Epigenetics, nuclear organization and gene function: with implications of epigenetic regulation and genetic architecture for human development and health
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Oxford
Oxford University Press
[2019]
|
| Ausgabe: | 1. edition |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XVIII, 286 Seiten Illustrationen, Diagramme |
| ISBN: | 9780198831211 9780198831204 |
Internformat
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| 245 | 1 | 0 | |a Epigenetics, nuclear organization and gene function |b with implications of epigenetic regulation and genetic architecture for human development and health |c John C. Lucchesi |
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| 300 | |a XVIII, 286 Seiten |b Illustrationen, Diagramme | ||
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Datensatz im Suchindex
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| adam_text | Contents
Part I An Introduction to Epigenetics and
Epigenetic Regulation 1
1 Epigenetic phenomena in fungi, plants and animals 3
Selective gene activity is the basis of cellular and tissue differentiation
and of organismal development 3
The concept of one genome but multiple epigenomes 4
Epigenetic memory 5
Epigenetics and the human condition 5
Chapter summary 5
References 6
2 The basic structure of chromatin 7
Organization of DNA and histones in the nucleosome 7
Assembly of the chromatin fiber 9
Transitions of the chromatin fiber into different states of condensation 11
The different faces of chromatin 12
Euchromatin vs heterochromatin 12
The molecular biology of heterochromatin 14
Euchromatin and heterochromatin have specific locations in the nucleus 14
Heterochromatic regions lag behind during genome replication 15
Chapter summary 15
References 15
Box 2 1: Repetitive sequences and transposable elements 13
3 The basic mechanism of gene transcription 17
The pre-initiation complex 17
Transcription initiation 18
Promoter clearance and early elongation 21
Pausing 21
Productive elongation 22
Co-transcriptional RNA processing events 24
Capping 24
Transcript splicing 25
Transcription termination and processing of the transcript s 3 end 25
Polymerase recycling and reinitiation of transcription 29
Chapter summary 29
xii CONTENTS
References
Box 3 1: Mediator
Box 3 2: Serine 2 (S2) phosphorylation
Box 3 3: Two examples of regulatory alternative splicing
Sex determination in Drosophila
A role for alternatively spliced transcripts in oncogenesis
Part II Transcription is Regulated by Epigenetic Mechanisms
4 Chromatin modification and remodeling
Gene transcription in the context of chromatin
Post-translational modifications (PTMs) of histones
Acetylation
Methylation
Phosphorylation
Ubiquitination
Sumoylation
Glycosylation
ADP ribosylation
Hydroxyisobutyrylation
Remodeling complexes
Histone variants and nucleosome turnover
Histone H3 variants
Histone H2A variants
Histone H2B variants
Histone HI variants
DNA modifications
Chapter summary
References
Box 4 1: Examples of human diseases associated with histone
and DNA modifications
Alzheimer s disease (AD)
Parkinson s disease (PD)
Huntington s disease (HD)
Rubinstein-Taybi syndrome (RSTS)
5 Epigenetic chromatin changes and the transcription cycle
Role of remodeling complexes
Phosphorylation of RNA polymerase
Role of histone covalent modifications
Histone acetylation
Histone methylation
Transcription without covalent modification
Role of histone variants
Interactions among transcription regulators
Epigenetic changes at enhancers
Bivalent promoters
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CONTENTS xiii
Many genes are subjected to monoallelic expression 63
Heterogeneous gene expression among the cells of a particular tissue 63
Repression of transcription 64
Transcriptional configuration of the genome 64
Chapter summary 64
References 65
6 The role of non-coding RNAs 69
Long non-coding RNAs 69
LncRNAs and lincRNAs repress or enhance the transcription of target genes 69
Some IncRNAs transcribed from enhancers promote the association of these
regulatory modules with their target genes 71
LincRNAs can affect gene activity by interacting directly with transcription
co-factors 71
LincRNAs contribute to the topological organization of chromatin 71
Short non-coding RNAs 72
Micro RNAs (miRNAs) 72
Endogenous small interfering RNAs (siRNAs) 73
Piwi-interacting RNAs (piRNAs) 73
Small nuclear RNAs (snRNAs) 74
tRNA-derived non-coding RNAs 74
Antisense non-coding RNAs are a common byproduct of transcription 74
RNA editing 74
Chapter summary 75
References T7
Box 6 1: Transposable elements 75
7 Maintenance of the active and inactive states 80
PcG gene products guard against improper HOX gene expression 81
PcG activity is mediated through the action of repressive protein complexes 81
The mechanistic basis of PcG repression 83
PRC2 83
PRC1 83
PcG proteins alter the three-dimensional structure of the genome 84
Repression can occur without the intervention of PRC complexes 84
Normal levels of homeotic gene expression are maintained by the TrxG genes 84
TrxG complexes function by preventing PcG silencing 84
TrxG proteins participate in the general transcription process 85
The role of cohesin 85
Transvection 87
Paramutations: a special case of transvection in plants 88
Chapter summary 88
References 88
8 DNA methylation and gene expression 93
Established silencing by DNA methylation 94
The role of DNA methylation in single-copy gene regulation 94
Klv i ON I l N I li
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iennmlc Iniprlriffrig
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Reference#
Box 8 1: Kelt syndrome (Ktt;
Itox 8 2: Imprinting diseases
lieckwith-Wiedemann syndrome fBV/3;
Prader-Willi (i’WSf and Angelman AS s- rdre—es
9 Regulation of domains and whole chromosomes
Transcriptional regulation of gene dusters
The ß-globin genes
rRNA genes and the nudeolus
Histone genes
Transcriptional regulation of whole chromosomes
Dosage compensation in DrosopkEa m amp;SKC amp;sier
Dosage compensation in Caenorkibdiiis eU-^nj
Dosage compensation in mammals
Dosage compensation in birds
Gene duplication is a corollary* to dosage compersaäon
Chapter summary
References
Box 9 1: Human aneuploidy
Different events can cause variation in the chromosomal
constitution (karyotype)
Autosomal aneuploidy
Sex chromosome aneuploidy*
Part III The Interplay Between Transcription and Nudear Structures
10 Architectural organization of the genome
Evidence for the existence of chromosome territories
The arrangement of CTs within a nucleus
Chromatin domains
Promoters physically associate with distant enhancers
Insulators circumscribe the activity of enhancers
Insulators subdivide the genome into functional units
Topologically associating domains (TADs)
1 ,oop extrusion ns a basis of TAD formation
TADs enn be visualized in Pnsopln/ i polytene chromosomes
TAD formation during early development
Insulator bodies and I’cG bodies
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CONTENTS xv
Transcription and DNA replication can be regulated by relocating genes to
different nuclear sub-compartments 134
Chapter summary 135
References 135
Box 10 1: Chromosome conformation capture techniques 127
Box 10 2: Multiplexed reporter assay 131
11 The nuclear envelope 140
Inner and outer membranes 140
The nuclear envelope through the cell cycle 140
The nuclear lamina 141
The lamina is a mesh of protein fibers consisting mostly of lamins 141
Association of the genome with the nuclear lamina 141
Transcriptional and epigenetic features of genes associated
with the lamina 142
Facultative LADs 142
Nuclear pore complexes 143
Nuclear pore complexes (NPCs) are large multiprotein structures 143
Nuclear pores participate in the regulation of gene expression 144
Chapter summary 144
References 145
12 The nucleolus 147
Ribosome biogenesis 147
The nucleolus as a gene-silencing environment 149
The nucleolus is the site of many diverse molecular processes 150
Telomerase assembly 150
Regulation of p53 stability 150
Modifications and processing of non-ribosomal RNAs 150
Chapter summary 151
References 151
13 Nuclear bodies 153
The perinucleolar compartment 153
The Cajal bodies 153
Gemini of coiled bodies and histone locus bodies 154
Redundancy or collaboration? Storage or active processing? 154
Nuclear speckles 155
Paraspeckles 155
PML nuclear bodies 156
Nuclear stress bodies 157
Transcription factories 157
Dynamic association of polymerases and transcription units 157
Co-localization of genes in transcription factories may lead to their
co-regulation 158
xvi CONTENTS
How do transcription factories originate?
Chapter summary
References
PART IV Inheritance of Chromatin Structure and Functional States
14 Chromatin replication
An overview of the process of DNA replication
Coordination of DNA replication with histone synthesis and nucleosome
assembly
Errors can occur during DNA replication
The DNA damage response
Chromosome replication in the context of nuclear organization
Chapter summary
References
15 DNA repair and genomic stability
Mismatch repair
Nucleotide excision and base excision repair pathways
DNA breaks
Single-strand break repair
Double-strand break repair
Detection of the double-strand break
Non-homologous end-joining repair pathway
The homologous recombination pathway
Epigenetic modifications in double-strand break repair
The conformation of chromatin at the site of a double-strand break
The three-dimensional arrangement of double-strand breaks
Chapter summary
References
16 Inheritance of chromatin modifications through the cell cycle
Transcription factors and co-factors
DNA methylation
Histone modifications
Re-establishment of the chromatin landscape in daughter cells
Nucleosome positioning following DNA replication
Transmission of genomic loop domains from parent to daughter cells
Epigenetic specification of centromeres
Chapter summary
References
17 Stem cells
Characteristics of stem cells
Totipotent cells
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CONTENTS xvii
Pluripotent cells 191
Multipotent adult stem cells 194
The stem cell niche concept 194
Maintenance of pluripotency during stem cell proliferation 195
Epigenetic marks of stem cell self-renewal and differentiation 196
The role of non-coding RNAs 197
X chromosome inactivation in female stem cells 198
Chromatin architecture of stem cells 198
Chapter summary 199
References 199
18 Nuclear reprogramming and induced pluripotency 205
Methods for reprogramming somatic cells 205
Molecular aspects of reprogramming 206
Epigenetic changes during reprogramming 208
Histone modifications 208
DNA methylation 208
Therapeutic applications of iPSCs 208
Chapter summary 209
References 210
19 Transgenerational inheritance of epigenetic traits 213
Adult effects of embryonic exposure to particular environmental factors 213
Epigenetic transgenerational transmission 214
Physiological stress and chronic metabolic diseases 214
Endocrine disruptors 215
Neurodevelopmental, behavioral and psychiatric effects 216
Mechanisms of transgenerational inheritance 217
DNA methylation 217
Histone modifications 217
Epigenetic inheritance must overcome germline reprogramming 218
Small non-coding RNAs 220
Chapter summary 221
References 221
Box 19 1: The parameters of transgenerational epigenetic inheritance 214
Part V Epigenetics, Human Health and Development 225
20 Aging, cellular senescence and cancer: the role of genomic instability,
cellular homeostasis and telomeres 227
Genomic instability 227
Mitochondrial DNA (mtDNA) 229
Changes in cellular homeostasis 229
Telomeres 230
Telomere biogenesis 231
Telomere protection 232
xviii CONTENTS
Control of telomerase levels and telomere length
The role of telomeres in aging and cancer
Chapter summary
References
21 Aging, cellular senescence and cancer: epigenetic alterations
and nuclear remodeling
Changes in DNA methylation
Changes in histone modifications
Changes in histone variants
Chromatin remodeling
Changes in nuclear architecture
Changes in the size and shape of nuclei
Changes in the arrangement of the chromosomes
Changes in the A (active) and B (inactive) compartments
Changes in nucleolar size
Changes in the topological organization of the genome
The role of non-coding RNAs
Cellular (replicative) senescence as a native defense against cancer
Chapter summary
References
22 Developmental systems and their dysfunction
Neuronal regulation of learning and memory formation
Development of the nervous system
Learning and memory
Molecular events underlying memory establishment and consolidation
Epigenetic modifications associated with learning and memory
DNA methylation
Chromatin remodeling
Non-coding RNAs
Genome topology
Cognitive diseases
Development and dysfunction of the cardiovascular system
Epigenetic regulation of cardiac differentiation
Cardiovascular diseases
Epigenetics and immune system disorders
Systemic lupus erythematosus (SLE)
Rheumatoid arthritis (RA)
Chapter summary
References
Box 22 1: Interferons and interleukins
Interferons (IFNs)
Interleukins (ILs)
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Index
|
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| id | DE-604.BV045293498 |
| illustrated | Illustrated |
| indexdate | 2024-07-10T08:14:03Z |
| institution | BVB |
| isbn | 9780198831211 9780198831204 |
| language | English |
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| publishDate | 2019 |
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| publisher | Oxford University Press |
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| spelling | Lucchesi, John C. Verfasser (DE-588)1180052919 aut Epigenetics, nuclear organization and gene function with implications of epigenetic regulation and genetic architecture for human development and health John C. Lucchesi 1. edition Oxford Oxford University Press [2019] XVIII, 286 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Epigenetik (DE-588)7566079-9 gnd rswk-swf Genregulation (DE-588)4122166-7 gnd rswk-swf Zellkern (DE-588)4067544-0 gnd rswk-swf Epigenetik (DE-588)7566079-9 s Genregulation (DE-588)4122166-7 s Zellkern (DE-588)4067544-0 s DE-604 HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030680823&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Lucchesi, John C. Epigenetics, nuclear organization and gene function with implications of epigenetic regulation and genetic architecture for human development and health Epigenetik (DE-588)7566079-9 gnd Genregulation (DE-588)4122166-7 gnd Zellkern (DE-588)4067544-0 gnd |
| subject_GND | (DE-588)7566079-9 (DE-588)4122166-7 (DE-588)4067544-0 |
| title | Epigenetics, nuclear organization and gene function with implications of epigenetic regulation and genetic architecture for human development and health |
| title_auth | Epigenetics, nuclear organization and gene function with implications of epigenetic regulation and genetic architecture for human development and health |
| title_exact_search | Epigenetics, nuclear organization and gene function with implications of epigenetic regulation and genetic architecture for human development and health |
| title_full | Epigenetics, nuclear organization and gene function with implications of epigenetic regulation and genetic architecture for human development and health John C. Lucchesi |
| title_fullStr | Epigenetics, nuclear organization and gene function with implications of epigenetic regulation and genetic architecture for human development and health John C. Lucchesi |
| title_full_unstemmed | Epigenetics, nuclear organization and gene function with implications of epigenetic regulation and genetic architecture for human development and health John C. Lucchesi |
| title_short | Epigenetics, nuclear organization and gene function |
| title_sort | epigenetics nuclear organization and gene function with implications of epigenetic regulation and genetic architecture for human development and health |
| title_sub | with implications of epigenetic regulation and genetic architecture for human development and health |
| topic | Epigenetik (DE-588)7566079-9 gnd Genregulation (DE-588)4122166-7 gnd Zellkern (DE-588)4067544-0 gnd |
| topic_facet | Epigenetik Genregulation Zellkern |
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