Gene Activity in Early Development

677 Pages·1986·19.785 MB·English

by  Arnold I. Davidson (Auth.)

Gene Activity
in Early
Development
Third Edition
Eric H. Davidson
Division of Biology
California Institute of Technology
Pasadena, California
ACADEMIC PRESS, INC.
Harcourt Brace Jovanovich, Publishers
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Library of Congress Cataloging in Publication Data
Davidson, Eric H., Date
Gene activity in early development.
Bibliography: p.
Includes index.
1. Developmental genetics. I. Title.
QH453.D38 1986 574.3'3 86-Ί734Ί
ISBN 0-12-205161-0 (alk. paper)
PRINTKD IN THH I'NITHI) STATHS OF AMHRICA
9 8 7 6 5 4 3 2 I
This work is dedicated to the memory of my father,
Morris Davidson (1898-1979), in his time a leading
American painter. Only in recent years have I realized
how much I learned from him about the ordering of
complex perceptions.
Acknowledgments
Though entitled the third edition of "Gene Activity in Early Develop-
ment," this is a wholly new book. Perhaps this book contains more molecu-
lar and genetic evidence that is of biological import than did its predecessor.
Certain conceptual themes, some organizational aspects, and various figures
and calculations are all that survive from the second edition. The discoveries
that have been achieved in the decade since the appearance of the second
edition have largely transformed this domain of biological science. Were I to
have succeeded in fulfilling the objectives of this endeavor, the following
pages would provide an interpretive, synthetic review, presented in suffi-
cient detail and with sufficient accuracy to serve also as a scholarly work of
reference for interested students and for my scientific colleagues. I have
realized that it may not be possible to write a book that truly accomplishes
these objectives. The technological variety and the depth of available experi-
mental evidence, and the rate at which new results appear, preclude real
accuracy. Even more problematic is the task of constructing from the frag-
mentary insights that our field now affords a consistent image of the develop-
mental systems that are the ultimate subject of this essay. The scope of the
subject matter and the comparative approach I have chosen have denied me
refuge within the narrower conceptual purviews of any one system. Thus it
is my hope that despite its many deep imperfections, this book may provide
an analysis of early development that is more united than those available, for
example, in most multiauthored treatises or symposium volumes.
I would probably have never embarked on this project but for the urging
and advice of colleagues whose views I deeply respect. At several junctions
I would surely have abandoned it, had it not been for those on whom I have
depended throughout for wisdom, knowledge, and criticism. I have been the
beneficiary, on each of the hundreds of days on which I struggled with this
manuscript, of essential support and encouragement. The manuscript was
read, corrected, and in innumerable ways improved within my Caltech labo-
ratory by my long time associate and colleague, Dr. Barbara R. Hough-
Evans, and by Dr. Frank J. Calzone, at the time a Senior Research Fellow.
Dr. L. Dennis Smith of Purdue University, and Dr. Roy J. Britten, Dr. Elliot
Meyerowitz, and Dr. Ellen V. Rothenberg of the Caltech Division of Biology
all reviewed critically the entire manuscript, a thankless and extensive ef-
fort. I am extremely grateful for their encouragement, their criticism, and in
general their diverse and perspicacious insights. Various chapters or sec-
tions were also reviewed by Dr. Richard Axel of Columbia University Col-
xiii
XIV Acknowledgments
lege of Physicians and Surgeons; Dr. Gary Freeman of the University of
Texas at Austin; Dr. William H. Klein of the M. D. Anderson Hospital,
University of Texas Medical Center; and Drs. Edward B. Lewis, Mark
Konishi, and Barbara Wold of the Caltech Division of Biology. It is my
pleasure to acknowledge the debt that I owe to the scholarship and interest
of these scientists, who in their individual ways contributed essentially to
this work, though it is important to stress that they bear no responsibility for
my oversights.
The manuscript was put together with the close collaboration of Ms. Jane
Rigg. She served at once as bibliographic researcher, compiler of figures,
editor, proofreader, interpreter, and advisor. Her informed intuitions, deter-
mination, indefatigable energy, and professional expertise were truly crucial
at every stage. Ms. Stephanie Canada, who expertly converted my initial
handwritten scrawl (which is generally considered illegible) and all the sub-
sequent drafts of each chapter into a finished manuscript, also made this
project her own. Her contributions from beginning to end were invaluable.
Ms. Rene Thorf provided extensive and characteristically accurate secretar-
ial assistance as well. I should also like to acknowledge, with sadness as well
as gratitude, the role played by the late Mr. Ryo Arai, the Academic Press
editor who organized the production of the second edition and initiated the
commitment that led to this third edition. Mr. William Woodcock, the editor
who inherited the problems of this enterprise, has been an understanding,
effective, and above all intelligent agent and friend, and for his support and
surveillance I am indeed grateful.
I
From Genome to Embryo:
The Regulation of Gene Activity
in Early Development
1. Introductory Comments 2
2. Synopsis of Major Themes 3
3. Historical Antecedents: A Very Brief Summary of the Origins of the
Variable Gene Activity Theory of Cell Differentiation 8
4. Is There Structural and Functional Change in the Genome during
Development? 12
(i) Ontogeny and the Structure of Specific Genes 12
(ii) Activation of Silent Genes in Differentiated Adult Cells 16
(iii) Developmental Capacities of Nuclei Transplanted into Eggs 17
Transplantation of Differentiated Amphibian Cell Nuclei into
Enucleated Eggs 18
Developmental Potentiality of Transplanted Nuclei in Other
Organisms 23
5. Gene Regulation in Development 25
(i) Developmental Activation of Genes by Interaction with
7raws-Regulators 25
Evidence from Somatic Cell Transformation 25
Transgenic Animals: Ontogenic Function of Exogenous Genes
Introduced into the Germ Line 28
(ii) Regulation of Gene Activity during Embryogenesis 32
Mechanism of Repression of Late Genes during Early Development;
Genomic Methylation 33
Evidence That Oocyte Cytoplasm Contains Factors That Can Affect
Nuclear Gene Expression 37
Activation of the Maternal Gene Set in the Embryo 38
Activation of Embryonic Genes Not Previously Expressed 42
2 /. From Genome to Embryo
1. INTRODUCTORY COMMENTS
It has been understood for almost a century that the process of develop-
ment is itself a heritable feature of the organism, and that construction of the
organism from the egg is the consequence of genomic expression. Modern
measurements demonstrate that early development, including both oogene-
sis and embryogenesis, involves a huge outlay of genomic information. By
the time of fertilization the egg has been equipped with a unique set of
biosynthetic capabilities, and in most forms it is endowed with structural
polarities that are ultimately reflected in the spatial organization of the em-
bryonic cell lineages. With the current formulation of the molecular mecha-
nisms by which gene expression establishes the properties of differentiated
cells, and the development of potent new experimental technologies, the
process of embryogenesis has become more accessible. A fundamental ex-
planation would require understanding at the molecular level of exactly what
developmental information is encoded in the genome; how it is utilized in
morphogenetic time and space; how its expression is regulated; and exactly
how its products endow the differentiated cells of the embryo with their
functional characteristics. As yet, though we know that they exist, most of
the crucial causal links between genome and embryo remain largely unde-
scribed.
The objective of this book, as of the two previous editions (1968, 1976), is
to provide a meaningful interpretation, and critical review, of those aspects
of the molecular biology of the embryo that reflect on the role of genomic
information in early development. The areas considered extend from gene
expression during oogenesis to the establishment of an asymmetric pattern
of lineage-specific gene expression in the embryo. The depth and the variety
of the relevant literature presents a formidable challenge. It is easy for the
reviewer to feel that less knowledge has been extracted than is actually
available in the mass of current experimental data.
The molecular mechanisms required to produce a differentiated animal
embryo are anything but obvious. The paradigms that emerge from molecu-
lar analyses of terminal cell differentiation, or of systems that do not un-
dergo embryonic development, provide essential information as to molecu-
lar mechanisms of animal cell function, insights into the differentiation
process, and comparative points of reference. However, as more is learned
it becomes increasingly evident that to understand early development it is
necessary to study oocytes, eggs and embryos. Developmental problems
that are intrinsic to embryogenesis include the creation of a three-dimen-
sional cellular morphology where there was none before; the determination
ab initio of cell lineage precursors; the requirement for active biosynthesis
within an enormous mass of cytoplasm that at first contains very few nuclei;
the need to produce large numbers of new cells at a rate higher than at any
other time in the life cycle (at least in some organisms), and within a constant
volume of cytoplasm; and so forth. A fundamental difference from later
2. Synopsis of Major Themes 3
cells, at least in higher animals, is that the genomes of the early blastomeres
are "naive, "and in some organisms demonstrably totipotent. During the
ontogeny of the lineages leading to given differentiated cell types interac-
tions with other molecules occur that stably, if not irreversibly, distinguish
genes never to be utilized in these cells from genes whose expression is or
will be required. This deep-seated difference between the adult and early
embryonic genomic apparatus can be shown experimentally, both by gene
transfer and by nuclear transfer, as discussed later in this chapter.
Observations on four experimental systems account for most of our cur-
rent knowledge of oogenesis and early development. These are Xenopus,
sea urchins of various species, the mouse, and Drosophila. For certain areas
other organisms have proved extremely valuable as well, such as the nema-
tode Caenorhabditis, ascidians of various species, ctenophores, gastropod
molluscs, etc. Each system has its strong points and its weak points as an
experimental object, and it is impossible to obtain anything but a partial view
of the processes of oogenesis and early development through the lens that
any one system provides. The approach taken in the following review is thus
comparative. By this route it becomes evident that many of the special
devices utilized during early development can be interpreted in terms of their
adaptive value, given the special biological constraints to which each species
is exposed, for example the time available for oogenesis or embryogenesis,
and the conditions in which these processes must occur. Thus in different
organisms there is significant variation in the relative importance even of
basic, common phenomena such as cell-cell interaction, the initial spatial
organization of the egg cytoplasm, the utilization of maternal transcripts,
and many other particular mechanistic features, as will become apparent in
following chapters.
2. SYNOPSIS OF MAJOR THEMES
Chapter I: From Genome to Embryo: The Regulation of Gene Activity
in Early Development
The modern theory that different sets of genes are active in different cells
developed originally from classical studies that were focussed on the role of
the genome in embryogenesis. It was concluded that early embryo nuclei are
functionally equivalent, and by the first decades of the 20th century leading
investigators had correctly perceived the determinative significance of ge-
nomic expression during oogenesis and embryogenesis. Current evidence
regarding genomic equivalence among differentiated cells later in develop-
ment includes examples in which alteration of the primary gene structure is
required for expression, e.g., in the vertebrate immune system, but in most
genes examined the DNA itself appears to remain unchanged during ontog-
eny. Evidence from cell fusion experiments, and from regeneration and
4 /. From Genome to Embryo
other examples of transdifferentiation, suggests that genes normally des-
tined to remain silent in differentiated cells are retained intact and can be
reactivated. When reimplanted into eggs, differentiated cell nuclei of am-
phibians and several other groups display the ability to direct embryogenesis
and the formation of many differentiated larval tissues. Particular genes are
activated and others repressed on introduction of somatic nuclei into eggs
and oocytes. Somatic cell and germ line transformation experiments have
confirmed that developmental activation as well as inductive modulation of
genes functional in highly differentiated cell types ("late genes") are pro-
cesses usually mediated by interactions of trans-regulators with eis se-
quences located in the vicinity of the gene. Late genes are probably engaged
in cell-heritable, repressive chromatin complexes early in development, and
remain so in all cell lineages save those requiring their expression. Activa-
tion of the large set of genes utilized very early in embryogenesis may be
mediated by factors present in egg cytoplasm, and in some organisms these
genes may also be premarked during gametogenesis for expression in the
early embryo.
Chapter II: The Nature and Function of Maternal Transcripts
RNAs synthesized during oogenesis support all or most of the biosyn-
thetic activities carried out in early embryos. The utilization of these tran-
scripts is triggered by maturation or fertilization, and they persist until re-
placed by zygotic transcripts emanating from the blastomere nuclei.
Maternal transcripts include messenger RNAs, ribosomal RNAs, various
low molecular weight RNAs, and a prominent class of large nontranslatable
poly (A) RNA molecules, the significance of which is yet unknown. The
complexity of genomic information represented in the maternal RNA is high,
relative to that expressed in many somatic cells, and is almost the same in
the eggs of many different species, irrespective of genome size. The extent
of dependence on maternal transcripts both in real and in developmental
time varies according to species, and to the particular genes considered. A
number of instructive examples of such genes have now been cloned and the
disposition of their transcripts quantitatively characterized. The develop-
mental functions for which maternal mRNAs code are illuminated by ge-
netic, molecular, and cytological evidence. Among these functions are the
provision of specific embryo nucleoproteins, cytoskeletal proteins, cell sur-
face proteins, and enzymes. Maternal transcripts may also code for regula-
tory proteins that affect blastomere lineage fate.
Chapter III: Transcription in the Embryo and Transfer of Control
to the Zygotic Genomes
The genomes of early embryos characteristically express a set of se-
quences that are largely the same as those transcribed during oogenesis. The
2. Synopsis of Major Themes 5
pattern of transcription changes as some new genomic sequences are acti-
vated and some genes expressed early are repressed. The level of expression
of any given gene that is utilized in early development, i.e., the quantity of
cytoplasmic message of that species, is given by the amount of surviving
maternal transcript, the rate of flow into the cytoplasmic compartments of
newly synthesized embryo transcripts, and their rate of turnover, which in
the embryo varies sharply among different mRNA species. The stage of
development at which newly synthesized embryonic gene products become
dominant with respect to maternal transcripts varies according to the organ-
ism, and when closely examined this crucial switch occurs at different times
for each individual gene or functionally related set of genes. The major
embryonic transcript class is high complexity nuclear RNA (nRNA), >90%
of which never accumulates outside the nuclear compartment. Measure-
ments of the kinetics of nRNA biosynthesis and decay, and of nRNA popula-
tion complexities, show that when considered with respect to genome size
the numbers of nRNA species transcribed, the synthesis rates, the turnover
rates, and the fractions of nRNA exported as processed message are very
similar in sea urchin, Drosophila, and Xenopus embryos. Over 104 transcrip-
tion units appear to be utilized in sea urchin embryos. Thus early develop-
ment requires an enormous amount of genomic information, as well as a
complex regulatory apparatus to direct its expression. Ribosomal RNA
genes are highly repressed in invertebrate and lower vertebrate embryos that
develop as closed systems, i.e., without net growth, but they function ac-
tively from early cleavage onward in mammalian embryos. Many specific
genes, the expression of which is not restricted to given cell types, are in the
early embryo subject to ontogenic programs of control, while later, after an
adult nucleus-to-cytoplasm ratio is attained, they are controlled in response
to physiological cues. The best known are the histone genes, particularly in
the sea urchin, where separate sets of genes code for the histones utilized at
a high rate early in development. Additional examples are afforded by other
genes that in adult cells are under cell cycle regulation, e.g., those coding for
ribosomal proteins; and by environmental response genes known to be ac-
tive in some embryos, e.g., metallothionein and heat shock genes.
Chapter IV: Differential Gene Function in the Embryo
Biochemical and cytological evidence indicates that after an initial phase
of cell division there occurs the onset of active differentiation in particular
regions of the early embryo. By differentiation is meant the imposition of
specialized programs of cytoplasmic biosynthesis directed by zygotic
mRNAs. The biological and molecular processes leading to the appearance
of differentiated cells in Caenorhabditis, sea urchin, Xenopus, and Drosoph-
ila embryos are considered in some detail. In C. elegans cell lineage is
largely invariant, and with a few exceptions the fate of each cell is deter-