Epigenetics and Systems Biology

Leonie Ringrose is Professor of Quantitative Biology at the Integrated Research Institute for Lifesciences and Humboldt University Berlin, Germany. Her laboratory studies quantitative epigenetics

Section I. Introduction

Section II: Where Am I? Genomic Features and DNA Sequence Principles Defining Sites of Epigenetic Regulation: Machine Learning1. Computational Identification of Polycomb/Trithorax Response Elements2. Modeling Chromatin States3. Crossing Borders: Modeling Approaches to Understand Chromatin Domains and Their Boundaries4. Inferring Chromatin Signaling From Genome-Wide ChIP-seq Data

Section III. Everything’s Moving: In Vivo Dynamics of Epigenetic Regulators: Kinetic Models Based on Ordinary Differential Equations5. “In Vivo Biochemistry”: Absolute Quantification and Kinetic Modeling Applied to Polycomb and Trithorax Regulation6. Modeling Distributive Histone Modification by Dot1 Methyltransferases: From Mechanism to Biological Insights

Section IV: Reconciling Randomness and Precision: Bistable Epigenetic Memory and Switching: Stochastic Models7. Modeling Bistable Chromatin States8. Quantitative Environmentally Triggered Switching Between Stable Epigenetic States

Section V: The Third and Fourth Dimensions: Chromosomal Long Range Interactions: Polymer Models9. On the Nature of Chromatin 3D Organization: Lessons From Modeling10. From Chromosome Conformation Capture to Polymer Physics and Back: Investigating the Three-Dimensional Structure of Chromatin Within Topological Associating Domains11. A Combination Approach Based on Live-Cell Imaging and Computational Modeling to Further Our Understanding of Chromatin, Epigenetics, and the Genome12. Capturing Chromosome Structural Properties From Their Spatial and Temporal Fluctuations