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Molecular principles of animal development / by Alfonso Martinez Arias, Alison Stewart. — Oxford ; New York : Oxford University Press, 2002.—(58.178/M385) |
Contents
Contents
1 Introduction: Towards a molecular analysis of development 1
The rationale for a different approach 3
Beginnings 7
The heyday of descriptive embryology 8
Experimental embryology is born 10
Morgan's 'deviation': Genetics 12
The impasse 13
Genetics meets molecular biology 13
Lessons from history? 13
About this book 14
2 Programs and regulatory elements in DNA and RNA 19
The DNA during development 19
Types of DNA sequences 22
Genes and genomes 24
Regulatory sequences in DNA 27
Irreversible modifications of the DNA sequence 33
Regulatory regions in RNA 33
Coordination of gene expression 35
Developmental programs 36
Higher-order programs 39
3 Decoding the program: Transcription 43
Transcription in prokaryotes 43
The transcriptional machinery in eukaryotes 46
Enhancers and gene-specific transcription factors 49
DNA-binding specificity of transcription factors 51
Assembly of complexes at enhancers: Enhanceosomes 52
Interactions between promoters and enhancers 58
The role of chromatin in transcription 59
The dynamics of transcriptional activation and chromatin remodeling 61
Transcriptional repression in eukaryotes 62
The transcriptional machinery and regulated transcription 64
Transcriptional regulation during development: From domains to stripes in the
Drosophila blastoderm 65
Transcriptional regulation during development: Regulation of the
immunoglobulin I1 heavy-chain gene 68
Transcriptional elongation and termination 69
The stability of the transcriptionally active or inactive state 70
RNA-binding proteins 72
RNA localization and the establishment of the body plan in Drosophila 76
4 Cell surface proteins: Receptors， ligands， and their environment 79
Intercellular communication: Cell signaling 79
Indentification of signalling molecules and receptors 81
Characterization of signalling molecules and receptors 83
Types of signalling molecules 86
Low-molecular-mass signalling molecules 87
Peptide and protein signalling molecules 90
Receptors 94
Cell-surface receptors 95
Receptor tyrosine kinases 95
Serine/threonine kinase receptors 97
Receptor phosphatases 99
Receptors associated with cytoplasmic kinases 99
Seven transmembrane domain receptors 101
Other cell-surface receptors 102
Signalling proteins as receptors 104
Intracellular receptors 106
Regulation of ligand-receptor interactions 107
The vertebrate organizer as a source of signal modulators 111
The extracellular environment and cell signaling 111
5 Intracellular effectors of cell and networks 115
interactions: Signalling pathways 116
Epistasis and the analysis of signalling pathways 116
Signalling currencies 119
Adaptor motifs 119
A tool for detecting molecular interactions 123
Modular protein kinases and phosphatases 123
G proteins and intracellular switches 124
Signalling pathways 127
Routes triggering nuclear translocation of the effector 127
Delta-Notch signaling 127
NFKB/dorsal signaling 128
JAK-STAT signaling 128
TGFI]-Smad signaling 129
Membrane-nucleus relays: Mitogen-activated protein kinase (MAPK) signalling cascades 133
Second-messenger signalling pathways 137
Cyclic AMP and protein kinase A 137
Lipid second-messenger pathways 138
Hedgehog and Wnt signaling 139
Hedgehog signaling 141
Wnt signaling 143
Dynamics and regulation of signal transduction during cell interactions 145
Changes in activity of signalling pathway components 146
Changes in the concentration or stability of signalling pathway components 146
Compartmentalization 150
Integration of signalling pathways 151
Connectivity and integration of signalling networks 154
Signal integration in the nucleus 155
6 Cells and their interactions 161
The extracellular matrix 163
The cytoskeleton 165
intermediate filaments 165
Microtubules 167
Actin filaments 169
Cell adhesion and cell junctions 174
Molecular mediators of cell adhesion 176
Cell adhesion and signaling 179
Cell polarity 183
Apico-basal polarity 184
Planar polarity 187
Cell shape， movement， and migration 189
Cues for cell movement 195
7 Basic cellular routines: Division， differentiation， and cell death 197
The cell cycle 197
Uncovering the cell-cycle regulators 199
The cell-cycle machinery at work 201
Cell-cycle checkpoints: Integration and surveillance 205
The cell cycle in early development 205
Coordinating cell division with cell growth 208
Extracellular regulation of the link between growth and proliferation 211
The cell cycle and cell differentiation 211
Cell death: The ultimate 'differentiation' 216
The cell death machinery 218
Death signals during development 221
Regulation of cell survival during development 221
Cell numbers and overall size 222
8 The generation of lineages: A developmental routine 227
Cell lineages and cell interactions 227
Lineages and fate maps 229
Stem cell lineages 229
Stem cell factors 232
Stem cell-like lineages 234
Complex determinate lineages 234
The leech Helobdella triserialis 238
The nematode Caenorhabditis elegans 238
Cell fate determination within lineages 240
Mechanisms of segregation of determinants of lineage identity in S. cerevisiae and C. elegans 242
Mechanisms of segregation of determinants of lineage identity in the development of the nervous system 245
Notch signalling: A recurring element in the lineage-mediated assignment of cell fates 249
The spatial and temporal regulation of Notch signaling 253
Iterative molecular mechanisms for cell fate assignment 254
Indeterminate lineages and polyclonal lineage compartments 256
9 Long- and short-range influences in the generation of cell diversity 261
Induction and positional information 261
Long- and short-range inductive molecules 265
Cellular responses to inductive signals: Competence 269
Signalling-induced modifications of the inductive event 271
The morphogen concept: Graded responses to diffusible signals 274
Candidate morphogens 274
Candidate morphogens in Drosophila 276
Bicoid 278
Dorsal 280
Dpp 283
Candidate morphogens in vertebrates 283
Activin 283
Limitations of the classical concept of the morphogen 285
The generation of graded molecular information 288
The interpretation of graded molecular information 288
Long- versus short-range patterning mechanisms in pattern formation 291
10 Cell-type specification: A developmental operation 295
Methods for the spatial and temporal analysis of gene activity 295
Muscle development: Myogenesis 298
The origins of muscle cells 298
Establishment of different mesodermal fates 301
Myogenic regulatory factors and the commitment to the myogenic pathway 305
Muscle differentiation 312
Neurogenesis: The central nervous system 314
The origins of the central nervous system 314
The emergence of neural tissue 315
Axial organization of the nervous system 319
The commitment to the neurogenic pathway 320
The birth of neurons: Individual cell-type specification 323
Neurogenesis in Drosophila 325
Regulatory hierarchies in the establishment of cell fates 325
11 Patterns in one and two dimensions 333
Development and patterning of the Caenorhabditis elegans vulva 333
Generation and specification of the vulva precursor cells (VPCs) 335
The signal from the anchor cell: Ras signalling and the specification of VPCs 335
VPCs: lin-12 signalling 341
Execution of the fates of the VPCs 343
Morphogenesis of the vulva 344
Development and patterning of the larval epidermis of Drosophila 345
Establishment of references and polarity 346
Generation of cell diversity with respect to the coordinates 351
The emergence of the pattern 354
Development and patterning of the teeth 354
initiation of tooth development 357
Morphogenesis and differentiation 358
Different types of teeth 359
General principles for the patterning of two-dimensional cellular assemblies 361
12 Patterns in three dimensions 363
Limbs and appendages 363
Initiation of vertebrate limb development 365
Establishment of AP and DV coordinates in the limb bud 367
nitiation of appendage development in insects 368
Cellular parameters of vertebrate limb development 368
AER-driven initiation of PD patterning and growth 372
Molecular mediators of growth and positional information in the growing bud 374
Integration of information from the ZPA and the AER 377
The role of the DV axis in limb patterning 377
Growth and patterning along the PD axis 377
Hox codes and the registration of the positional information 380
The patterning of the digits 380
Development and patterning of the appendages of Drosophila 382
The initiation of wing development 383
Patterning and growth of the wing 386
The patterning of the wing: Veins 388
Common strategies in the development and patterning of vertebrate limbs and the appendages of insects 389
Branched structures: The insect tracheal system and vertebrate lungs 392
The tracheal system of Drosophila 392
Cell-type specification in the tracheal system 393
Branching morphogenesis in the tracheal system 395
Specification of cell types within the migrating branch 397
The development of the vertebrate lung 398
Are there general principles for three-dimensional patterning? 400
Index 403
