The Regulatory Genome in Adaptation, Evolution, Development, and Disease
- 1st Edition - March 10, 2023
- Imprint: Academic Press
- Author: Moyra Smith
- Language: English
- Paperback ISBN:9 7 8 - 0 - 4 4 3 - 1 5 3 5 2 - 5
- eBook ISBN:9 7 8 - 0 - 4 4 3 - 1 5 3 5 3 - 2
The Regulatory Genome in Adaptation, Evolution, Development, and Disease synthesizes insights from recent genomic and gene expression studies across organisms, from humans to… Read more
Purchase options
Institutional subscription on ScienceDirect
Request a sales quoteThe Regulatory Genome in Adaptation, Evolution, Development, and Disease synthesizes insights from recent genomic and gene expression studies across organisms, from humans to plants, animals, and single cell life, exploring common roles gene regulation plays in adaptive evolution, developmental biology and susceptibility to disease. The book sheds light on gene regulation across evolutionary timelines, illuminating new areas of focus and future research. Chapters consider key elements in gene expression regulation, fundamentals of genomic alterations over time, and in response to environmental and local conditions, epigenetics in adaptive evolution, and adaptive gene regulation in healthy processes and developmental biology, and in disease biology.
Throughout the book, a comparative approach is adopted across organisms to highlight common evolutionary themes and genome diversity revealed by recent sequencing and GWAS studies, as well as how this informs our understanding of human adaptive evolution. The book finishes by detailing how we can use this knowledge to impact disease outcomes and healthy human metabolism, development, and physiology.
- Reviews key elements in the regulation of gene expression and modes of studying gene regulation across evolutionary timelines
- Adopts a cross-species view, synthesizing recent sequencing and GWAS studies across organisms to draw out fresh meaning and highlight pathways for future research
- Considers altered gene expression associated with developmental defects and disease, as well as healthy biology and physiology, and our adaptive response to disease influence
Human geneticists; human genomicists; translational researchers in medical genetics, genomic medicine, epigenetics, neuroscience, toxicology, public health, and environmental science; life science researchers; developmental biologists; and evolutionary biologists. Students and clinicians
- Cover image
- Title page
- Table of Contents
- Copyright
- Dedication
- Preface
- Acknowledgments
- Epigraph
- Part I. Progress in determining key elements in regulation of gene expression
- Chapter 1. Gene regulation in physiological processes
- Eukaryotic core promoters function, diversity
- Enhancers
- Core promoters and interactions
- Assays used in determining key elements in gene regulation
- New insights into transcriptomics through the ENCODE project and categories of RNAs
- Noncoding RNAs
- Elements in gene expression activation and expression of enhancers
- Enhancer analysis and chromatin modifications and looping
- TADs transcription-associated domains
- Single nucleotide polymorphisms impacting regulatory elements and expression
- ENCODE project
- Database of enhancer elements
- Cell-type specific enhancers
- Lineage-determining transcription factors
- Cell-specific regulatory factors
- Negative regulation of expression
- Environments, nutrients, metabolites, mechanisms through which they impact gene expression
- Metabolic regulation and gene expression
- Stimulus for gene transcription
- Pioneer transcription factors
- Enhancers and metabolites and metabolic disorders
- Exercise training epigenetic rewiring and enhancers
- Silencers (repressors) of gene expression
- Alternative pre-mRNA splicing
- Gene products related to alternative pre-mRNA splicing: spliceosome
- Ribosomal genes and proteins
- Ribosomal gene-encoded mRNA stability
- Translation and ribosome profiling
- Transfer RNAs
- Translation elongation
- Chapter 2. Epigenetics, the nonprotein coding genome, and human accelerated sequences
- DNA methylation
- Metabolic signaling and chromatin remodeling
- Enhancers and gene expression
- Enhancer redundancy and phenotypic robustness
- Cell type specific enhancers
- Epigenetics, DNA methylation, and cell identity in development
- Epigenetic reprogramming and germ cell preimplantation zygote and early embryo
- Enhancer activation
- Enhancers as recruiting sites for specific transcription factors
- Human-accelerated sequences
- Significant regulatory differences were found to coincide with transcription factor binding sites
- Enhancer RNA
- Developmental enhancers
- Gene regulation and enhancer redundancy
- Factors that are required for optimal enhancer function
- Evolutionary changes in regulatory regions and protein-coding regions
- Part II. Evolution and adaptation
- Chapter 3. Gene expression and regulation relative to specific tissues and functions
- Erythropoiesis
- Sonic hedgehog
- Regulatory switches
- Silencers of gene expression
- Silencing of specific enhancers in later stages of development globin gene expression
- Integration of multiple signals
- Growth factors
- Cell identity
- Human developmental cell atlas
- Specific studies to define cell types
- Integration of single-cell data
- Spatio-temporal transcription analysis
- Alternative splicing as a regulator
- Brain transcriptome and splicing
- MRNA expression, alternate splicing, and alternate polyadenylation relative to neuronal identity
- Eye development
- Gene expression relevant to specific systems and processes, for example, brain connectome
- Mammalian neocortex evolution and neuronal diversity
- Spatial transcriptomics and single-cell RNA sequencing
- Aspects of functions in particular cellular organelles that are present in almost all tissues
- The lysosome endosome system and autophagy
- Peroxisomes
- Evolution of peroxisomes
- Chapter 4. Evo-Devo and morphological diversity
- HOX genes as toolkit genes
- Enhancers
- Transposable elements and evolution
- Evolution enzyme activity and nonprotein coding region regulatory mutations
- Epidermal barrier development
- Signaling pathways across species
- Gill regions and branchial arches
- Branchial arches and related developmental defects
- Human HOX genes and HOX gene disorders
- Placental evolution
- Chapter 5. Adaptation and evolution
- Archaea and eukaryotic origins
- The ribosomal tree of life
- Extremophiles
- Investigating genomes
- Gene duplication events leading to emergence of new genes, new traits, new sites of gene expression
- Adaptive evolution in the noncoding genome sequence
- Genome assemblies using long-read sequencing
- Updated versions of the human genome sequence
- Genome sequencing of different animal species
- Chromosome rearrangements and evolution
- Chromosome and chromatin domains and revelations from conformation capture
- Evolutionary innovations at the levels of regulatory regions in the genome
- Introgression of specific gene variants from Neanderthals and Denisovans into modern humans
- Melanocortin receptor
- Evolution of bone
- Bone metabolism and adaptation
- Metazoan cell signaling pathways
- Hedgehog signaling system
- Variation in gene expression, molecular, and evolutionary processes
- Metabolism and organelles
- Lysosomes
- Peroxisomes
- Mitochondria
- Steps in the delineation of concepts of genetics and epigenetics and evolution
- Epigenetics and adaptation
- Phenotypic plasticity, adaptation, and evolution
- Environmental stress and adaptation
- Polygenic adaptation
- Quantitative trait loci and evolutionary adaptation
- Innate immune system
- Changes and adaptations in the immune system throughout life
- Major histocompatibility complex Histocomplatibilty associated (HLA) system
- Transitions from unicellularity to multicellularity
- Hormones and evolution
- Hormones, insulin, and insulin-like growth factor in life history
- Epigenetics in evolution phenotypic plasticity and adaptation
- Resistance to environmental extremes
- Human eye regions
- The visual cycle in vertebrates and role of vitamin A
- Opsins
- Hearing evolution
- Vocal communication and conspecific voice perception
- Adaptive evolution: insight from genes leading to hearing loss in humans
- Pathogen–host interactions and adaptations
- Evolution, adaptation through interaction with the environment and other life forms
- Architecture of the intestinal system
- Genomes and adaptations present in ruminants
- Humans as cucinivores
- Humans, diet, and microbiota
- Evolution and symbiosis
- Phenotypic convergence
- Chapter 6. Adaptations metabolic and genomic to environmental changes
- Nutrient sensing
- Phenotypic plasticity
- MTOR metabolism and evolution
- Metabolic state and gene expression
- One-carbon metabolism and epigenetics
- Genomic changes associated with environmental adaptations
- Convergent evolution to high altitude in different species
- Diet and convergent evolution
- Genetics and climate adaptation
- Part III. Adaptation
- Chapter 7. Regulatory elements relevant to brain, connectome, and neurodevelopmental disorders
- Neocortical expansion during the course of evolution
- Mammalian neocortex evolution and neuronal diversity
- Connectivity in the human cortex
- FOXP2 and speech and language
- Cortical folding and defects
- Neurodevelopmental disorders and defects in the nonprotein coding genome
- The connectome
- Single-cell epigenomics cortical development
- Retinoic acid
- Chapter 8. Altered gene expression associated with developmental defects and disease
- Toolkit genes: developmental regulatory genes
- HOX genes and human developmental defects
- Genomic changes involved in cerebral cortex development
- Epilepsy in inborn errors of metabolism
- Vitamin responsive epilepsies
- Developmental epileptic encephalopathies
- Polygenic epilepsy
- Retinitis pigmentosa
- Autosomal recessive retinitis pigmentosa
- X-linked retinitis pigmentosa
- Other forms of deafness
- Autosomal-dominant nonsyndromic hearing loss
- Primary cilia: function and defects
- Calcium signaling in nodal flow
- Genotype–phenotype exome-sequencing study in children with heterotaxia and heart disease
- Chapter 9. Metabolic, epigenetic functions and correlations with phenotype
- Nutrients
- Metals, micronutrients, and metabolic functions
- Insights into metabolic functions through studies of specific genetic diseases
- Lysosomes their functions and defects
- Epigenetics in lysosomal storage diseases
- Epigenetics and transthyretin amyloidosis
- Peroxisomes
- Cofactors in metabolic enzyme reactions, vitamin-related insight through inborn errors
- Glycogen
- Inborn errors of metabolism with implications for dietary intake of specific aminoacids in protein
- Impaired metabolism of branched chain amino acids and organic acidurias
- Defects in fatty acid oxidation
- Carnitine metabolism and inborn errors of metabolism
- Inborn errors of protein metabolism and urea cycle defects
- Vitamins
- Folate
- Vitamin B12 (cobalamin)
- Micronutrients
- Calcium and vitamin D
- Metabolism and epigenetic functions
- NAD homeostasis
- Cholesterol metabolism: insights through analyses of hypercholesterolemia
- Chapter 10. Aging, genomic mitochondrial, and regulatory changes
- Longevity
- Mitochondria
- Iron–sulfur cluster biosynthesis
- Mitochondrial iron–sulfur cluster dysfunction
- Mitochondrial sirtuins, NAD, and aging
- DNA damage in aging
- Telomeres
- Brain aging neurodegeneration mitochondria
- Vascular aging
- Oxidative stress
- Evolution of the vascular system
- Hypertension
- Atherosclerosis
- Calcific aortic valve disease
- Immune system evolution
- Immunosenescence
- DNA methylation, epigenetics, and aging
- Aging and metabolites
- Osteoarthritis
- Neurodegenerative diseases and aging
- Alzheimer disease
- Parkinson's disease
- International studies in Parkinson's disease
- Amyotrophic lateral sclerosis
- Cell senescence
- Part IV. Altered gene expression associated with developmental defects and disease
- Chapter 11. The regulatory genome and defects in monogenic diseases
- Transcriptional enhancers impacted in human disorders
- Nonprotein coding genomic elements leading to altered gene expression
- Defining how genetic variants influence biology
- Congenital heart disease
- Immunodeficiencies
- Homeostasis, iron regulation, and erythropoiesis
- Copper metabolism and monogenic disorders
- Regulatory pathways potentially implicated in monogenic disorders
- Copy number variants in noncoding genomic regions
- Neurodevelopmental disorders
- The regulatory genome in neural crest cell development and differentiation and in neural crest disorders
- Neural crest development and the associated gene regulatory network
- Cardiac neural crest
- Hirschsprung disease
- Cis-regulatory control of mammalian sex determination
- Manifestations of a neurodevelopmental disorder due to gene enhancer network compromise
- Promoter enhancer interactions in inborn errors of metabolism
- Structural chromosome rearrangements and impact on gene enhancer interactions
- Clinical disorders and the search for regulatory defects through transcription analyses
- Transcriptomics in molecular diagnosis of inborn errors of metabolism
- Transcriptional silencers
- Dual functionality of specific genomic elements
- The 3-prime end of gene transcripts alternated cleavage and polyadenylation
- Genetic modifiers in rare Mendelian diseases
- Chapter 12. Epigenetics and human disease
- Epigenetics and cortical development
- Chromatinopathies
- Gene products that bind to modified nucleotides
- Metabolic factors that influence chromatin
- Pericentromeric heterochromatin
- Examples of the impact of specific epigenetic changes in cancer
- Availability of acetyl CoA for histone acetylation
- Chapter 13. Connecting developmental defects and evolutionary findings
- Origins of chromosome aneuploidy
- Documentation of specific birth defects in humans
- Stem cells
- TGF β and extracellular matrix
- Bone and skeletal development and patterning
- TGF β signaling and fibrosis
- Carnitine acylcarnitine carrier SLC25A20
- Transporters of vitamins
- Channelopathies
- Evolution of voltage-gated ion channels
- Ion channels in epilepsy
- Neurotransmitter receptors, neurotransmitter transporters
- Evolution of neurotransmitters and receptor systems
- GABA and GABA receptors involved in epilepsy
- Chapter 14. The regulatory genome and complex common diseases
- RNA splicing defects
- From GWAS association to function
- Disorders due to regulatory variants, single gene variants, and polygenic variants
- Variable penetrance and variable expressivity of disease-causing variants
- Chronic metabolic conditions including familial hypercholesterolemia
- Lipid disorders
- Parkinson's disease Mendelian and non-Mendelian inheritance
- Alzheimer disease
- Autism
- Chromosome 22q11.2 copy number variants in neuropsychiatric disorders including autism
- Attention deficit hyperactivity disorder
- Brain disorders neuronal and glial 3-D chromatin architecture
- Increased susceptibility to infections and immunodeficiency, including gene defects and regulatory genome variants
- Genome-wide polygenic risk scores in common diseases
- Polygenic and monogenic risk for genomic conditions associated with cancer
- A new approach to genetic variant analyses
- Gene environment interactions in complex diseases
- Psychiatric disorders as complex common disorders
- Transcriptomic profiling in psychiatric disease
- Index
- Edition: 1
- Published: March 10, 2023
- No. of pages (Paperback): 418
- No. of pages (eBook): 418
- Imprint: Academic Press
- Language: English
- Paperback ISBN: 9780443153525
- eBook ISBN: 9780443153532
MS
Moyra Smith
Dr. Moyra Smith is a Professor Emerita in the Department of Pediatrics and Human Genetics, College of Health Sciences, at the University of California, Irvine, and in past years has held appointments at the National Institutes of Health and Johns Hopkins University. In 2017, the UCI Emeriti Association awarded Dr. Smith the UCI Outstanding Emerita Award in recognition of her continuing research on genetics and genomics, strong record of publications, active engagement with programs in the Department of Pediatrics, mentoring of graduate students, and involvement with the CART Autism Center at UCI. Dr. Moyra Smith has published more than 100 scientific articles in peer-reviewed journals such as Frontiers in Molecular Biosciences, Molecular Psychiatry, the Journal of Medical Genetics (JMG), and Cytogenetics Cell Genetics.
Affiliations and expertise
Professor Emerita, Department of Pediatrics and Human Genetics, College of Health Sciences, University of California, Irvine, CA, USARead The Regulatory Genome in Adaptation, Evolution, Development, and Disease on ScienceDirect