**Meet the editors**

Born in Brussels, Colin Logie studied Genetics and Molecular Biology at Glasgow University, graduating in 1991. For his PhD, he built the first ligand-regulated site-specific DNA recombinases with A. Francis Stewart at the EMBL, Heidelberg, Germany, in 1995. He went on to engineer nucleosome remodelling assays during his postdoc with Craig L. Peterson at the UMASS, Worcester, MA,

USA. Since 1999 he has conducted academic research on chromatin remodelling complexes at the Radboud University Science Faculty Molecular Biology Department (RIMLS), Nijmegen, The Netherlands, which is a joint venture with the Medical Faculty of the Radboud University. For the past seven years he has focused on human blood monocytes, and the cell types they can differentiate into such as macrophages, dendritic cells, and osteoclasts as an experimental research system. He is interested in the systems-wide integration of nuclear receptor action in health and disease. Through the COST-funded Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC) he became a member of the Gene Ontology Consortium. There he participates in setting the stage for computer-readable gene annotation for the 21st century, with a focus on 'breaking through the DNA wall' so as to enable automated reasoning through cellular signal transduction all the way to the trans-acting sequence-specific DNA binding transcription factors and their co-factors that act in concert on cis-acting chromosomal DNA sequences to permit cell type- and environmentally-conditioned gene transcription regulation. This includes the concepts of epigenetic memory embodied by post-replicational DNA modifications such as DNA methylation, nucleosome-borne epigenetic information in the form of histone post-translational modifications, nucleosome remodelling, and the positioning of nucleosomes along the length of chromosomes. Also chromatin domain boundaries have been a focus of his recent research. Over the years, his research has been funded by EMBL, Human Frontiers Science Program (HFSP), the Dutch Research Organisation NWO, the European Science Foundation (ESF), and indirectly by the European Research Council (ERC) with Hendrik G. Stunnenberg and Stefano Ceri.

Born in the Rhein-Neckar region Mannheim/Heidelberg, Germany, Dr. Knoch studied Physics, Mathematics, and Biology at the University of Heidelberg. In 1998, he graduated in (bio-)physics with "Three-Dimensional Organization of Chromosomes domains in Simulation and Experiment", followed by his dissertation "Approaching the Three-Dimensional Organization of the Human Genome"

both at the German Cancer Research Center (DKFZ), Heidelberg, in 2002. In 2002/2004 Dr. Knoch founded his group Biophysical Genomics located at the Kirchhoff Institute for Physics, University of Heidelberg, and until today at the Cell Biology Department, Erasmus Medical Center, Rotterdam, The Netherlands. His work is focusing on the determination and understanding of genome organization from the DNA sequence level to the entire nuclear morphology. Therefore, approaches from theoretical physics have been combined with molecular biology in highly interdisciplinary projects ranging from advanced DNA sequence analyses, parallel high-performance computer modelling of genomic architectures, and new image analysis methods, to advanced fluorescence in situ hybridization and high-resolution chromatin conformation interaction genome mapping. Major achievements have been: an artefact-free in vivo labelling method of nuclear chromatin, the first system-biological genome browser (GLOBE 3D Genome Browser), the setup of one of the largest desktop computing grids, and last but not least the final determination of the general structural organization of higher mammalian genomes leading to a consistent systems genomics view of genomes from genotype to phenotype. All this has resulted in patents, publications, the foundation/coordination of international interdisciplinary cooperative networks, and consortia. He also (co-)founded many initiatives improving institutional/university study and management performance including the science outreach to the public and industry. Besides, he also conducts environmental and human ecology research, has achieved law-changing contributions in the human-rights sector, is an increasingly recognized artist in the fine arts, and last but not least has founded and is running two companies in the renewable energy production and development sector. His achievements have resulted in prestigious scholarships, awards, and prices as early as 1983.

Contents

**Preface VII**

**Gene Regions 1** Metin Budak

Tobias A. Knoch

**Regulation 125**

Chapter 7 **Epigenome Editing 145** Paul Enríquez

**Protein Complexes 21**

Velten Horn and Hugo van Ingen

Chapter 3 **Chromatin Dynamics upon DNA Damage 47** Judith Miné-Hattab and Xavier Darzacq

**and Dynamics of Genomes 67**

Chapter 1 **Logic of Epigenetics and Investigation of Potential**

Chapter 2 **Recognition of Nucleosomes by Chromatin Factors: Lessons**

Chapter 4 **A Consistent Systems Mechanics Model of the 3D Architecture**

Chapter 5 **Apicomplexa and Histone Variants: What's New? 95**

Tatsunosuke Tomita and Yoshiaki Onishi

Chapter 8 **Resetting Cell Fate by Epigenetic Reprogramming 165**

Molly Pui Man Wong and Ray Kit Ng

Chapter 6 **Epigenetic Modulation of Circadian Rhythms: Bmal1 Gene**

**from Data-Driven Docking-Based Structures of Nucleosome-**

Laura Vanagas, Susana Marisol Contreras and Sergio Oscar Angel
