Molecular Basis of Developmental and Stem Cell Regulation: Classical Models Revised (Results and Problems in Cell Differentiation, 72)

Preface
Contents
Part I: Somatic Cell Development from the Epiblast
	Chapter 1: The Epiblast and Pluripotent Stem Cell Lines
		1.1 The Epiblast
		1.2 Mouse ESCs and Their Prototype Embryonal Carcinomas
		1.3 Human ESCs Representing a Postimplantation Developmental Stage
		1.4 Mouse Epiblast Stem Cells (EpiSCs)
		References
	Chapter 2: Different Types of Pluripotent Stem Cells Represent Different Developmental Stages
		2.1 The Sox2-Pou5f1 Complex as the Core Transcription Factor (TF) Pair of the Preimplantation Inner Cell Mass and ESCs
		2.2 Expression Profiles of the Core TFs in Epiblasts
		2.3 Chromatin Immunoprecipitation Sequencing (ChIP-Seq) Analysis of the TF-Binding Genomic Sites in EpiSCs Revealed Zic2 and O...
		2.4 Shift of the Core TFs from Sox2-Pou5f1 in mESCs to Zic2-Otx2 in EpiSCs
		2.5 Culture Medium-Dependent Distinct Cell States of mESCs and Their In Vitro Derivatives, EpiSCs and Epiblast-Like Cells (Epi...
		2.6 From Human ESCs to a Preimplantation Stage
		References
	Chapter 3: Gastrulation: Its Principles and Variations
		3.1 The Generic Aspects of Gastrulation
		3.2 Gastrulation in Chicken Embryos
			3.2.1 Primitive Streak and Node Development in Chicken Embryos
			3.2.2 Gastrulation at Hensen´s Node in Chicken Embryos
			3.2.3 Gastrulation Along the Primitive Streak in Chicken Embryos
			3.2.4 Neuromesodermal Progenitors (NMPs) in Chicken Gastrulation Marked by N1 Enhancer Activity
		3.3 Gastrulation in the Mouse Embryo
			3.3.1 Pregastrulation Embryo Patterning
			3.3.2 Early-Stage Gastrulation
			3.3.3 Endoderm Gastrulation as Cell Bundles Activated by the Interaction with the Basement Membrane, Modeled in EpiSCs
			3.3.4 Neuromesodermal Progenitors (NMPs) in Mouse Embryos
			3.3.5 The Regulation of the NMPs
			3.3.6 Switching from Mesoderm-Dedicated Progenitors to NMPs During Embryo Axial Elongation
		3.4 The Panamniote and Panvertebrate Features of Gastrulation
			3.4.1 Primitive Streak-Forming Gastrulation Is Not Common
			3.4.2 Gastrulation Manages Two Processes: Head Development via AME Production and Trunk Development via Posterior Axial Tissue...
		References
	Chapter 4: How the Brain Develops from the Epiblast: The Node Is Not an Organizer
		4.1 The Limitation of Experimental Embryology and the Advantages of Live Imaging-Based Modern Analyses
		4.2 Two Initial Paradoxes Concerning the Early-Stage Brain Development
		4.3 Long-Range Cell Migration of Anterior Epiblast Cells to Form the Region-Specified Brain Primordium and the Covering Head E...
		4.4 The Developmental Outcome of Exogenous Node Grafts Depends on Whether the Graft Position Is in the Anterior or Posterior H...
		4.5 Node Graft-Derived AME or Isolated AME Elicits Local Gathering of Anterior Epiblast, Leading to Secondary Brain Tissue Dev...
		4.6 The Development of Brain Portions in the Secondary Brain Depends on the Positions of the Grafted AMEs
		4.7 Epiblast Brain Field
		4.8 The Node Is Not an Organizer
		4.9 Conclusion and Future Perspectives
		References
Part II: New Conceptions of Developmental Regulations
	Chapter 5: Multiple Cell Lineages Give Rise to a Cell Type
		5.1 Epigenetic Landscape
		5.2 Multiple Myogenic Domains of Embryos Develop into Skeletal Muscle
			5.2.1 Trunk Myogenesis Starting from Somites
			5.2.2 Cranial Muscles Develop via Distinct Regulatory Pathways
			5.2.3 Cranial Muscle Satellite Cells Are Capable of Regenerating Limb Skeletal Muscles
		5.3 Multiple Cell Lineages Give Rise to Lens Tissues
			5.3.1 Normal Lens Development
			5.3.2 Embryonic Neural Retina Developing into Lenses
			5.3.3 Lens Development from the Pituitary Precursor under Inhibited Hedgehog Signaling in Zebrafish and Avian Embryos
		5.4 Hematopoietic Development Arguing against Cell Lineage-Dependent Cell Specification
			5.4.1 The Advantages of the Study of Hematopoietic Development
			5.4.2 A Model of Hematopoiesis Based on the Cell Lineage Branching Model
			5.4.3 Multiple Developmental Pathways in Hematopoiesis Indicated by Single-Cell Transcriptome Analysis
		5.5 Cardiomyocyte Progenitors Develop into Neural Tissues Under Conditions of Disturbed Epigenetic Regulation
		5.6 The Synthesis of the Observations
		References
	Chapter 6: Organ Regeneration Without Relying on Regeneration-Dedicated Stem Cells
		6.1 Liver Regeneration
		6.2 Lens Regeneration from the Dorsal Iris of the Newt
		6.3 Amputated Limb Regeneration in Newts and Salamanders
		6.4 Routes to Central Nervous System Regeneration: Implications from Amphibians and Fish Cases
			6.4.1 The Repair of the Injured Spinal Cord by Ependymal Cell Activation
			6.4.2 The Regeneration of Retinal Neurons from Müller Cells
		References
	Chapter 7: Reciprocal Interactions Between the Epithelium and Mesenchyme in Organogenesis
		7.1 The Embryonic Gut Tube as a Platform to Investigate Epithelial and Mesenchymal Interactions
		7.2 A Lack of Sox2 Expression in the Anterior Foregut Epithelium Results in the Development of the Trachea Instead of the Esop...
		7.3 Mesenchymal Characteristics Accord with Those of the AFG
		7.4 Wnt Signaling from the AFG in the Absence of Sox2 Expression Triggers Tbx4 Expression in the Mesenchyme and Allows it to A...
		References
	Chapter 8: The Significance of Repressive Processes in Developmental Regulation
		8.1 Nervous System Development Escaping from Repressive Signals
			8.1.1 A Period of Confusion in Neural Inducer Research
			8.1.2 The Discovery of Chordin and Derepression Mechanisms
		8.2 Epigenetic Regulation: Differentiating Cranial and Trunk Neural Crest Development Via the Polycomb Group Protein Ezh2
			8.2.1 Polycomb Group and Trithorax Group Protein Complexes
			8.2.2 Cranial Neural Crest
			8.2.3 The Impact of Neural Crest-Specific Inactivation of the PRC2 Component Ezh2
		8.3 Sonic Hedgehog Signaling Outputs Counterbalancing Transcriptional Activation and Repression
			8.3.1 Sonic Hedgehog Signaling in Limb Development
			8.3.2 The Hedgehog Signaling-Dependent Regulation of Gli Transcription Factors
			8.3.3 Limb Digit Patterning by Gli Transcription Factor Activities
		8.4 Lifting the Gli3 Repressor Activity with miR-133a
		References
Part III: Transcriptional Regulation of Development
	Chapter 9: Enhancer Arrays Regulating Developmental Genes: Sox2 Enhancers as a Paradigm
		9.1 A Brief History of Enhancer Studies
		9.2 Screening Sox2 Neural Enhancers Using Reporter Assays in Developing Chicken Embryos
		9.3 Neural Enhancers Identified in Chicken Embryos and Conserved in the Mouse Genome
		9.4 Conservation of the Sox2 Neural Enhancer Sequences Across Vertebrate Species
		9.5 More Neural Enhancers Are Distributed in a Broader Genomic Region
		9.6 A Cluster of mESC-Specific Downstream Enhancers Composing the Sox2 Control Region (SCR)
		9.7 DNA Looping and the Topologically Associated Domains (TADs) of the Genome; Involvement of Their Subtypes in Cell Type-Spec...
		9.8 The DNA Looping Between the Sox2 Gene and the SCR Occurs Independently of TADs
		9.9 During the Bursts of Sox2 Transcription, the SCR Enhancer Sequence Does Not Approach Near to the Gene
		References
	Chapter 10: Enhancer Activation by Transcription Factors and Underlying Mechanisms
		10.1 Two Classes of Enhancers in Developmental Regulation
		10.2 Organization of Class I Enhancers
			10.2.1 Class I Enhancers Consist of a Core Region That Determines the Cell Type Specificity and a Subsidiary Region to Augment...
			10.2.2 The Core Sequence Provides Binding Sites for a Limited Number of TFs That Activate and Determine the Specificity of the...
		10.3 The Sox-Partner Code for Cell Specification
		10.4 Structural Basis of Sox2-Partner TF-DNA Ternary Complex Formation
			10.4.1 Features of the Functional Binding Sequences for Sox2-Pou5f1 and Sox2-Pax6 Hetero Dimers
			10.4.2 The Requirement of a Nonstandard Pax6 Binding Sequence for Sox2-Pax6 Cooperative Binding and Transcriptional Activation
			10.4.3 DNA Bending in the Sox2-Pax6-DC5 Ternary Complex
			10.4.4 Molecular Interfaces for the Cooperative Binding of Partner TFs with Sox2
		10.5 ``Super-Enhancers´´ and the Enhancers with Reiterated Binding of Core TFs of the Cells
		10.6 How Transcription Factors Search and Stay on the Enhancers: Single-Molecule Live Imaging of Sox2 in the ESC Nuclei
		10.7 Sox2-Partner Factor Complexes Search for and Bind to the Chromosomal Target Sites; Evidence from FRAP Analysis
		References
	Chapter 11: Molecular Basis of Cell Reprogramming into iPSCs with Exogenous Transcription Factors
		11.1 The Discovery of MyoD
		11.2 Pioneer Transcription Factors in Developmental Regulation
		11.3 Transcription Factor Requirements of iPSC Production from Dermal Fibroblasts
		11.4 iPSC-Producing Reprogramming Proceeds in Two Steps
		11.5 Initial Attack of the Fibroblast Genome by OSKM Occurs on Nucleosomes in the Closed Chromatin Region
		11.6 Sox2 and Pou5f1 Binding to Nucleosomes In Vitro
		11.7 DNA Demethylation Process: Insight from B-Cell-Derived iPSC Production
		11.8 Trajectories of OSKM Binding from MEFs to iPSCs
		11.9 Cellular and Culture Conditions for the Enhanced Derivation of iPSCs
			11.9.1 Reprogramming of Neural Stem Cells into iPSCs
			11.9.2 The Correspondence Between the Initial OSKM Attack Sites in the Fibroblast Genome and the Sox2-Bound Regions Across Ste...
			11.9.3 Neural Crest-Derived Embryonic Fibroblasts as the ``Elite´´ Population in iPSC Reprogramming
			11.9.4 iCD1 Culture Medium Supports a High Efficiency of MEF Reprogramming with OSK TFs
		11.10 Feedback to the Developmental Regulation: A Promise
		References
Postface
Appendix A: Molecular Interactions Involved in the Cooperative Binding of Sox2-Pax6 to the DC5 Enhancer Sequence to Elicit Enh...
	The DC5 Core Enhancer Sequence Allows the Cooperative Binding of Sox2 and Pax6
	Deviation of Bases at Positions 9, 10, and 12 of the Pax6-Binding Site from the Standalone Binding Consensus Is Essential for ...
	The N-terminal β-Sheet Interacting with the Target DNA Is Involved in Sox2-Pax6 Cooperative Binding
	The Interface Between Sox2 and Pax6 in the Complex with DC5-like DNA Sequences Inferred from Human Mutant Cases
	A Quest for DC5-type Consensus DNA Sequences for Sox2-Pax6 Cooperative Binding
	The Case of DC5-con Derivatives
	References
Appendix B: The List of Genomic Loci Commonly Occupied by Sox2 Among mESCs, EpiSCs, and Neural Progenitors (Section 11.9.2)
	References
Appendix C
	References
Index