Developmental Genetics
Developmental Genetics
Gurbachan S. Miglani
Ph.D. (Howard)
I.K. International Publishing House Pvt. Ltd.
New Delhi
•
Bangalore
•
Mumbai
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© 2006 I.K. International Publishing House Pvt. Ltd.
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Dedication
To
Dr Kulbir S. Gii
A Role Model Teacher
Preface
Development is behind what one looks like. Development is directed by genes, the units of heredity,
which are made up of deoxyribonucleic acid (DNA) in all animals (including man), plants, microorganisms
and most of the viruses except in some viruses where ribonucleic acid (RNA) is the genetic material.
Integrated study of genetics and development is the subject matter dealt with in Developmental Genetics.
Here one tries to understand role of genes in development, which starts from the very moment an egg is
fertilized and proceeds till the individual dies.
Keeping in view importance of developmental genetics as a science, a section comprising of the
subject matter in this branch of science has been included in University Grants Commission (UGC)
Council of Scientific and Industrial Research (CSIR)—National Entrance Test (NET) in Life Science.
Developmental Genetics is taught in almost all the conventional and agricultural Universities of India.
A course on Developmental Genetics was included in the postgraduate curricula of the Punjab Agricultural
University (PAU), Ludhiana in 1998 and since then I have been teaching Developmental Genetics at
PAU.
As a teacher of developmental genetics, it was challenging to collect the material from many different
books and research papers even for a single topic as there was no single book available to cater our
needs. This necessitated compilation of different lectures into “Class Notes on Developmental Genetics”,
which were found to be very useful by the students attending this course and those preparing for UGC/
CSIR-NET. My other colleagues also found these notes invaluable source of reference. My continued
interest in developmental genetics, experience of teaching the subject, lack of a book on developmental
genetics by an Indian author, and above all, request from students studying developmental genetics
prompted me to write the present book.
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Developmental Genetics
This book is intended to serve as a textbook for a postgraduate course in developmental genetics in
Indian and foreign universities and a reference book for the teachers teaching this course and for the
developmental biologists who conduct research in this area. Attempt has been made to explain various
phenomenons of developmental genetics, wherever possible, taking examples from animals, plants,
bacteria and viruses. Responsibility of including or not including certain topics or examples entirely rests
with me. Style of presentation of material is my choice.
This book has been divided into 20 chapters. Each chapter begins with a brief background, matter
in the subject is explained with the help of suitable tables, diagrams and flow charts, as felt necessary.
Thought provoking questions are given at the end of every chapter. Separate sections on Bibliography
and Glossary of useful terms are also included. Author and Subject Indexes given at the end of the book
will have special value for the reader.
While writing this book I have consulted a large number of old and new textbooks, original research
papers, review articles, dictionaries and encyclopedias. My head bows with respect before all these
authors. My colleague, Dr Sudagar Singh, Professor of Genetics made his lecture notes available to me
for consultations. I am thankful to him for his gesture.
Mr. Gagandeep Singh of Ludhiana typed the manuscript of the book and made all the figures on the
computer with utmost care and efficiency.
My wife Harjit, son Jemmy, daughter-in-law Parvi, son-in-law Shelly and daughter Simmi deserve
to be acknowledged for their patience and co-operation during writing of the book. My grand children
Sehaj and Prabhasis, always cheered me up and were source of energy, which is required in abundance
for such projects. I am thankful to M/s I.K. International Pvt. Ltd., New Delhi, for bringing out this
book, as per my wishes, in excellent format and design.
Gurbachan S. Miglani
Professor of Genetics (Retd.)
147-D, BRS Nagar
Ludhiana – 141 004
India
Contents
ix
Contents
1. INTRODUCTION
1
1.1 Preformation Versus Epigenesis........................................................................................ 1
1.2 Ontogeny, Phylogeny and Recapitulation ......................................................................... 2
1.3 Mosaic and Regulation Eggs ............................................................................................. 4
1.4 Genetics ............................................................................................................................ 4
1.5 Development ..................................................................................................................... 5
1.6 Developmental Genetics ................................................................................................... 5
1.7 Steps in Development ....................................................................................................... 8
1.8 Role of Genes in Development ......................................................................................... 9
1.9 Understanding Development in Genetics Terms ............................................................. 10
2. INHERITANCE OF DEVELOPMENTAL DIFFERENCES
12
2.1 Early Ideas about Heredity .............................................................................................. 12
2.2 Continuity of Life ............................................................................................................ 13
2.3 Qualitative and Quantitative Traits .................................................................................. 13
2.4 Genotype and Phenotype ................................................................................................ 13
2.5 Genotypic and Environmental Variation .......................................................................... 14
2.6 Mendelian Principles ....................................................................................................... 14
2.7 Concept of Dominance ................................................................................................... 17
2.8 Heterosis and Hybrid Vigour ........................................................................................... 19
2.9 Reverse Genetics in Mendel’s Wrinkled Character ......................................................... 19
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Developmental Genetics
2.10 Molecular Basis of Mendelian Genetics .......................................................................... 20
2.11 Mendelism—An Exception or Rule ................................................................................ 21
2.12 Mendel’s Results and Linkage ........................................................................................ 22
2.13 Chromosome Theory of Inheritance .............................................................................. 22
2.14 Sex-Linked, Sex-Limited and Sex-Influenced Inheritance ............................................. 24
2.15 Multiple Allelism .............................................................................................................. 25
2.16 Gene-Gene Interactions .................................................................................................. 26
2.17 Time of Segregation ....................................................................................................... 29
2.18 Endosperm Genetics ....................................................................................................... 29
2.19 Mutations ........................................................................................................................ 30
2.20 Quantitative Traits .......................................................................................................... 34
2.21 Penetrance and Expressivity ........................................................................................... 36
2.22 Pleiotropy ........................................................................................................................ 37
2.23 Phenocopies .................................................................................................................... 40
2.24 Homeostasis .................................................................................................................... 42
3. GENOME CONSTANCY IN DEVELOPMENT
47
3.1 Totipotency ..................................................................................................................... 47
3.2 Exceptions to Genome Constancy .................................................................................. 51
4. NUCLEUS AND NUCLEO-CYTOPLASMIC INTERACTIONS
62
4.1 Nucleus ........................................................................................................................... 62
4.2 Nucleo-cytoplasm Interactions ....................................................................................... 76
5. GENE-PROTEIN-PHENOTYPE RELATIONSHIP
83
5.1 Chemical Nature of the Genetic Material ........................................................................ 83
5.2 Molecular Structure of DNA .......................................................................................... 86
5.3 Molecular Structure of RNA .......................................................................................... 89
5.4 Properties of the Genetic Material .................................................................................. 91
5.5 DNA Replication ............................................................................................................. 91
5.6 Biological Function of the Gene ...................................................................................... 97
5.7 Gene Expression ........................................................................................................... 104
5.8 Analysis of Gene Expression ......................................................................................... 111
5.9 Environment and Gene Expression ............................................................................... 128
Contents
xi
5.10 Types of Transcripts .................................................................................................... 131
5.11 Genetic Code ................................................................................................................ 134
5.12 Protein Biosynthesis ...................................................................................................... 136
5.13 Protein Targeting .......................................................................................................... 144
5.14 Protein Secretion .......................................................................................................... 145
5.15 Molecular Chaperone .................................................................................................... 147
5.16 Protein Turnover .......................................................................................................... 148
5.17 Protein Degradation ...................................................................................................... 148
5.18 Protein-Phenotype System ........................................................................................... 149
6. GENE REGULATION AND DIFFERENTIATION
154
6.1 Gene Regulation in Prokaryotes .................................................................................... 154
6.2 Gene Regulation in Lambda Phage ............................................................................... 164
6.3 Gene Regulation in Eukaryotes ..................................................................................... 167
6.4 Messenger RNA and Differentiation ............................................................................. 201
6.5 Circadian Clock ............................................................................................................ 202
7. CELLS IN DEVELOPMENT
206
7.1 Cell Cycle ...................................................................................................................... 206
7.2 Cell Proliferation ........................................................................................................... 224
7.3 Cell Division Axis .......................................................................................................... 226
7.4 Cell Elongation .............................................................................................................. 228
7.5 Cell Determination and Differentiation .......................................................................... 229
7.6 Transdetermination ....................................................................................................... 233
7.7 Pattern Formation in Polytene Puffs ............................................................................ 235
7.8 Trans differentiation ..................................................................................................... 236
7.9 Cell Polarity ................................................................................................................... 237
7.10 Cellular Homeostasis ..................................................................................................... 239
7.11 Regulation of Diverse Cellular Activities ....................................................................... 239
7.12 Cell and Tissue Regeneration ........................................................................................ 240
7.13 Cell Adhesion ................................................................................................................ 243
7.14 Cell Commitment .......................................................................................................... 244
7.15 Cell Migration ................................................................................................................ 244
7.16 Cell Motility ................................................................................................................... 244
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Developmental Genetics
7.17 Cellular Responses ........................................................................................................ 245
7.18 Cell Competition ............................................................................................................ 245
7.19 Intercellular Junctions................................................................................................... 245
7.20 Cell-Cell Interactions .................................................................................................... 246
7.21 Cytoskelton ................................................................................................................... 248
8. CELL-SPECIFIC GENE ACTIVATION AND TISSUE DIFFERENTIATION
252
8.1 Origin of Different Cell Types ...................................................................................... 252
8.2 Cell-Specific Gene Activation ....................................................................................... 257
8.3 Specificity in Eukaryotic Transcription ........................................................................ 258
8.4 Tissue Differentiation ................................................................................................... 261
9. PLANT EMBRYOLOGY
278
9.1 Meiosis .......................................................................................................................... 278
9.2 Fertilization in Angiosperms .......................................................................................... 288
9.3 Endosperm Development .............................................................................................. 289
9.4 Embryo Formation ........................................................................................................ 290
9.5 Storage Proteins ............................................................................................................ 298
10. GAMETE FORMATION, FERTILIZATION AND CLEAVAGE IN ANIMALS
304
10.1 Primordial Germ Cells................................................................................................... 304
10.2 Spermatogenesis ........................................................................................................... 306
10.3 Oogenesis ..................................................................................................................... 312
10.4 Fertilization ................................................................................................................... 318
10.5 Cleavage ........................................................................................................................ 322
11. ANIMAL DEVELOPMENT
329
11.1 Drosophila ..................................................................................................................... 330
11.2 Sea Urchin .................................................................................................................... 348
11.3 Mammals ...................................................................................................................... 356
11.4 Frog .............................................................................................................................. 361
11.5 Caenorhabditis Elegans ................................................................................................. 364
11.6 Zebrafish ....................................................................................................................... 368
11.7 Blastogenesis ................................................................................................................. 368
11.8 Bone Marrow Stem Cells .............................................................................................. 368
Contents
12. DOSAGE COMPENSATION AND SEX DETERMINATION
xiii
373
12.1 Dosage Compensation .................................................................................................. 373
12.2 Mechanisms of Dosage Compensation ........................................................................ 379
12.3 Sex Determination ........................................................................................................ 381
12.4 Noncoding DNA Hypothesis for Sex-Determination.................................................... 385
12.5 Evolutionary Relationships Among Sex-Determining Mechanisms .............................. 388
12.6 Sex Differentiation ........................................................................................................ 389
12.7 Events in Sex Determination ......................................................................................... 389
13. AGEING AND APOPTOSIS
391
13.1 Ageing ........................................................................................................................... 391
13.2 Theories of Ageing ........................................................................................................ 397
13.3 Genetics of Ageing ........................................................................................................ 404
13.4 Postponement of Ageing ............................................................................................... 407
13.5 Apoptosis ...................................................................................................................... 410
13.6 Reaper Model ................................................................................................................ 413
13.7 Regulators of Apoptosis ................................................................................................ 416
13.8 Miotchondrial Pathway of Apoptosis ............................................................................ 419
13.9 Role of Morphogens in Apoptosis ................................................................................ 420
13.10 Programmed Cell Death in Plants ................................................................................. 421
14. PATTERN FORMATION AND EPIGENETICS
424
14.1 Pattern Formation ......................................................................................................... 424
14.2 Positional Information and Developmental Patterns ..................................................... 429
14.3 Epigenetics .................................................................................................................... 433
14.4 DNA Methylation and Epigenetics ................................................................................ 434
14.5 Epigenetic Reprogramming ........................................................................................... 440
14.6 Linking Conventional Genetics with Development ....................................................... 441
14.7 Epigenetic Code ............................................................................................................ 443
15. MORPHOGENESIS
445
15.1 Morphogens .................................................................................................................. 446
15.2 Morphogenesis in Viruses ............................................................................................. 450
15.3 Morphogenesis in Bacillus Subtilis ................................................................................ 453
15.4 Morphogenesis in Slime Mold ...................................................................................... 453
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Developmental Genetics
15.5 Morphogenesis in Green Algae ..................................................................................... 455
15.6 Morphogenesis in Animals ............................................................................................ 455
15.7 Binary Switch Genes .................................................................................................... 464
15.8 Process of Morphogenesis ........................................................................................... 465
15.9 Organ Development ...................................................................................................... 466
15.10 Plant Morphogenesis .................................................................................................... 473
16. HOMEOSIS
483
16.1 Drosophila Homeosis .................................................................................................... 483
16.2 Silkworm Homeosis ...................................................................................................... 492
16.3 Tribolium Homeosis ...................................................................................................... 492
16.4 Mode of Action of Specification ................................................................................... 493
16.5 Common Coding Motifs ............................................................................................... 494
16.6 Coordination of Development and Proliferative Pool .................................................... 494
16.7 Antennapedia Type Genes in Xenopus ......................................................................... 495
16.8 Deciphering Function of the Hox Genes ...................................................................... 495
16.9 Pou Domain in Mammals ............................................................................................. 498
16.10 Homeosis in Plants ........................................................................................................ 498
16.11 Micro RNAs in Development ....................................................................................... 500
16.12 Homeo Domains ........................................................................................................... 500
16.13 Development—A Cascade of Gene Expression ............................................................ 502
17. STEM CELLS
507
17.1 Stem Cell Biology .......................................................................................................... 507
17.2 Embryonic Stem Cells .................................................................................................. 512
17.3 Adult Stem Cells ........................................................................................................... 514
17.4 Neural Stem Cells ......................................................................................................... 515
17.5 Mesenchymal Stem Cells .............................................................................................. 515
17.6 Develpmental Potency .................................................................................................. 517
17.7 Uses of Pluripotent Stem Cells ..................................................................................... 517
17.8 Violating the Rules of Embryology ............................................................................... 518
18. SIGNAL TRANSDUCTION
521
18.1 Diffusible Signals .......................................................................................................... 521
18.2 Signalling Pathways ...................................................................................................... 522
Contents
xv
18.3 Signal Transducers and Activators of Transcription .................................................... 527
18.4 Regulators of Developmental Timing ........................................................................... 532
18.5 Signal Transduction Knowledge Environment ............................................................. 532
18.6 Plant Signal Transduction ............................................................................................. 534
19. RECENT PROGRESSES IN DEVELOPMENTAL GENETICS
537
19.1 Areas of Current Interest .............................................................................................. 537
19.2 Need to Know More About ........................................................................................... 541
20. SYNTHESIS
545
20.1 The Conception and Birth of Evo-Devo ....................................................................... 546
20.2 Developmental Machinery ............................................................................................ 547
20.3 Evolutionary Developmental Mechanisms .................................................................... 548
20.4 Evolution of Biosynthetic and Morphogenetic Pathways ............................................. 549
Glossary ................................................................................................................ 553-663
Bibliography ......................................................................................................... 664-709
Author Index ....................................................................................................... 710-735
Subject Index ....................................................................................................... 736-765
Developmental Genetics
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