Epigenetics and systems biology:
Saved in:
| Other Authors: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
London
Academic Press
[2017]
|
| Series: | Translational epigenetics series
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Item Description: | Includes bibliographical references and index |
| Physical Description: | xii, 273 Seiten Illustrationen, Diagramme |
| ISBN: | 9780128030752 |
Staff View
MARC
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| 245 | 1 | 0 | |a Epigenetics and systems biology |c edited by Leonie Ringrose |
| 264 | 1 | |a London |b Academic Press |c [2017] | |
| 300 | |a xii, 273 Seiten |b Illustrationen, Diagramme | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 490 | 0 | |a Translational epigenetics series | |
| 500 | |a Includes bibliographical references and index | ||
| 650 | 4 | |a Epigenetics | |
| 650 | 4 | |a Systems biology | |
| 650 | 0 | 7 | |a Epigenetik |0 (DE-588)7566079-9 |2 gnd |9 rswk-swf |
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Record in the Search Index
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|---|---|
| adam_text | Contents
List of Contributors xi
Section Introduction
Section m Where Am I? Genomic Features and DNA
Sequence Principles Defining Sites of Epigenetic
Regulation: Machine Learning
CHAPTER 1 Computational Identification of Polycomb/Trithorax
Response Elements 7
Marc Rehmsmeier
Introduction to Polycomb/Trithorax Response Elements 7
2003 Ad Hoc Approach to PRE Prediction, Together With Its
Particular Motivations 8
Evaluating Classification Performance 11
Results of 2003 PRE Prediction 13
New Motifs Discovered 14
Recasting PRE Prediction as a Machine Learning Problem 14
Misclassification Costs and the Trade-Off Dimension 16
Evolutionary Analysis and Search-Space Reduction 17
Today: Genome-Wide Profiling Data 18
How Good Is Our Method When Evaluated Under These Data? 19
Sensitivity and Specificity of Genome-Wide Profiling 19
Conclusion 21
References 21
Glossary 23
List of Acronyms and Abbreviations 24
CHAPTER 2 Modeling Chromatin States 25
Marc Corrales and Guillaume J Filion
The Purpose of Modeling Chromatin States
The Common Approach
25
26
v
What Have We Learned From Those Models? 30
Static Versus Dynamical Models 35
Chromatin States Are Attractors 36
References 40
Glossary 42
List of Acronyms and Abbreviations 43
CHAPTER 3 Crossing Borders: Modeling Approaches to Understand
Chromatin Domains and Their Boundaries 45
Benjamin L Moore and Colin A Semple
Introduction 45
The Expanding Universe of Structural Domains 47
Experimental Techniques 50
Modeling Higher Order Chromatin Structure 54
Formalizing Compartment Calling and Boundary Prediction 57
Outlook 63
References 65
List of Acronyms and Abbreviations 67
CHAPTER 4 Inferring Chromatin Signaling From Genome-Wide
ChIP-seq Data 69
Juliane Perner and Ho-Ryun Chung
Introduction 69
Experimental Techniques 71
Modeling 74
Perturbing the System 81
Outlook 81
References 83
Glossary 85
List of Acronyms and Abbreviations 85
Sec nun Hi Everything s Moving: In Vivo Dynamics of
Epigenetic Regulators: Kinetic Models
Based on Ordinary Differential Equations
CHAPTER 5 In Vivo Biochemistry”: Absolute Quantification and Kinetic
Modeling Applied to Polycomb and Trithorax Regulation 89
Leonie Ringrose
Introduction 89
The Journey Begins: DNA Recombinases Yield Their
Secrets to Mathematics 89
The Journey Continues: Epigenetics Meets Mathematics 90
CHAPTER 6
Contents
Absolute Quantification In Vivo: A Technical Challenge 91
Fluorescent Tagging: A Powerful Tool for Live Imaging 93
Absolute Quantification of Molecule Numbers: Double Check! 95
Everything’s Moving: Methods for Measuring Kinetic
Parameters In Vivo 97
In Vivo Biochemistry of an Epigenetic System: What Did
We Learn? 97
Mathematical Modeling of the System: Defining What
We Don t Know 102
Basic Principles of Kinetic Modeling 102
Kinetic Modeling of Polycomb and ASH 1 Makes
Mechanistic Predictions 103
Back to the Bench: Testing the Model by Perturbing the System 107
Outlook 109
Acknowledgments 111
References 111
Glossary 114
List of Acronyms and Abbreviations 114
Modeling Distributive Histone Modification by
Dotl Methyltransferases: From Mechanism to
Biological Insights 117
Dirk De Vos, Hanneke Vlaming, Barbara M Bakker
and Fred van Leeuwen
Introduction 117
Modeling Histone Modification by Dotl 119
Dotl Action: Distributive Versus Processive 119
A Distributive Mechanism of Methylation Provides an
Explanation for Transhistone Cross-Talk Phenotypes 125
Histone Dilution as a Mechanism to Counteract the
Distributive Build-Up of H3K79 Methylation 126
A Single-Cell Model of H3K79 Methylation to Describe
the Dynamics During the Cell Cycle 126
Extending the Single-Cell Model With Demethylation 128
Modeling H3K76 Methylation by Dotl in African
Trypanosomes 128
A Two-Enzyme Single-Cell Model to Describe the Cell Cycle
Control of H3K76 Methylation in Trypanosomes 129
Future Developments and Applications of the Models 130
Acknowledgments 131
References 131
Glossary 135
List of Acronyms and Abbreviations 135
Appendix: Parameter Estimation and Formal Mathematical
Description of the Models 135
Section l¥ Reconciling Randomness and Precision: Bistable
Epigenetic Memory and Switching: Stochastic
Models
CHAPTER 7 Modeling Bistable Chromatin States 145
Ian B Dodd and Kim Sneppen
Cell Memory by Chromatin-Based Epigenetics 145
Modeling Approach and Philosophy 147
Benefits of Mathematical Modeling 747
Our Modeling Approach—Simplified Stochastic Simulations 747
Nucleosome-Mediated Epigenetics 147
Fundamental Lessons From Modeling Nucleosome-
Mediated Bistability in Fission Yeast 749
Different Reaction Schemes 753
Temporal Regulation—Tilting the System 754
Spatial Regulation—Containing Positive Feedback 756
DNA Methylation-Mediated Epigenetics 158
CpG Methylation 758
Modeling Bistability Through CpG Collaboration 160
Outlook 165
References 165
Glossary 168
List of Acronyms and Abbreviations 168
CHAPTER 8 Quantitative Environmentally Triggered Switching
Between Stable Epigenetic States 169
Rea Antoniou-Kourounioti and Martin Howard
Introduction 169
Memory of the Cold Is Digital and Is Stored Locally in the
Chromatin 173
Memory 7 73
Switching 7 77
Cold Registration Is Digital 178
Model Validation 181
Outlook 183
References 185
Glossary 186
List of Acronyms and Abbreviations 187
Section V The Third and Fourth Dimensions: Chromosomal
Long Range Interactions: Polymer Models
CHAPTER 9 On the Nature of Chromatin 3D Organization: Lessons
From Modeling 191
Mario Nicodemi and Ana Pombo
Introduction 191
Polymer Models of Chromatin 191
Polymer Models of TADs 193
Polymer Models of Mitotic Chromosomes 196
Models to Reconstruct 3D-Conformation From Contact Data 197
Conclusions 198
References 199
Glossary 201
CHAPTER 10 From Chromosome Conformation Capture to Polymer
Physics and Back: Investigating the Three-Dimensional
Structure of Chromatin Within Topological Associating
Domains 203
Guido Tiana, Edith Heard and Luca Giorgetti
Introduction 203
From 5C/Hi-C Maps to Three-Dimensional Structures 207
Description of the Data-Driven Polymer Model 210
What Can Be Learned From Data-Driven, Polymer-Based
Reconstructions of Chromosome Structure? 213
What Are the Molecular Mechanisms Behind Interaction
Energies? 217
Conclusions and Perspectives 220
References 220
Glossary 224
List of Acronyms and Abbreviations 224
CHAPTER 11 A Combination Approach Based on Live-Cell Imaging
and Computational Modeling to Further Our Understanding
of Chromatin, Epigenetics, and the Genome 225
Kayo Hibino, Kazunari Kaizu, Koichi Takahashi and
Kazuhiro Maeshima
Introduction: Genomic DNA, Nucleosomes, and Chromatin 225
Experimental Techniques: Single-Nucleosome Imaging in
Living Cells Using Super-Resolution Microscopy 227
Modeling: Monte Carlo Simulation of Chromatin Dynamics 229
Another Result From the Model: Physical Size of
Transcription Complexes 232
Contents
Perspective 235
References 236
Glossary 238
List of Acronyms and Abbreviations 238
CHAPTER 12 Capturing Chromosome Structural Properties From
Their Spatial and Temporal Fluctuations 239
Aurelien Bancaud, Olivier Gadal and Kerstin Bystricky
Introduction 239
Chromosome Labeling Technologies 241
Spatial Dynamics: Real-Time Imaging and Tracking of Single
Chromosome Loci 244
Imaging Experiments 244
A Few Facts on the Signal-to-Noise Ratio in Single
Particle Experiments 244
Tracking and Trajectory Reconstruction 246
Data Analysis 247
Mapping Chromosome Conformational Dynamics by
Single/Multi Loci Positioning 250
Single Locus Localization in the Nucleus in a
Large Population of Cells 250
Multilocus Localization for Chromosome Conformation
Analysis 253
Real-Time Tracking of Multiple Loci 254
Outlook—Future Developments 255
Technological Pipeline 255
Chromosome Structure and Dynamics and Their Link
to Genome Transactions 256
References 256
Glossary 263
Index
|
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| series2 | Translational epigenetics series |
| spelling | Epigenetics and systems biology edited by Leonie Ringrose London Academic Press [2017] xii, 273 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Translational epigenetics series Includes bibliographical references and index Epigenetics Systems biology Epigenetik (DE-588)7566079-9 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Epigenetik (DE-588)7566079-9 s DE-604 Ringrose, Leonie (DE-588)1136276629 edt HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029753512&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Epigenetics and systems biology Epigenetics Systems biology Epigenetik (DE-588)7566079-9 gnd |
| subject_GND | (DE-588)7566079-9 (DE-588)4143413-4 |
| title | Epigenetics and systems biology |
| title_auth | Epigenetics and systems biology |
| title_exact_search | Epigenetics and systems biology |
| title_full | Epigenetics and systems biology edited by Leonie Ringrose |
| title_fullStr | Epigenetics and systems biology edited by Leonie Ringrose |
| title_full_unstemmed | Epigenetics and systems biology edited by Leonie Ringrose |
| title_short | Epigenetics and systems biology |
| title_sort | epigenetics and systems biology |
| topic | Epigenetics Systems biology Epigenetik (DE-588)7566079-9 gnd |
| topic_facet | Epigenetics Systems biology Epigenetik Aufsatzsammlung |
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