Perinatal and Developmental Epigenetics

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Perinatal and Developmental Epigenetics
Translational Epigenetics Series
Translational Epigenetics Perinatal and Developmental Epigenetics
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Contents
Contributors
1 -
The ever-growingcomplexity ofepigenetic regulationof gene expression
1 - Epigenetic regulation of gene expression: an overview of classical and recently discovered novel players
Introduction
DNA methylation
DNMTs and DNA-binding proteins
Importance of epigenetic reprogramming during development
Role of DNA methylation in embryonic stem cells
Pathological impact of altered DNA methylation
Genomic imprinting
Epigenetic mechanisms of gene regulation for imprinted genes
Establishing epigenetic marks on imprinted genes
Role of genomic imprinting in development
Role of genomic imprinting in fetoplacental development
Genomic imprinting and X-chromosome inactivation
Histone modifications
Types of histone modifications
Regulation of gene expression by histone modifications during embryonic and perinatal development
Nucleosome remodeling
Chromatin structure of embryonic stem cells
Ontogeny of chromatin remodeling
Higher-order chromatin organization (topologically associating domains)
Pathological impact of deregulation in histone modifications
Noncoding RNAs
Regulation of gene expression by noncoding RNAs during embryonic and perinatal development
Small noncoding RNAs (miRNAs and siRNAs)
Piwi-interacting RNAs
Long noncoding RNAs
Interaction of lncRNAs with chromatin-modifying complexes
Pathological impact of deregulation in lncRNAs
Effect of different conditions on Epigenetic mechanisms and programming of human health and disease risk
Impact of prenatal stress on epigenetic modifications
Long-term impacts of epigenetic deregulation during childhood
Effect of acute intrapartum events on epigenetic mechanisms
References
2 - Histone modifications in germline development and maintenance
Cécile Bedet, Francesca Palladino, Valérie J. Robert
Dynamic reorganization of histone PTMs supports germ cell development, identity, and functions in mammals
Description of histone PTMs and their dynamics
From PGC specification to birth
During gametogenesis
Histone PTMs cooperate to regulate germline functions and shape the epigenetic landscape
Histone PTMs in meiotic recombination
Histone PTMs and meiotic sex chromosome inactivation
Histone PTMs and transcriptional control during gametogenesis
Histone PTMs distribution and function in Caenorhabditis elegans hermaphrodite germ cells
Distribution of histone PTMs in the Caenorhabditis elegans germline
Repressive chromatin structure in the P blastomeres and PGC
Chromatin landscape in the adult hermaphrodite germline
Role of histone PTMs in transcriptional regulation in the Caenorhabditis elegans germline
X chromosome silencing
Histone PTMs and transcriptional memory
Histone PTMs and maintenance of germline identity
Histone PTMs and transgenerational epigenetic inheritance of environmental conditions
H3K9 methylation and genome stability
Concluding remarks
References
3 - Epigenetic regulation of cis-regulatory elements and transcription factors during development
Epigenetic mechanisms govern developmental processes via Genome regulation
cis-regulatory elements and trans-acting factors orchestrate Cell type–specific gene transcription
Trans-acting factors
Transcription factors
Noncoding RNAs
Making the connections: readers and writers program the epigenome during early development
Three-dimensional genome organization
Identification and characterization of cis-regulatory elements and trans-acting factors
Conserved sequences and chromatin features aid in the identification of regulatory elements
Sequence conservation and characteristic motifs
Chromatin features
Emergent approaches for the identification of regulatory elements
Computational methods for harnessing epigenomic data sets to predict regulatory elements
Epigenetic programming in perinatal and early development
Switching chromatin states—dynamic epigenomic landscape at developmental cis-regulatory elements
Trans-regulatory networks govern stem cell pluripotency and differentiation
Regulatory elements in early development inform adult health and disease states
Conclusion
References
4 - Genomic imprinting and developmental physiology: intrauterine growth and postnatal period
Genomic imprinting: discovery and early work
Imprinted gene functions converge on neuronal and metabolic processes that govern early development: The cost of altered im ...
Genomic imprinting-mediated control of fetal growth and placental resources
Genomic imprinting and human imprinting disorders
Imprinted genes regulate multiple maternal–fetal interactions and are essential for early survival
Postnatal control of growth and development is mediated by imprinted genes via key metabolic systems and is crucial for pre ...
Final comments
References
5 - Role of RNA epigenetics in development
Introduction
RNA modifications
RNA N6-methyladenosine modification (m6A)
RNA 5-methylcytosine (m5C) modification
RNA A-to-I editing
Role of RNA modifications in development
Conclusion and future perspective
References
2 -
Epigenetic programming of placenta regulatesshort-term and long-term health outcomes
6 - Epigenetic regulation of placental function
Introduction
Epigenetic regulation during placentation
Epigenetics and human placenta development
Epigenetics and mouse placental development
Transcriptional factors and trophoblast lineage differentiation
Epigenetics and regulation of trophoblast functions
Epigenetic mechanisms regulating placental development and function
DNA methylation
DNA methylation in trophoblast
DNA methylation and regulation of placental nutrient transfer
Genomic imprinting
Genomic imprinting and regulation of placental endocrine function
Histone modifications and placental functions
Noncoding RNA
miRs
C19MC in placental functions
C14MC in placental function
C2MC in placental functions
Long noncoding RNAs
Epigenetics and placenta-related pathologies
Epigenetics and preeclampsia
Epigenetics and gestational diabetes
Epigenetics and intrauterine growth restriction
Conclusion
References
7 - Role of placenta in developmental programming of sex-specific adult outcomes
Mechanisms of developmental programming
Sex-specific effects and disease programming in utero
References
Further reading
3 -
Epigenetics,hormones, sex,and developmental programming
8 - Role of epigenetics in shaping sex differences in brain development and behavior
Introduction
Introduction to epigenetics
Gonadal steroid hormones drive sexual differentiation and are epigenetic modifiers
An extreme sex difference in epigenetic regulation: X chromosome inactivation
Sex differences in the human epigenome: normal development
DNA methylation
Histones and microRNAs
Genomic imprinting
Implications for neurological disorders and diseases
Sex differences in the brain epigenome: rodent studies
DNA methylation
Histone modifications
Sex differences in the epigenetic writers, erasers, and readers
DNA methylation
Histone modifications
MicroRNAs
Manipulating epigenetic marks during development: effects on sexual differentiation of neural morphology and behavior
Manipulating epigenetic marks during development: sexual differentiation of neurochemistry
Future directions
References
4 - Epigenetic programming by adverse perinatal influences
9 - Early-life stress exposure and epigenetic programming
Introduction to epigenetics
History of epigenetics
Epigenetic mechanisms
DNA methylation
Histone modifications
Nucleosome positioning
Small noncoding RNAs
Mechanisms of stress
Stress and early-life stress
The hypothalamic–pituitary–adrenal and sympathetic–adrenal–medullary axes
Developmental and physiological overview
Stress and oxytocin
Stress and the serotonergic system
Stress and brain-derived neurotrophic factor
Candidate early-life stress–mediated epigenetic markers
The glucocorticoid receptor (NR3C1)
FK506-binding protein
The mineralocorticoid receptor (NR3C2)
The oxytocin receptor
Solute carrier family 6 member 4 and monoamine oxidase-A
Brain-derived neurotrophic factor
Conclusion
References
10 - Early life substance abuse and epigenetic programming
Substance abuse and substance use disorders
Epigenetics and gene expression regulation
Histone modification
DNA methylation
RNA-associated modifications
Inherited predispositions (i.e., susceptibility of future generations)
Early drug use and epigenetic modifications
Nicotine
Alcohol
Cocaine
Marijuana/THC
Opioids
Molecular strategies targeting epigenetic modifications as novel therapeutics for treatment
Conclusions
References
11 - Paternal and maternal environmental influences on offspring health: inter- and transgenerational epigenetic in ...
Introduction
Germline epigenome and reprogramming
DNA methylation
Histone modifications
Small RNAs
Germline epigenetic inheritance in mammals
Inheritance of paternal environmental exposure effects
Paternal environmental influences on offspring health
Paternal dietary exposure
Paternal exposure to traumatic stress
Paternal toxicant exposure
Mechanisms of inheritance of paternal environmental effects
DNA methylation
Histone modifications
Small RNAs
Inheritance of maternal environmental exposure effects
Maternal environmental influence on offspring health
Maternal toxicant exposure
Maternal dietary effects
Mechanisms of inheritance of maternal environmental effects
DNA methylation
Histone modifications
Small RNAs
Mitochondrial inheritance and the metabolome
Signaling environmental information to germline
Conclusions and future perspective
References
12 - Modeling early-life adversity in the laboratory: animal models, their advantages, and future directions in ext ...
Introduction
The advantage of animal models
Animal models used to study the consequences of early adversity
Consequences of early adversity
Behavioral analyses
Consequences of early adversity
Biological analyses
Recovery interventions
Summary
References
5 -
Pharmacological and nonpharmacological approaches to reprogram the developmental programming to improve the health outcomes
13 - The Emerging field of epigenetic editing: implication for translational purposes for diseases with development ...
Summary of the epigenetic editing field
Epigenetic writers, erasers, and their small molecule inhibitors
Targeted epigenetic editing
Targeted DNA methylation editing
Targeted gene activation by erasing DNA methylation
Targeted gene repression by inducing DNA methylation
Targeted histone modification editing
Targeted gene activation by editing histone modification
Targeted gene silencing by editing histone modification
Target noncoding RNA
Developmental disease that have the potential to be treated with epigenetic editing
Imprinting disorders
Angelman syndrome
Etiology
Previous efforts to develop treatment
Epigenetic editing to treat Angelman syndrome
Prader–Willi syndrome
Etiology
Previous efforts to develop treatment
Potential therapy by specific epigenetic editing
X-linked intellectual disability
Rett syndrome
Etiology
Previous efforts to develop treatment
Developing specific epigenetic editing therapy
Fragile X syndrome
Etiology
Previous approach to develop treatment
Targeted epigenetic editing to treat FXS
Insights for the Application of epigenetic editing in the treatment of these developmental diseases
Off-target effects
Efficacy of influencing transcription
Phenotypical potency of the epigenetic editing
Persistency of the epigenetic change
Future direction: manipulation of 3D chromatin topology to treat developmental diseases
References
Index
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