expression. These marks are present especially within the regulatory region known as imprinting control region (ICR). ICRs are associated with different epigenetic marks such as DNA methylation, histone modifications, noncoding RNA, and chromatin organizations, resulting in parent-of-origin-specific expression of imprinted genes. ⁶ , ⁶⁵ These imprints are not only faithfully replicated during the cell division but also are perfectly established on the maternal and paternal allele during gamete formation. The acquittance of these imprinting marks in germline cells and their maintenance after fertilization has been well studied. The epigenetic reprogramming occurs in germ cells during gametogenesis ensuring independent establishment of parental-specific imprints that drives proper embryonic development. ¹ Methylation imprints are erased actively to reset imprinting during the development of PGCs ⁶⁶ and reestablished in allele-specific manner during oogenesis and spermatogenesis. ¹⁶ De novo DNA methyltransferase 3a (DNMT3A) establishes DNA methylation with the help of DNMT3L, which has no methyltransferase activity, but acts as an accessory protein in germlines. ¹⁹ In H19/Igf2 locus, paternal-specific methylation is established in male germline in prospermatogonia, ⁶⁷ while methylation at ICR occurs in growing oocytes in maternal-specific manner. ⁶⁸

During PGC reprogramming, various epigenetic remodeling steps occur in addition to DNA demethylation, resulting in the increased expression of DNA-binding factors Stella, TET1, and cell cycle that arrest the G2 phase. Enhanced levels of TET1 are observed at germline gene promoters and ICRs, ⁶⁹ which play a role in the activation of germline-associated genes and global hydroxymethylcytosine (hmC) during PGC progression. ⁷⁰ PGCs also have lower expression of DNMT1 destabilizing factor UHRF1 and DNMT3; thus, global demethylation is eased by cell division in the absence of methyltransferase activity. ⁶⁹ , ⁷¹

Erasure of DNA methylation and an extensive genome reprogramming occur after fertilization; however, the parental-specific imprints are maintained by DNA methyltransferase DNMT1. In addition, during early embryonic development, proteins such as STELLA (maternal factor PGC7) ⁷² and zinc finger protein homolog 57 (ZFP57) ⁷³ play a role in protecting and regulating DNA methylation at ICRs. In somatic cells, such imprints are retained throughout lifetime. However, the biparental imprints are finally erased in PGCs recruited from somatic cells. ⁷ This process is carried out by various active and passive events, such as translocation (Tet) family of methyl cytosine dioxygenases oxidizing 5-methylcytosine to 5-hydroxymethylcytosine ⁷⁰ and action of DNA repair machinery. ⁷⁴ In PGCs, DNMT1 is blocked from reaching to replication fork by repression of Uhrf1, hence preventing methylation of newly replicated DNA. ⁷¹

Imprinting loci show differential rates of de novo methylation, suggesting the role of epigenetic memory in reestablishing methylation marks. Proteins zinc finger protein ZFP57 and TRIM28 play a role in maintaining imprints. In embryos, ZFP57 recruits TRIM28 to imprints, while in ESCs, ZFP57 recruits a complex containing TRIM28, the DNMT3s, and UHRF1 to a methylated CpG-containing motif. ⁹

In addition to DNA methylation, PGCs also show demethylation of histones. H3K9me2 marks are erased by decreased levels of binding partner of G9A, GLP, ⁷⁵ and recruitment of histone chaperones. ⁷⁶ Interestingly, global H3K27 methylation occurs to compensate demethylation at H3K9 and DNA levels. ⁷⁵

Role of genomic imprinting in development

Increased evidence of gene imprinting disorders associated with various assisted reproductive techniques (ART) emphasize the importance of genomic imprinting in early embryonic development. ⁷ Imprinted genes have a vital role in mammalian development regulating fetal and placental growth, pluripotency, differentiation, and behavior. ⁶⁵ These genes regulate embryogenesis, placental implantation, and fetal growth during fetoplacental development including both fetal growth–promoting and fetal growth–restricting pathways. ⁷⁷

Role of genomic imprinting in fetoplacental development

Genomic imprinting is observed only in the placental mammals with various genes showing placenta-specific imprinting. ⁷⁸ Imprinting genes are conserved between species. Placenta is a vital organ for proper fetal development. ⁷⁹ Many imprinted genes exhibit splice variants specific to placenta based on their expression from placenta-specific promoter. ⁷⁸

Imprinting disorders have been associated with several placental abnormalities such as (1) abnormal placental weights, ⁸⁰ (2) defective proliferation, apoptosis, and differentiation of trophoblasts, ⁷⁹ (3) malfunctioning spongiotrophoblast, (4) morphological abnormalities related to disproportionate labyrinth and junctional, (5) the number of glycogen cells, (6) placental vascularity zones, (7) imperfect fetal/placental weight ratio, (8) atypical placental endocrine function, ⁸¹ and (9) altered nutrient uptake. ⁷⁸ , ⁷⁹ , ⁸¹

Altered expression of imprinted gene can also pose a potential threat for proper fetal growth, leading to large-for-gestational-age (LGA) fetus, ⁸² abnormal birth weight, head circumference of newborn, ⁷⁷ neurobehavioral development, ⁸³ and altered invasive potential of trophoblasts. ⁸⁴ Placental growth and functions are more prone to environmental cues such as air pollution, alcohol consumption, and exposure of pregnant women to endocrine disruptors (phthalates, BPA, and phthalates), leading to imprinting defects in placenta and developing fetus. ⁷

Genomic imprinting especially has a critical role in the brain and neuronal development. Studies based on gynogenic and androgenetic mouse chimeras have emphasized the developmental regulation of imprinted genes in the brain. These chimeras have revealed the effect of abnormal genomic imprinting on the brain size. ⁸⁵ Transcriptome sequencing analysis has shown differential expression of imprinted genes in different brain regions, with higher proportion of these genes within hypothalamus and hindbrain. Higher maternally expressed genes are found during early embryonic development, compared with higher expression of paternally expressed genes in adult brain regions. ⁸⁶

Imprinted genes such as Dlk1, Igf2, and Ube3a show diverse transcriptional dosage in brain during neuronal development. ⁸⁷ In brain development, several genes also show brain-specific imprinting bias related to parental allele expression. ⁸⁶

Imprinted genes influence both embryonic neurodevelopmental processes, such as proliferation, differentiation, migration, self-renewal, axonal, and dendritic outgrowth, and functioning of adult brain such as regulating synaptic plasticity, transmission, and action potentials. ⁸⁸  Table 1.2 shows a list of imprinted genes with altered expression related to fetal/neonatal and placental abnormalities and known disorders.

Genomic imprinting and X-chromosome inactivation

Like genomic imprinting, X-chromosome inactivation is recognized by monoallelic gene expression. Several mechanisms are involved in maintaining the inactivation of X-chromosome, which includes DNA methylation, expression of ncRNA Xist, and state of deacetylation of histones. ¹⁰⁰ DNMT1 plays a crucial role in maintaining X-chromosome inactivation. ¹⁰¹ While in somatic cells, X inactivation is random, in extraembryonic lineages, it is regulated by parental origin. The inactive X chromosome is determined by the expression of Xist from X inactivation center (Xic) and its coating of the specific X chromosome. ¹⁰² Furthermore, the expression of Xist is regulated by a noncoding antisense transcript known as Tsix, ¹⁰³ with the mediation of CTCF that binds Tsix ICR, ¹⁰⁴ hence, modulating X inactivation.

Table 1.2

Histone modifications

After Allfrey's pioneering studies in the 1960s, it is known that histones are posttranslationally modified. Histone modification is a covalent posttranslational modification (PTM) to histones. These influence chromatin structure and employ remodeling enzymes for repositioning nucleosomes. ¹⁰⁵ These modifications act in various biological processes—transcriptional activation/inactivation, chromosome packaging, and DNA damage/repair.

Types of histone modifications

Numerous modifications mark histone, which alters the gene expression, which is given in Table 1.3. Acetylation and phosphorylation caused transcriptional activation; SUMOylation, deimination, and proline isomerization usually exist in transcriptionally silent regions; methylation and ubiquitination are known to influence both activation and repression. ¹²⁰ However, whether histones are conjugated to O-GlcNAc in mammals is still unknown. ¹²¹ The noncovalent proline isomerization on H3 holds an impact on H3K36 methylation to boost transcription. ¹²² The deimination of arginine by PADI4 provokes arginine methylation and converts arginine/methylarginine to citrulline. ¹²³ , ¹²⁴ Hypercitrullination encourages chromatin decondensation. ¹²⁵ In general, these newly recognized histone modifications can affect conventional modifications such as methylation etc. via competing for the same site or via cross-talk conferring a conformational transformation, thus altering the downstream signaling and finally gene expression. ¹²⁶

Regulation of gene expression by histone modifications during embryonic and perinatal development

Histone methylation is linked to early differentiation processes, i.e., trophectoderm (TE) and inner cell mass (ICM) formation. ¹²⁷ A few histones directly inherited from the sperm contain increased hyperacetylated H4K8 and K12 and could transmit epigenetic information. ¹²⁸ ESCs involve hydroxylation of methylated cytosines by the Tet family of enzymes. ¹²⁹ Embryonic system exhibits distinctive histone methylation patterns of bivalent (activating and repressive) marks at lineage-specific genes that get converted to monovalent marks while differentiation, to define apt gene expression in tissues. ¹³⁰ Methylation and demethylation of both activating and repressive marks are essential for establishing embryonic and extraembryonic lineages. ¹³⁰ Altered methylation throughout embryogenesis can induce faulty development of organs and body patterning. ¹³⁰ Histone modifications play a role in the segregation between ICM and TE, with a higher H3K27me3 and lower H2A and/or H4 phosphorylation in ICM. These changes, however, cannot be directly correlated to gene expression. ¹³¹ In four-celled mouse embryo, one blastomere showed hypomethylated H3H3R26, diminished H3R26me3, and upregulated Nanog and Sox2, thus promoting ICM fate of these cells. ¹³² The acetylated lysine and methylated arginine decline globally on egg chromatin. ¹³³ H3K27me3 is vital in development and is reversible, and therefore acts as an on–off switch according to developmental signals. ¹³⁴ H3K9me3 is a feature of heterochromatin, whereas H3K9me2 is restricted to null or less expressive genes of euchromatin. ¹³⁵–¹³⁷ H3K4 methylation commonly occurs at transcription start sites in hESCs (human), zebrafish, and mouse embryos. H3K4me3-marked genes were 80% expressed in hESCs, marginally expressed in early embryos of zebrafish, whereas H3K4 methylation sites were common between the TE and ICM in mouse embryos. ¹³⁸ , ¹³⁹ H3K27me was found in certain discrete genes in mouse embryos. ¹²⁷ In ESCs, H3K27me3 domains were less broadened when compared with differentiated cells. ¹⁴⁰ , ¹⁴¹ During biological development, H3K9me3 was dynamically altered; lineage-specific genes activate by losing it, while pluripotency genes gain this mark. ¹⁴² In early embryogenesis, in zebrafish and mouse, H3K4me3 and H3K27me3 bivalently marked genes were absent. ¹⁴³ , ¹⁴⁴ Bivalently marked genes were initially considered peculiar to early embryo; they play special roles in later developmental stages; however, some studies explained mechanisms separate from bivalency for gene suppression. ¹⁴⁵ , ¹⁴⁶ Mouse embryos showed H3K27 marks in gametes, which disappeared postfertilization and reestablished after implantation. ¹⁴⁶ On the contrary, maternal genome of preimplantation embryos has broad, noncanonical tracts of H3K4me3; these were associated with gene suppression in mouse embryos. ¹⁴⁶ H3K4me3 and H3K27me3 are elevated in the ova compared with sperm chromatin, which during development progressively attains these marks. ¹⁴⁷ Also, immunostaining for histone marks has depicted an unequal distribution of histone modifications among the parental genomes. ¹³¹ , ¹⁴⁸ , ¹⁴⁹ H4 hyperacetylated lysine and H3 andand H4 methylated arginine at 17th andand third positions, respectively, are reduced in metaphase II eggs, fertilized eggs, and early embryonic metaphase stage blastomeres, which is pivotal for transition from egg to embryo during genomic reprogramming. ¹³³ Carrozza et al. found that Rpd3 removes histone acetylation marks associated with gene elongation. ¹⁵⁰ Out of all histone modifications, methylation is the most studied and has been detailed in Table 1.4.

Table 1.3