1. Early Embryonic Cell Fate Decisions in the Mouse Yojiro Yamanaka and Amy Ralston Abstract Introduction Lineage Establishment and the Pre?stem Cell Program: Formation of the Blastocyst Lineage Maintenance and the Stem Cell Program: Beyond the Blastocyst The Second Lineage Decision: Subdividing the ICM Cell Signaling Regulates PE/EPI Specification Establishment and Modulation of Pluripotency in the EPI Lineage Conclusion 2. Nuclear Architecture in Stem Cells Kelly J. Morris, Mita Chotalia and Ana Pombo Abstract Introduction Functional Compartmentalization of the ES Cell Nucleus Stem Cell Features of Other Nucleoplasmic Subcompartments Chromatin Features Characteristic of ES Cell Nuclei Conclusion 3. Epigenetic Regulation of Pluripotency Eleni M. Tomazou and Alexander Meissner Abstract Introduction Epigenetic Modifications The Epigenome of ES Cells Conclusion 4. Autosomal Lyonization of Replication Domains During Early Mammalian Development Ichiro Hiratani and David M. Gilbert Abstract Introduction Replication Timing Program: An Elusive Measure of Genome Organization An Evolutionarily Conserved Epigenetic Fingerprint Replication Timing as a Quantitative Index of 3?Dimensional Genome Organization Replication Timing Reveals An Epigenetic Transition: Autosomal Lyonization at the Epiblast Stage Replication Timing and Cellular Reprogramming: Further Support for Autosomal Lyonization Maintenance and Alteration of Replication Timing Program and Its Potential Roles Conclusion 5. PRESERVATION OF GENOMIC INTEGRITY IN MOUSE EMBRYONIC STEM CELLS Peter J. Stambrook and Elisia D. Tichy Abstract Introduction and Historical Perspective Mutation Frequencies in Somatic Cells Protection of the Mouse ES Cell Genome Conclusion 6. Transcriptional Regulation in Embryonic Stem Cells Jian?Chien Dominic Heng and Huck?Hui Ng Abstract Introduction Embryonic Stem Cells as a Model to Study Transcriptional Regulation Transcription Factors Governing ESC Pluripotency TranscriptionalRegulatory Network Technologies for Dissecting the Transcriptional Regulatory Network The Core Transcriptional Regulatory Network: Oct4, Sox2 and Nanog Expanded Transcriptional Regulatory Network Enhanceosomes: Transcription Factor Complex Integration of Signaling Pathways to Transcriptional Network Interface Between Transcriptional and Epigenetic Regulation Conclusion 7. ALTERNATIVE SPLICING IN STEM CELL SELF?RENEWAL AND DIFERENTIATION David A. Nelles and Gene W. Yeo Abstract Introduction Introduction to Alternative Splicing Alternative Splicing of Genes Implicated in Stemness and Differentiation Genome?Wide Methods to Identify and Detect Alternative Splicing Events Regulation of Alternative Splicing by RNA Binding Proteins Conclusion and Perspectives 8. MicroRNA Regulation of Embryonic Stem Cell Self?Renewal and Differentiation Collin Melton and Robert Blelloch Abstract Introduction: The Self?Renewal Program Embryonic Stem Cells miRNA Biogenesis and Function ESCC miRNAs Promote Self?Renewal miRNAs Induced during ESC Differentiation Suppress the Self?Renewal Program Regulatory Networks Controlling miRNA Expression miRNAs Can Promote or Inhibit Dedifferentiation to iPS Cells miRNAs in Somatic Stem Cells miRNAs in Cancer Cells Conclusion 9. TELOMERES AND TELOMERASE IN ADULT STEM CELLS and PLURIPOTENT EMBRYONIC STEM CELLS Rosa M. Marión and Maria A. Blasco Abstract Introduction Regulation of Telomeres and Telomerase Role of Telomeres and Telomerase in Adult SC Compartments Telomeres and Telomerase Regulation During Reprogramming by SCNT Telomeres and Telomerase Regulation During iPS Cell Generation Telomerase Activation is Essential for the "Good" Quality of the Resulting iPS Cells Regulation of Telomere Reprogramming Conclusion 10. X Chromosome Inactivation and Embryonic Stem Cells Tahsin Stefan Barakat and Joost Gribnau Abstract Introduction Cis Acting Factors in XCI Trans Acting Factors in XCI Counting and Choice Silencing and Maintenance of
About the Author: Eran Mes horer, PhD, is studying chromatin plasticity in embryonic and neuronal stem cells at the Department of Genetics at the Hebrew University of Jerusalem. He received his PhD in Molecular Neuroscience from the Hebrew University and conducted his post-doctoral studies at the National Cancer Institute, NIH. His lab focuses on understanding pluripotency, differentiation and reprogramming from a chromatin perspective, taking both genome-wide and single cell approaches. He is a member of the International Society for Stem Cell Research and holds the Joseph H. and Belle R. Braun Senior Lectureship in Life Sciences. Kathrin Plath, PhD, is an Assistant Professor in the Department of Biological Chemistry at the University of California Los Angeles since 2004. After she received her PhD from the Humboldt University at Berlin in Germany, she was at the University of California San Francisco and the Whitehead Institute in Cambridge, MA for her postdoctoral studies. Dr. Plath's main research interest is to understand how developmental cues induce changes in chromatin structure at the molecular level, and how these changes regulate cell fate decisions and gene expression in mammalian development. She is a member of the International Society for Stem Cell Research and of the editorial board of several stem cell journals.