21BTE418T - Developmental Biology

UNIT - I
 Introduction to Developmental Biology
• Between fertilization and birth, the developing organism is known as
an embryo.
– As an embryo, you had to build yourself from a single cell.
– You had to respire before you had lungs, digest before you had a gut, build
bones when you were pulpy, and form orderly arrays of neurons before you
knew how to think.
• Multicellular organisms do not spring forth fully formed. Rather, they
arise by relatively slow process of progressive change that we call
development.
– In nearly all cases, the development of a multicellular organism begins with a
single cell-the fertilized egg, or zygote, which divides mitotically to produce all
the cells of the body.
– The study of animal development has traditionally been called embryology,
after that phase of an organism that exists between fertilization and birth.
– Developmental biology is the discipline that studies embryonic and other
developmental processes.
 The Questions of Developmental Biology
• Aristotle, the first known embryologist said that wonder was the
source of knowledge and animal development
– This development, this formation of an orderly body from relatively
homogeneous material, provokes profound and fundamental questions that
Homo sapiens have asked since the dawn of self-awareness
– A geneticist might ask how globin genes are transmitted from one generation
to the next
– A physiologist might ask about the function of globin proteins in the body.
– But the developmental biologist asks how it is that the globin genes come to
be expressed only in red blood cells and how these genes become active only
at specific times in development.
• Development accomplishes two major objectives. First it generates
cellular diversity and order within the individual organism; second,
it ensures the continuity of life from one generation to the next.
• These questions can be subdivided into several categories of questions
scrutinized by developmental biologists:
– The question of differentiation How a single cell, the fertilized egg, gives
rise to hundreds of different cell types? muscle cells, epidermal cells,
neurons, lens cells, lymphocytes, blood cells, fat cells, and so on. This
generation of cellular diversity is called differentiation.
– The question of morphogenesis How can the cells in our body organize into
functional structures? Our fingers are always at the tips of our hands, never in
the middle; our eyes are always in our heads, not in our toes or gut. This
creation of ordered form is called morphogenesis, and it involves
coordinating cell growth, cell migration, and cell death.
– The question of growth If each cell in our face were to undergo just one more
cell division, we would be considered horribly malformed. Our arms are
generally the same size on both sides of the body. How is cell division so
tightly regulated?
– The question of reproduction The sperm and egg are highly specialized cells,
and only they can transmit the instructions for making an organism from one
generation to the next. How are these germ cells set apart, and what are the
instructions in the nucleus and cytoplasm that allow them to form the next
generation?
 – The question of regeneration Some organisms can regenerate every part of
their bodies. Some salamanders regenerate their eyes and their legs, while many
reptiles can regenerate their tails. There are some cells in our bodies-stem cells-
that are able to form new structures even in adults. How do stem cells retain
this capacity, and can we harness it to cure debilitating diseases?
– The question of environmental integration The development of many
(perhaps all) organisms is influenced by cues from the environment that
surrounds the embryo or larva. Certain chemicals in the environment can disrupt
normal development, causing malformations in the adult. How is the
development of an organism integrated into the larger context of its
habitat?
– The question of evolution Evolution involves inherited changes of
development. How do changes in development create new body forms?
Which heritable changes are possible, given the constraints imposed by the
necessity of the organism to survive as it develops?
• The questions asked by developmental biologists have become critical in
molecular biology, physiology, cel1 biology, genetics, anatomy, cancer
research, neurobiology, immunology, ecology, and evolutionary biology.
 The Cycle of Life
• Each animal whether earthworm or eagle, termite or beagle, passes through
similar stages of development: fertilization, cleavage, gastrulation,
organogenesis, birth, metamorphosis, and gametogenesis.
• The stages of development between fertilization and hatching (or birth) are
collectively called embryogenesis.
– Fertilization involves the fusion of the mature sex cells, the sperm and egg, which are
collectively called the gametes
– Cleavage is a series of extremely rapid mitotic divisions that immediately follow
fertilization. During cleavage, the enormous volume of zygote cytoplasm is divided into
numerous smaller cells called blastomeres. By the end of cleavage, the blastomeres have
usually formed a sphere, known as a blastula.
– The blastomeres undergo dramatic movements and change their positions relative to one
another. This series of extensive cell rearrangements is called gastrulation, and the
embryo is said to be in the gastrula stage. As a result of gastrulation, the embryo
contains three germ laryers (endoderm, ectoderm, and mesoderm) that will interact to
generate the organs of the body.
– Organogenesis: the cells interact with one another and rearrange themselves to produce
tissues and organs through the exchange of chemical signals between the cells of the
germ layers
– The organism needs to
undergo metamorphosis to
become a sexually mature
adult. In most animals, the
young organism is a called a
larva, and it may look
significantly different from
the adult.
– In many species, a group of
cells is set aside to produce
the next generation. These
cells are the precursors of
the gametes. The gametes
and their precursor cells are
collectively called germ
cells, and they are set aside
for reproductive function.
All other cells of the body
are called somatic cells. The
development of gametes,
called gametogenesis, is
usually not completed until
the organism has become
physically mature.
 Comparative Embryology
• In The Generation of Animals (ca. 350 BCE), Aristotle noted some of the variations
on the life cycle themes: some animals are born from eggs (oviparity, as in birds,
frogs, and most invertebrates); some by live birth (viviparity, as in placental
mammals); and some by producing an egg that hatches inside the body
(ovoviviparity, as in certain reptiles and sharks).
• Aristotle also identified the two major cell division patterns by which embryos are
formed: the holoblastic pattern of cleavage (in which the entire egg is divided into
successively smaller cells, as it is in frogs and mammals) and the meroblastic
pattern of cleavage (as in chicks, wherein only part of the egg is destined to become
the embryo while the other portion-the yolk-serves as nutrition for the embryo).
• After Aristotle, it was only in 1651 that William Harvey concluded that all animals
even mammals-originate from eggs. He was first to see the blastoderm of the chick
embryo, and he was the first to notice that "islands" of blood tissue form before the
heart does
• Marcello Malpighi published the first microscopic account of chick development
in 1672. Here, for the first time, the neural groove (precursor of the neural tube), the
muscle-forming somites, and the first circulation of the arteries and veins-to and
from the yolk-were identified.
Patterns of Cleavage
• The pattern of embryonic
cleavage peculiar to a
species is determined by
two major parameters: (1)
the amount and
distribution of yolk
protein within the
cytoplasm, which
determine where cleavage
can occur and the relative
sizes of the blastomeres;
and (2) factors in the egg
cytoplasm that influence
the angle of the mitotic
spindle and the timing of
its formation.
 Gastrulation: "The most
important time in your
life"
• Gastrulation is what
makes animals.
(Animals gastrulate;
plants and fungi do
not.)
• Gastrulation usually
proceeds by some
combination of several
types of movements
• These movements
involve the entire
embryo, and cell
migrations in one part
of the gastrulating
embryo must be
intimately coordinated • Although patterns of gastrulation vary enormously
with other movements throughout the animal kingdom, all of the patterns are
that are taking place different combinations of the five basic types of cell
simultaneously. movements-invagination, involution, ingression,
delamination, and epiboly
• In addition to establishing which cells will be in which germ layer, embryos must
develop three crucial axes that are the foundation of the body: the anterior-
posterior axis, the dorsal-ventral axis, and the right-left axis
• The anterior-posterior (AP or anteroposterior) axis is the line extending from head
to tail (or mouth to anus in those organisms thai lack a head and tail).
• The dorsal-ventral (DV or dorsoventral) axis is the line extending from back
(dorsum) to belly (ventrum).
• The right-left axis separates the two lateral sides of the body.
– Although humans (for example) may look symmetrical, recall that in most of us, the heart is in the
left half of the body, while the liver is on the right.
– Somehow the embryo knows that some organs belong on one side and other organs go on the other.
 Naming the parts: The primary germ layers and early organs
• The end of preformationism did not come until the 1820s, when a combination of
new staining techniques, improved microscopes, and institutional reforms in
German universities created a revolution in descriptive embryology.
• The work of Christian Pander, Heinrich Rathke, and Karl Ernst von Baer
transformed embryology into a specialized branch of science.
• Studying the chick embryo, Pander discovered that the embryo was organized into
germ layers
– The ectoderm generates the outer layer of the embryo. It produces the surface layer
(epidermis) of the skin and forms the brain and nervous system.
– The endoderm becomes the innermost layer of the embryo and produces the epithelium
of the digestive tube and its associated organs (including the lungs).
– The mesoderm becomes sandwiched between the ectoderm and endoderm. It generates
the blood, heart, kidney, gonads, bones, muscles, and connective tissues.
• Rathke followed the intricate development of the vertebrate skull, excretory
systems, and respiratory systems, showing that these became increasingly complex.
– Rathke was the first to identify the pharyngeal arches. He showed that these same
embryonic structures became gill supports in fish and the jaws and ears (among other
things) in mammals.
 The four principles of Karl Ernst von Baer
• Karl Ernst von Baer extended Pander's studies of the chick embryo. He recognized that
there is a common pattern to all vertebrate development-that each of the three germ
layers generally gives rise to the same organs, whether the organism is a fish, a frog, or a
chick.
• From his detailed study of chick development and his comparison of chick embryos with
the embryos of other vertebrates, von Baer derived four generalizations. Now often
referred to as "von Baer's laws," they are stated here with some vertebrate examples.
– The general features of a large group of animals appear earlier in development than do the
specialized features of a smaller group. Although each vertebrate group may start off with different
patterns of cleavage and gastrulation, they converge at a very similar structure when they begin
forming their neural tube.
– Less general characters develop from the more general, until finally the most specialized appear. All
vertebrates initially have the same type of skin. Only later does the skin develop fish scales,
reptilian scales, bird feathers, or the hair, claws, and nails of mammals.
– The embryo of a given species, instead of passing through the adult stages of lower animals, departs
more and more from them. For example, as seen in Figure 1.8, the pharyngeal arches start off the
same in all vertebrates. But the arch that becomes the jaw support in fish, becomes part of the skull
of reptiles and becomes part of the middle ear bones of mammals.
– Therefore, the early embryo of a higher animal is never like a lower animal, but only like its early
embryo. Human embryos never pass through a stage equivalent to an adult fish or bird. Rather,
human embryos initially share characteristics in common with fish and avian embryos. Later in
development, the mammalian and other embryos diverge, none of them passing through the stages of
the others.
 Keeping Track of Moving Cells: Fate Maps and Cell Lineages
• There are two major types of cells in the embryo: epithelial cells, which are tightly
connected to one another in sheets or tubes; and mesenchymal cells, which are
unconnected or loosely connected to one another and can operate as independent
units.
• Within these two types of arrangements, morphogenesis is brought about through a
limited repertoire of variations in cellular processes:
– Direction and number of cell divisions.
– Cell shape changes. Cell shape change is a critical feature of development‘ Changing the shapes of
epithelial cells often creates tubes out of sheets (as when the neural tube forms), and a shape change
from epithelial to mesenchymal is critical when individual cells migrate away from the epithelial
sheet (as when muscle cells are formed).
– Cell migration. Cells have to move in order to get to their appropriate locations. For e.g., The germ
cells have to migrate into the developing gonad
– Cell growth. Cells can change in size. This is most apparent in the germ cells: the sperm eliminates
most of its cytoplasm and becomes smaller
– Cell death. Death is a critical part of life. The embryonic cells that constitute the webbing between
our toes and fingers die before we are born. The orifices of our mouth, anus, and reproductive glands
all form through apoptosis-the programmed death of certain cells at particular times and places.
– Changes in the composition of the cell membrane or secreted products. Cell membranes and
secreted cell products influence the behavior of neighboring cells.
• Given such a dynamic situation, one of the most important programs of
descriptive embryology became the tracing of cell lineeages: following
individual cells to see what those cells become.
• In many organisms, resolution of individual cells is not possible, but one can
label groups of embryonic cells to see what that area becomes in the adult
organism. By bringing such studies together, one can construct a fate map.
 Evolutionary Embryology
• Charles Darwin's theory of evolution restructured comparative
embryology and gave it a new focus.
• After reading Johannes Müller's summary of von Baer's laws in 1842,
Darwin saw that embryonic resemblances would be a strong argument
in favor of the genetic connectedness of different animal groups.
"Community of embryonic structure reveals community of descent,"
he would conclude in on the origin of species in 1859.
• In the 1830s, for instance, J. V. Thompson demonstrated that larval
barnacles were almost identical to larval shrimp, and therefore he
(correctly) counted barnacles as arthropods rather than mollusks
(FIGURE l.17)
• One could emphasize common descent by pointing out embryonic
similarities between two or more groups of animals, or one could
emphasize the modifications to show how development has been
altered to produce structures that enable animals to adapt to particular
conditions.
 Embryonic homologies
• Homologous structures are those organs whose
underlying similarity arises from their being
derived from a common ancestral structure. For
example, the wing of a bird and the arm of a
human are homologous, both having evolved from
the forelimb bones of a common ancestor.
Moreover, their respective parts are homologous
• Anologous structures are those whose
similarity comes from their
performing a similar function rather
than their arising from a common
ancestor. For example, the wing of a
butterfly and the wing of a bird are
analogous; the two share a common
function (and thus both are called
wings), but the bird wing and insect
wing did not arise from a common
ancestral structure that became
modified through evolution into bird
wings and butterfly wings.
 Cell Specification: Mechanisms of Developmental
Patterning
• In 1883, one of America’s first embryologists, William Brooks, reflected on
"the greatest of all wonders of the material universe: the existence, in a
simple, unorganized egg, of a power to produce a definite adult animal.“
– Indeed, how to get from "a simple, unorganized egg" to an exquisitely ordered
body is the fundamental mystery of development.
• The concept of cell specification- how cells become specified to a
specific fate-and explore how cells of different organisms use
different “ mechanisms for determining cell fate.
Cell Differentiation
• The generation of specialized cell types is called differentiation, a process
during which a cell ceases to divide and develops specialized structural
elements and distinct functional properties.
• Differences in cellular biochemistry and function are preceded by a process that
commits the cell to a certain fate. During the course of commitment, the cell might
not look different from its nearest or most distant neighbors in the embryo and show
no visible signs of differentiation, but its developmental fate has become restricted.
Commitment
• The process of commitment can be divided into two stages.
• The first stage is specification. The fate of a cell or tissue is said to be
specified when it is capable of differentiating autonomously (i.e., by itself)
when placed in an environment that is neutral with respect to the
developmental pathway, such as in a petri dish or test tube.
– At the stage of specification, cell commitment is still labile (i.e., capable of being
altered). If a specified cell is transplanted to a population of differently specified
cells, the fate of the transplant will be altered by its interactions with its new
neighbors.
– It is not unlike many of you who may have entered your developmental biology
classroom interested in chemistry but after being exposed to the awesomeness
that is developmental biology, will be influenced to change your mind and
become a developmental biologist.
• The second stage of commitment is determination. A cell or tissue is said
to be determined when it is capable of differentiating autonomously even
when placed into another region of the embryo or a cluster of differently
specified cells in a petri dish.
– If a cell or tissue type is able to differentiate according to its specified fate even
under these circumstances, it is assumed that commitment is irreversible.
• During embryogenesis an undifferentiated cell matures
through specific stages that cumulatively commit it to a
specific fate: first specification, then determination, and
finally differentiation.
• During specification, there are three
major strategies that embryos can
exhibit: autonomous, conditional, and
syncytial.
 Autonomous Specification
• The blastomeres of the early embryo are apportioned a set of critical
determination factors within the egg cytoplasm.
– In other words, the egg cytoplasm is not homogeneous; rather, different regions
of the egg contain different morphogenetic determinants that will influence
the cell's development.
– These determinants are molecules- often transcription factors-that regulate
gene expression in a manner that directs the cell into a particular path of
development.
• In autonomous specification, the cell "knows" very early what it is
to become without interacting with other cells.
– For instance, even in the very early cleavage stages of the snail Patella,
blastomeres that are presumptive trochoblast cells can be isolated in a petri dish.
– There, they will develop into the same ciliated cell types that they would give
rise to in the embryo and with the same temporal precision
– This continued commitment to the trochoblast fate suggests that these particular
early blastomeres are already specified and determined to their fate.
 Conditional Specification
• Conditional specification is the process by which cells achieve
their respective fates by interacting with other cells.
• Here, what a cell becomes is specified by the array of interactions it
has with its neighbors, which may include cell-to-cell contacts
(juxtacrine factors), secreted signals (paracrine factors), or the
physical properties of its local environment (mechanical stress)
– For example, if cells from one region of a vertebrate blastula (e.g., frog,
zebrafish, chick, or mouse) whose fates have been mapped to give rise to the
dorsal region of the embryo are transplanted into the presumptive ventral region
of another embryo, the transplanted "donor" cells will change their fates and
differentiate into ventral cell types
– Moreover, the dorsal region of the donor embryo where cells were extracted
also ends up developing normally.
 Syncytial Specification
• Cytoplasm that contains many nuclei is called a syncytium and
the specification of presumptive cells within such a syncytium is
called syncytial specification.
– A notable example of an embryo that goes through a syncytial stage is found in
insects, as illustrated by the fruit fly, Drosophila melanogaster.
– During its early cleavage stages, nuclei divide through 13 cycles in the absence
of any cytoplasmic cleavage.
– This division creates an embryo of many nuclei contained within one shared
cytoplasm surrounded by one common plasma membrane.
– This embryo is called the syncytial blastoderm
– It is within the syncytial blastoderm that the identity of future cells is
established simultaneously across the entire embryo along the anterior-to-
posterior axis of the blastoderm.
– Therefore, identity is established without any membranes separating nuclei into
individual cells.
– Membranes do eventually form around each nucleus through a process called
cellularization, which occurs after mitotic cycle 13 just prior to gastrulation
Syncytia can be found
in many organisms,
from fungi to humans.
Examples are the
syncytium of the
nematode germ cells
(connected by
cytoplasmic bridges),
the multinucleated
skeletal muscle fiber,
and the giant cancer
cells derived from fused
immune cells.
 – A fascinating issue is how the cell fates-those cells determined to become
the head, thorax, abdomen, and tail-are specified before cellularization.
– Are there determination factors segregated to discrete locations in the
blastoderm to determine identity, as seen in autonomous specification?
– Or do nuclei in this syncytium obtain their identity from their position
relative to neighboring nuclei, akin to conditional specification?
– The answer to both these questions is yes
Opposing axial gradients define position
• The cytoplasm of the Drosophila egg is not uniform.
• Instead, it contains gradients of positional information that dictate cell fate
along the egg's anterior-posterior axis
• In the syncytial blastoderm, nuclei in the anterior part of the cell are
exposed to cytoplasmic determination factors that are not present in the
posterior part of the cell and vice versa.
• It is the interaction between nuclei and the differing amounts of
determination factors that specify cell fate.
• It is important that these gradients of determination factors are established
during maturation of the egg prior to fertilization.
• After fertilization, as nuclei undergo synchronous waves of division,
each nucleus becomes positioned at specific coordinates along the
anterior-posterior axis and experiences unique concentrations of
determination factors.
• How do the nuclei maintain a position within the syncytial
blastoderm?
– They do so through the action of their own cytoskeletal machinery: their
centrosome, affiliated microtubules, actin filaments, and interacting proteins.
– Specifically, when the nuclei are in between divisions (in interphase), each
nucleus radiates dynamic microtubule extensions organized by their centrosome
that establish an "orbit" and exert force on the orbits of other nuclei

• A hierarchy of genes (1) establish anterior-posterior polarity and (2) divide

the embryo into a specific chamber of segments each with different identity
• This hierarchy is initiated by maternal effect genes that produce mRNAs
localized to different regions of the egg
• These mRNAs encode transcriptional and translational regulatory proteins
that diffuse through the syncytial blastoderm and activate or repress the
expression of certain zygotic genes
• Keeping nuclear position stable during early development allows each
nucleus to be exposed to different amounts of the determination
factors distributed in gradients throughout the shared cytoplasmic
environment.
• A nucleus can interpret its position (whether to become part of the
anterior, midsection, or posterior part of the body) based on the
concentration of cytoplasmic determinants it experiences.
• Each nucleus thereby becomes genetically programmed toward a
particular identity.
• The determinants are transcription factors, proteins that bind DNA
and regulate gene transcription.
• The anterior-most portion of the Drosophila embryo produces a
transcription factor called Bicoid, with a concentration of both
mRNA and protein that is highest in the anterior region of the egg and
declines toward the posterior
– The Bicoid concentration gradient across the syncytium is the combined result
of diffusion with a mechanism of protein and mRNA degradation.
• In addition, the posterior-most portion of the egg forms a posterior-to-
anterior gradient of the transcription factor Caudal.
• Thus, the long axis of the Drosophila egg is spanned by opposing
gradients:
– Bicoid from the anterior and Caudal from the posterior (FIGURE 2.12D).
– Bicoid and Caudal are considered morphogens because they occur in a
concentration gradient and are capable of regulating different genes at different
threshold concentrations.
– As morphogens, Bicoid and Caudal proteins activate different sets of genes in
the syncytial nuclei.
– Those nuclei in regions containing high amounts of Bicoid and little Caudal are
instructed to activate the genes that produce the head.
– Nuclei in regions with slightly less Bicoid and a small amount of Caudal are
instructed to activate genes that generate the thorax.
– In regions with little or no Bicoid but plenty of Caudal, the activated genes form
abdominal structures
 A Rainbow of Cell Identities
• Is the designation of a "cell type" the most precise way of identifying a cell?
• To answer this question, we would have to be able to watch and analyze
individual cells in an embryo over time.
• Earlier, we discussed using fate mapping techniques, which enable the
marking of a single cell with something such as a dye that can be traced
through development to determine the cell's fate.
• A genetic approach to fate mapping has been developed to label cells
with a seeming rainbow of possible colors, which can be used to identify
each individual cell in a tissue or even a whole embryo.
– This method was named Brainbow because the initial study focused on
characterizing cells of the developing mouse brain.
– It can be applied to any organism, however, and has been called different
names, such as "Flybow" and "dBrainbow" for its use in Drosophila, "Rainbow"
and "Confetti" for its use in mouse , and "Zebrabow" for its use in zebrafish
– The Brainbow system triggers the expression of different combinations and
amounts of distinct fluorescent proteins
– Different cells are then distingulshable based on the hue of fluorescence created
by the different combinations of fluorescent proteins active in each cell.
– "Rainbow" system to label cells of the early cleavage stages of the mouse
embryo to address the following question
– Is the first lineage choice of becoming an embryonic cell or an extraembryonic
cell a random or a regulated process?
– They discovered that it is nonrandom
 Differential Gene Expression: Mechanisms of Cell
Differentiation
• Each somatic cell nucleus has the same chromosomes-and therefore the
same set of genes-as all other somatic cell nuclei. This fundamental concept
is known as genomic equivalence
– If every cell in the body contains the genes for hemoglobin and insulin, why are
Hb proteins made only in RBCs and insulin proteins only in certain pancreatic
cells?
• A consensus emerged in the 1960s that the answer lies in differential gene
expression. It is a process by which cells become different from one
another based upon the unique combination of genes that are active or
"expressed.“ There are three postulates of differential gene expression:
1. Every somatic cell nucleus of an organism contains the complete genome
established in the fertilized egg. In molecular terms, the DNAs of all differentiated
cells are identical.
2. The unused genes in differentiated cells are neither destroyed nor
mutated; they retain the potential for being expressed.
3. Only a small percentage of the genome is expressed in each cell, and a
portion of the RNA synthesized in each cell is specific for that cell type.
• Gene expression can be regulated at four levels such that different cell types
synthesize different sets of proteins:
1. Differential gene transcription regulates which of the nuclear genes are
transcribed into nuclear RNA.
2. Selective nuclear RNA processing regulates which of the transcribed RNAs (or
which parts of such a nuclear RNA) are able to enter into the cytoplasm and
become messenger RNAs.
3. Selective messenger RNA translation regulates which of the mRNAs in the
cytoplasm are translated into proteins.
4. Differential protein modification regulates which proteins are allowed to
remain and/or function in the cell.
• The central dogma pertains to the sequence of events that enables the use and
transfer of information to make the proteins of a cell
– double-stranded DNA that provides the informative code or blueprints for the
precise combination of amino acids needed to build specific proteins.
– Proteins are not made directly from DNA, however; rather, the information laid out in
the sequence of DNA bases is first copied or transcribed into a single-stranded
polymer of similar molecules called a nuclear ribonucleic acid (nRNA).
– The process of copying DNA into RNA is called transcription and the RNA
produced from a given gene is often referred to as a transcript.
• The nRNA strand will undergo processing
to excise the noncoding domains and
protect the ends of the strand to yield a
messenger RNA (mRNA) molecule.
• mRNA is transported out of the nucleus
into the cytoplasm where it can interact
with a ribosome and convey its message
for the synthesis of a specific protein.
• mRNA unveils the complementary
sequence of DNA three bases at a time,
each triplet being called a codon.
• Each codon calls for a specific amino
acid that will be covalently attached to
its neighboring amino acid denoted by
the codon next in line.
• In this manner, translation leads to the
synthesis of a polypeptide chain that will
undergo protein folding and potential
modification by the addition of various
functional moieties such as
carbohydrates, phosphates, or cholesterol
groups.
• The completed protein is now ready to
carry out its specific function
 Evidence for Genomic
Equivalence
• The first demonstration that a nucleus from an adult
mammalian somatic cell could direct the
development of an entire animal didn't come until
1997, when Dolly the sheep was cloned
• Of the 434 sheep oocytes originally used in this
experiment, only one survived: Dolly
• Cloning of adult mammals has been confirmed in
guinea pigs, rabbits, rats, mice, dogs, cats, horses,
and cows.
• In 2003, a cloned mule became the first sterile animal
to be so reproduced
 Modulating Access to Genes
• A fundamental difference distinguishing most eukaryotic genes from prokaryotic
genes is that eukaryotic genes are contained within a complex of DNA and protein
called chromatin.
• The protein component constitutes about half the weight of chromatin and is
composed largely of histones.
• The nucleosome is the basic unit of chromatin structure
– It is composed of an octamer of histone proteins (two molecules each of histones H2A, H2B, H3,
and H4) wrapped with two loops containing approximately 147 base pairs of DNA
– There are more than a dozen contacts between the DNA and the histones, which function to enable
the remarkable packaging of more than 6 feet of DNA into the approximately 6 micrometer (in
diameter) nucleus of each human cell
– Much of the time, the nucleosomes appear to be wound into tight structures called solenoids that are
stabilized by histone H1
– Chromatin regions that are tightly packed are called heterochromatin, and regions loosely packed
are called euchromatin.
– In general, histone acetylation-the addition of negatively charged acetyl groups to histones-
neutralizes the basic charge of lysine and loosens the histones, which activates transcription.
Enzymes known as histone acetyltransferases place acetyl groups on histones (especially on
lysines in H3 and H4), destabilizing the nucleosomes so that they come apart easily (become more
euchromatic).
– As might be expected, then, enzymes that remove acetyl groups-histone deacetylases-stabilize the
nucleosomes (which become more heterochromatic) and prevent transcription.
• Histone
methylation is
the addition of
methyl groups to
histones by
enzymes called
histone
methyltransfera
rses.
• Although
histone
methylation
more often
results in
heterochromati
c states and
transcriptional
repression, it
can also activate
transcription
depending on the
amino acid being
methylated and
the presence of
other methyl or
acetyl groups in
the vicinity
 Anatomy of the Gene
• Now that we understand that modifying histones can grant access to regions of the
genome, we can ask, what mechanisms exist to influence gene transcription
more directly?
• More simply, once a gene is accessible, how can it be turned on and off?
– Eukaryotic genes are not co-linear with their peptide products. Rather, the single nucleic acid strand
of eukaryotic mRNA comes from noncontiguous regions on the chromosome.
– Exons are the regions of DNA that code for parts of a protein; between exons, however, are
intervening sequences called introns that have nothing whatsoever to do with the amino acid
sequence of the protein.
– The gene, which encodes part of the hemoglobin protein of the red blood cells, consists of the
following elements:
• A promoter region, where RNA polymerase II binds to initiate transcription. The promoter region of the
human β-globin gene has three distinct units and extends from 95 to 26 base pairs before ("upstream
from") the transcription initiation site. Some promoters have the DNA sequence TATA (called the "TATA-
box"), which binds the basal or general transcription factor (TATA-binding protein, TBP) that helps
anchor RNA polymerase II to the promoter.
• The transcription initiation site, which for human β-globin is ACATTTG. This site is often called the
cap sequence because it is the DNA sequence that will code for the addition of a modified nucleotide
"cap" at the 5' end of the RNA soon after it is transcribed. The specific cap sequence varies among genes.
This cap sequence begins the first exon.
• The 5' untranslated region (5' UTR), also called the leader sequence. In the human β-globin
gene, it is the sequence of 50 base pairs intervening between the initiation points of transcription
and translation. The 5' UTR can determine the rate at which translation is initiated.
• The translation initiation site, ATG. This codon (which becomes AUG in mRNA) is located 50
base pairs after the transcription initiation site in the human β-globin gene (this distance differs
greatly among different genes). The ATG translation start sequence is the same in every gene.
• The protein-encoding portion of the first exon, which contains 90 base pairs coding for amino
acids 1-30 of human β-globin protein.
• An intron containing 130 base pairs with no coding sequences for β-globin. The structure of this
intron, however, is important in enabling the RNA to be processed into mRNA and exit from the
nucleus.
• An exon containing 222 base pairs coding for amino acids 31-104.
• A large intron-850 base pairs-having nothing to do with β-globin protein structure.
• An exon containing 126 base pairs coding for amino acids 105-146 of the protein.
• A translation termination codon, TAA. This codon becomes UAA in the mRNA. When a
ribosome encounters this codon, the ribosome dissociates, and the protein is released. Translation
termination can also be represented by the TAG or TGA codon sequences in other genes.
• A 3' untranslated region (3'UTR) that although transcribed, is not translated into protein. This
region includes the sequence AATAAA, which is needed for polyadenylation, the insertion of a
"tail" of some 200-300 adenylate residues on the RNA transcript, about 20 bases downstream of
the AAUAAA sequence. This polyA tall (1) confers stability on the mRNA" (2) allows the mRNA to
exit the nucleus, and (3) permits the mRNA to be translated into protein.
• A transcription termination sequence. Transcription continues beyond the AATAAA site for
about 1000 nucleotides before being terminated.
• The original transcription product is called nuclear RNA (nRNA) or,
sometimes, heterogeneous nuclear RNA (hnRNA) or pre-messenger RNA
(pre-mRNA).
– Nuclear RNA contains the cap sequence, the 5' UTR exons, introns, and the 3'UTR.
– Both ends of these transcripts are modified before these RNAs leave the nucleus.
– A cap consisting of methylated guanosine is placed on the 5' end of the RNA in
opposite polarity to the RNA itself which means that there is no free 5' phosphate group
on the nRNA.
– The 5' cap is necessary for the binding of mRNA to the ribosome and for subsequent
translation
– The 3' terminus is usually modified in the nucleus by the addition of a polyA tail.
The adenylate residues in this tail are added to the transcript enzymatically; they are
not part of the gene sequence.
• Both the 5' and 3' modifications may protect the mRNA from exonucleases that would
otherwise digest it
• The modifications thus stabilize the message and its precursor.
– Before the nRNA leaves the nucleus, its introns are removed and the remaining
exons spliced together.
– In this way, the coding regions of the mRNA-that is, the exons-are brought together to
form a single uninterrupted transcript, and this transcript is translated into a
protein. The protein can be further modified to make it functional
Cis regulatory elements: The on, off, and dimmer switches
of a gene
• In addition to the protein-encoding region of the gene, regulatory
sequences can be located on either end of the gene (or even
within it).
– These regulatory sequences-the promoter, enhancers, and silencers-are
necessary for controlling where, when, and how actively a particular gene
is transcribed.
– When located on the same chromosome as the gene (and they usually are),
they can be referred to as cis-regulatory elements
– Most of these promoters contain a stretch of about 1000 base pairs that is
rich in the sequence CG, often referred to as CpG (a C and a G connected
through the normal phosphate bond). These regions are called CpG
islands).
– The reason transcription is initiated near CpG islands is thought to involve
proteins called basal transcription factors, which are present in every cell
and specifically bind to the CpG-rich sites.
– These basal transcription factor proteins form a "saddle" that can recruit
RNA polymerase II and position it appropriately for the polymerase to
begin transcription
• RNA polymerase II does not bind to every promoter in the genome at the same
time, however. Rather, it is recruited to and stabilized on the promoters by DNA
sequences called enhancers that signal where and when a promoter can be used and
how much gene product to make.
– In other words, enhancers control the efficiency and rate of transcription from a
specific promoter.
• In contrast, DNA sequences called silencers can prevent promoter use and inhibit
gene transcription.
• Transcription factors are proteins that bind DNA with precise sequence
recognition for specific promoters, enhancers, or silencers.
– Transcription factors that bind enhancers can activate a gene by (1) recruiting
enzymes (such as histone acetyltransferases) that break up the nucleosomes in the
area or 2) stabilizing the transcription initiation complex as described above.
• In many genes, a bridge between enhancer and promoter is made by a large,
multimeric complex called the Mediator, whose nearly 30 protein subunits connect
RNA polymerase II to enhancer regions that relay developmental signals.
– This bridge forms the pre-initiation complex at the promoter.
• The boundaries of gene expression appear to be set by DNA sequences called
insulators. Insulator sequences limit the range in which an enhancer can activate
gene expression. They thereby "insulate" a promoter from being activated by
another gene's enhancers.
• Transcription factors have three major domains:
– The first is a DNA-binding domain that recognizes a particular DNA sequence
in the enhancer.
– The second domain is a trans-activating domain that activates or suppresses
the transcription of the gene whose promoter or enhancer it has bound
– Finally, there is usually a protein-protein interaction domain that allows the
trancriptlon factor's activity to be modulated by transcription-associated factors
or other transcription factors.
 Mechanisms of Differential Gene Transcription
• Differentiated proteins from high and low CpG-content
promoters
– There are two general classes of promoters that use different methods for
controlling transcription.
– These Promoter types are catalogued as having either a relatively high or a
relatively low number of CpG sequences at which DNA methylation can occur.
• High CpG-content promoters (HCPs) are usually found in "developmental
control genes," where they regulate synthesis of the transcription factors and other
developmental regulatory proteins used in the construction of the organism. The
default state of these promoters is "on," and they have to be actively repressed
by histone methylation.
• Low CpG-content promoters (LCPs) are usually found in those genes whose
products characterize mature cells (e.g., the globins of red blood cells, the
hormones of pancreatic cells, and the enzymes that carry out the normal
maintenance functions of the cell). The default state of these promoters is "off,"
but they can be activated by transcription factors. The nucleosomes on these
promoters have relatively few modified histones in the repressed state. Rather, their
CpG sites on the DNA are usually methylated, and this methylation is critical for
preventing transcription. When the DNA becomes unmethyiated, the histones
become modified with H3K4me3 and disperse so that RNA polymerase II can bind.
 Differential RNA Processing
• The regulation of gene expression is not confined to the differential
transcription of DNA. Even if a particular RNA transcript is
synthesized, there is no guarantee that it will create a functional
protein in the cell.
• To become an active protein, the nuclear RNA must be
– (1) processed into messenger RNA by the removal of introns,
– (2) translocated from the nucleus to the cytoplasm, and
– (3) translated by the protein-synthesizing apparatus.
– In some cases, even the newly synthesized protein is not in its mature form and
must be (4) posttranslationally modified to become active. Regulation during
development can occur at any of these steps.

• Differential RNA processing is the splicing of mRNA precursors into

messages that specify different proteins by using different
combinations of potential exons.
– If an mRNA precursor had five potential exons,
one cell type might use exons 1, 2, 4, and 5; a
different cell type might use exons 1, 2, and 3;
and yet another cell type might use all five.
– Thus, a single gene can produce an entire family
of proteins.
– The different proteins encoded by the same gene
 Control of Gene Expression at the level of
Translation
• The splicing of nuclear RNA is intimately connected with its export
through the nuclear pores and into the cytoplasm.
– As the introns are removed, specific proteins bind to the spliceosome and attach
the spliceosome-RNA complex to nuclear pores
– The proteins coating the 5' and 3' ends of the RNA also change. The nuclear cap
binding protein at the 5' end is replaced by eukaryotic translation initiation
factor eIF4E, and the polyA tail becomes bound by the cytoplasmic polyA
binding protein.
– Although both of these changes facilitate the initiation of translation, there is no
guarantee that the RNA will be translated once it reaches the cytoplasm.
– The control of gene expression at the level of translation can occur by many
means; some of the most important of them are described below.
– Differential mRNA longevity
– Stored oocyte mRNAs: Selective inhibition of mRNA translation
– Ribosomal selectivity: Selective activation of mRNA translation
– microRNAs: Specific regulation of mRNA translation and transcription
– Control of RNA expression by cytoplasmic localization
 Posttranslational Regulation of Gene Expression
• The story is not over when a protein is synthesized. Once a protein is
made, it becomes part of a larger level of organization.
– It may become part of the structural framework of the cell, for instance, or it
may become involved in one of the many enzymatic pathways for the
synthesis or breakdown of cellular metabolites.
– In any case, the individual protein is now part of a complex "ecosystem" that
integrates it into a relationship with numerous other proteins.
– Several changes can still take place that determine whether or not the
protein will be active.
– Some newly synthesized proteins remain inactive until certain inhibitory
sections are cleaved away. That is what happens when insulin is made from its
larger protein precursor.
– Some proteins must be "addressed" to their specific intracellular
destinations to function.
– Proteins are often sequestered in certain regions of the cell, such as
membranes, lysosomes, nuclei, or mitochondria.
– Some proteins need to assemble with other proteins to form a functional
unit.
• Differential gene expression is more like interpreting a
musical score than decoding a code script.
– lt is a stochastic phenomenon in which there are numerous
events that have to take place, each having numerous
interactions between component parts.
• A variety of molecular tools have enabled the study of
differentially expressed genes, such as
– in situ hybridization for gene expression,
– ChIP/Seq to identify regulatory regions of the DNA that proteins
bind to, and
– Gene knockdown (RNA interference) and knockout (CRISPR/
Cas9) to test gene function.
 Cell-to-Cell communication: Mechanisms of
Morphogenesis
• Development is more than just differentiation.
– The different cell types of an organism do not exist as random arrangements.
Rather, they form organized structures such as limbs and hearts.
– Moreover, the types of cells that constitute our fingers-bone, cartilage, neurons,
blood cells, and others-are the same cell types that make up our pelvis and legs.
• Somehow, the cells must be ordered to create different shapes and
make different connections. This construction of organized form is
called morphogenesis
• The twelfth-century rabbi and physician Maimonides framed the
question of morphogenesis beautifully when he noted that the pious
men of his day (around 1190 CE) believed that an angel of God had to
enter the womb to form the organs of the embryo.
• The problem addressed today is the secular version of Maimonides'
question: How can matter alone construct itself into the organized
tissues of the embryo?
• E. E. Just (1939) and Johannes Holtfreter (Townes and Holtfreter
1955) predicted that embryonic cells could have differences in their
cell membrane components that would enable the formation of
organs.
• The cells of an embryo are either epithelial or mesenchymal.
– Epithelial cells adhere to one another and can form sheets and tubes, whereas
mesenchymal cells often migrate individually and form extensive
extracellular matrices that can keep individual cells separate.
– An organ is formed from an epithelium and an underlying mesenchyme.
• There appears to be only a few processes through which cells create
structured organs, and all these processes involve the cell surface.
• There are three behaviors requiring cell-to-cell communication via the
cell surface: cell adhesion, cell shape, and cell signaling.
 A Primer on Cell-to-Cell Communication
• An embryo at any stage is held together, organized, and formed by the
interactions that occur between cells.
• The interactions exhibited by cells define their methods of
communication.
– For communication to occur successfully between humans, there needs to be
some initial "voice" or signal from one person that is "heard" or received by the
other person, which results in a specific response (a change in mood, a hug, or
perhaps a sarcastic remark back), much like friends conversing.
– Molecular communication between cells is largely carried out through highly
diverse and specific protein-protein interactions, which have evolved to elicit an
array of cellular responses, from changes in gene transcription and glucose
metabolism to cell migration and cell death.
• In an embryo, communication between cells can occur across short
distances, such as between two neighboring cells in direct contact, called
juxtacrine signaling, or across long distances through the secretion of
proteins into the extracellular matrix, called paracrine signaling.
– Proteins that are secreted from a cell and designed to communicate a response in
another cell are generally referred to as signaling proteins (generally called
ligands), while the proteins within a membrane that function to bind either
other membrane-associated proteins or signaling proteins are called receptors.
– A receptor in the membrane of one cell that binds the same type of receptor
in another cell represents a homophilic binding. In contrast, heterophilic
binding occurs between different receptor types
• Binding to a receptor of any kind generally alters the shape, or
conformation, of the receptor.
– This conformational change on the outside of the cell affects the shape of the
receptor inside the cell, and this latter change can give the intracellular portion
of the receptor a new property.
– It now has the ability to activate the enzymatic reactions that constitute a signal
transduction pathway.
• Often the "signal" is relayed or "transduced" through successive
conformational changes in the molecules of the pathway, changes
orchestrated through the binding of phosphate groups or other small
molecules (cAMP, Ca2+) that eventually lead to cellular responses.
• Signal transduction pathways that culminate in activating gene
expression in the nucleus are typically slower than those that
enzymatically activate biochemical pathways or regulate cytoskeletal
proteins, thereby affecting physiological functions or movement,
respectively.
• These signal transduction pathways are fundamental to animal
development.
 Adhesion and Sorting: Juxtacrine Signaling and the
Physics of Morphogenesis
Differential cell affinity
• Townes and Holtfreter found that reaggregated cells become spatially
segregated
– Thus, when epidermal (ectodermal) and mesodermal cells are brought together in a
mixed aggregate, the epidermal cells move to the periphery of the aggregate, and the
mesodermal cells move to the inside (FIGURE 4.3).
• Importantly, the researchers found
that the final positions of the
reaggregated cells reflect their
respective positions in the
embryo.
– The reaggregated mesoderm migrates
centrally with respect to the epidermis,
adhering to the inner epidermal surface
(FIGURE 4.4A).
– The mesoderm also migrates centrally
with respect to the gut or endoderm
(FIGURE 4.4B).
– When the three germ layers are mixed
together, however, the endoderm
separates from the ectoderm and
mesoderm and is then enveloped by
them (FIGURE 4.4C).
• In the final configuration, the
ectoderm is on the periphery,
the endoderm is internal, and the
mesoderm lies in the region
between them.
 The thermodynamic model of cell interactions
• Cells, then, do not sort randomly, but they can actively move to create tissue
organization.
• What forces direct cell movement during morphogenesis?
• In 1964, Malcolm Steinberg proposed the differential adhesion hypothesis,
a model that sought to explain patterns of cell sorting based on
thermodynamic principles.
– Using cells derived from trypsinized embryonic tissues, Steinberg showed that certain
cell types migrate centrally when combined with some cell types, but. migrate
peripherally when combined with others
– In several meticulous experiments using numerous tissue types, researchers showed that
those cell types that had greater surface cohesion migrated centrally compared to
cells that had less surface tension
• The tissue surface tensions of the individual germ layers were precisely
those required for the sorting patterns observed both in vitro and in vivo.
FIGURE 4,5 Hierarchy of cell sorting of
decreasing surface tensions.
(A) Simple schematic demonstrating a
logic statement for the properties
of differential cell adhesion.
 Cadherins and cell adhesion
• Several classes of molecules can mediate cell
adhesion, but the major ceil adhesion molecules
appear to be the cadherins.
– Cadherins are calcium-dependent adhesion molecules.
– They are critical for establishing and maintaining
intercellular connections, and they appear to be crucial to the
spatial segregation of cell types and to the organization of
animal form.
– Cadherins are transmembrane proteins that interact with
other cadherins on adjacent cells. The cadherins are anchored
inside the cell by a complex of proteins called catenins
– Cadherin-catenin complex forms the classic adherens
junctions that help hold epithelial cells together.
• Cadherins perform several functions
– First, their external domains serve to adhere cells together.
– Second, cadherins link to and help assemble the actin
cytoskeleton, thereby providing the mechanical forces for
forming sheets and tubes.
– Third, cadherins can serve to initiate and transduce signals that
can lead to changes in a cell's gene expression.
Several major cadherin types have been
identified
• E-cadherin is expressed on all early
mammalian embryonic cells, even at the
zygote stage.
– In the zebrafish embryo, E-cadherin is
needed for the formation and migration
of the epiblast as a sheet of cells during
gastrulation
– E-cadherin is restricted to epithelial
tissues of embryos and adults.
• P-cadherin is found predominantly on
the placenta, where it helps the placenta
stick to the uterus.
• N-cadherin becomes highly expressed
on the cells of the developing central
nervous system
• R-cadherin is critical in retina formation
• A class of cadherins called protocadherins lacks the attachment to
the actin cytoskeleton through catenins.
– Expressing similar protocadherins is an important means of keeping migrating
epithelial cells together, and expressing dissimilar protocadherins is an
important way of separating tissues (as when the mesoderm forming the
notochord separates from the surrounding mesoderm that will form somites)

QUANTITY AND COHESION

• The ability of cells to sort themselves based on the amount of
cadherin expression.
– When these two groups of cells, each expressing a different amount of P-cadherin,
were mixed, the cells that expressed more P-cadherin had a higher surface
cohesion and migrated internally to the lower-expressing group of cells.

TYPE, TIMING, AND BORDER FORMATION

– N-cadherin appears in the mesenchymal cells of the developing chick leg just
before these cells condense and form nodules of cartilage (which are the
precursors of the limb skeleton).
– N-cadherin is not seen prior to condensation, nor is it seen afterward.
– R-cadherin and B-cadherin do not bind well to each other. When two
populations of cells expressing either R-cadherin or B-cadherin at equal levels
are mixed together, they sort out into two opposing mounds of cells with a
distinct border between them
– The formation of boundaries is a critical physical achievement necessary for
many morphogenetic events.

FIGURE 4.9 lmportance of the types of cadherin for correct

morphogenesis. (A) The type of cadherin expressed can
result in different sorting behaviors, as seen when cells
expressing R-cadherin (red stain) are mixed together with
an equal number of cells expressing B-cadherin (green
stain). The cells form two distinct mounds with one common
boundary of contact.
 The Extracellular Matrix as a Source of Developmental
Signals
• Cell-to-cell interactions do not happen in the absence of an environment;
rather, they occur in coordination with and often due to the environmental
conditions surrounding the cells.
• This environment is called the extracellular matrix, which is an insoluble
network consisting of macromolecules secreted by cells.
– These macromolecules form a region of noncellular material in the interstices between
the cells. Cell adhesion, cell migration, and the formation of epithelial sheets and tubes
all depend on the ability of cells to form attachments to extracellular matrices.
• Proteoglycans play critically important roles in the delivery of the
paracrine factors
– These large molecules consist of core proteins (such as syndecan) with covalently
attached glycosaminoglycan polysaccharide side chains. Two of the most widespread
proteoglycans are heparan sulfate and chondroitin sulfate.
• Fibronectin is a very large (460-kDa) glycoprotein dimer synthesized by
numerous cell types.
– One function of fibronectin is to serve as a general adhesive molecule, linking cells to
one another and to other substrates such as collagen and proteoglycans .
• Laminin (another large glycoprotein) and type IV collagen are major
components of a type of extracellular matrix called the basal lamina.
The basal lamina is characterized by closely knit sheets that underlie
epithelial tissue
– The adhesion of epithelial cells to laminin (on which they sit) is much greater
than the affinity of mesenchymal cells for fibronectin (to which they must bind
and release if they are to migrate). Like fibronectin, laminin plays a role in
assembling the extracellular matrix, promoting cell adhesion and growth,
changing cell shape, and permitting cell migration

Fibronectin links together migrating cells,

collagen, heparan sulfate, and other extracellular
matrix proteins. This scanning electron
micrograph shows the extracellular matrix at the
junction of the epithelial cells (above) and
mesenchymal cells (below). The epithelial cells
synthesize a tight, laminin-based basal lamina,
whereas the mesenchymal cells secrete a loose
reticular lamina made primarily of collagen. (A
courtesy of M, Marsden and D. W. DeSimone; B
courtesy of R. L. Trelsted.)
 lntegrins: Receptors for extracellular matrix molecules
• The ability of a cell to bind to adhesive glycoproteins such as laminin
or fibronectin depends on its expressing membrane receptors for the
cell-binding sites of these large molecules.
– The main fibronectin receptor was found to be an extremely large protein that
could bind fibronectin on the outside of the cell, span the membrane, and bind
cytoskeletal proteins on the inside of the cell
• This family of receptor proteins are called integrins because they
integrate the extracellular and intracellular scaffolds, allowing them to
work together
– On the extracellular side, integrins bind to the amino acid sequence
arginine-glycine-aspartate (RGD), found in several extracellular matrix
adhesive proteins, including fibronectin, vitronectin (found in the basal
lamina of the eye), and laminin.
– On the cytoplasmic side, integrins bind to talin and α-actinin, two
proteins that connect to actin microfilaments.
• This dual binding enables the cell to move by contracting the actin
microfilaments against the fixed extracellular matrix.
• The presence of bound integrin prevents
the activation of genes that promote
apoptosis, or programmed cell death
• When focal adhesions linking an
epithelial cell to its extracellular matrix
are broken, the caspase-dependent
apoptosis pathway is activated, and the
cell dies.
• Such "death-on-detachment“ is a
special type of apoptosis called anoikis,
and it appears to be a major weapon
against cancer
• Although the mechanisms by which
bound integrins inhibit apoptosis remain
controversial, the extracellular
matrix is obviously an important
source of signals that can be
transduced into the nucleus to
produce specific gene expression.
 The Epithelial-Mesenchymal Transition
• One important developmental phenomenon, the epithelial-mesenchymal
transition, or EMT, integrates all the processes we have discussed so far in
this chapter.
– EMT is an orderly series of events whereby epithelial cells are transformed
into mesenchymal cells.
– In this transition, a polarized stationary epithelial cell, which normally
interacts with basal lamina through its basal lamina, becomes a migratory
mesenchymal cell that can invade tissues and help form organs in new places
• Examples of developmental processes in which this transition is active
include
– (1) the formation of neural crest cells from the dorsal most region of the neural
tube;
– (2) the formation of mesoderm in chick embryos, wherein cells that had been
part of epithelial layer become mesodermal and migrate into the embryo; and
– (3) the formation of vertebrae precursor ce1ls from the somites, wherein these
cells detach from somite and migrate around the developing spinal cord.
• EMT is also important in adults, in whom it is needed for wound healing.
• The most critical adult form of EMT, however is seen in cancer metastasis,
 Cell Signaling
• As you know the experiences one has in early life greatly influence the type
of person one becomes as an adult in terms of personality, career choice, or
food preferences.
– Similarly, the experiences a cell has in its embryonic position influence the gene
regulatory network under which it develops.
• Therefore, the real question is, in a given location, what defines the
cell's experience?
lnduction and competence
• The development of the vertebrate eye is a classic example used to describe
the modus operandi of tissue organization via intercellular interactions.
– In the vertebrate eye, light is transmitted through the transparent corneal tissue and
focused by the lens tissue (the diameter of which is controlled by muscle tissue),
eventually impinging on the tissue of the neural retina.
– The precise arrangement of tissues in the eye cannot be disturbed without
impairing its function.
– Such coordination in the construction of organs is accomplished by one group of
cells changing the behavior of an adjacent set of cells, thereby causing them to
change their shape, mitotic rate, or cell fate.
• This kind of interaction at close range between two or more cells or tissues
of different histories and properties is called induction.

Defining Induction and Competence

• There are at least two components to every inductive interaction.
• The first component is the inducer, the tissue that produces a signal (or
signals) that changes the cellular behavior of the other tissue.
• Often this signal is a secreted protein called a paracrine factor. Paracrine
factors are proteins made by a cell or a group of cells that alter the behavior
or differentiation of adjacent cells.
– In contrast to endocrine factors (hormones), which travel through the blood and
exert their effects on cells and tissues far away, paracrine factors are secreted
into the extracellular space and influence their close neighbors.
• The second component, the responder, is the cell or tissue being induced.
– Cells of the responding tissue must have both a receptor protein for the
inducing factor and the ability to respond to the signal.
• The ability to respond to a specific inductive signal is called competence
Reciprocal induction
• Another feature of induction is the reciprocal
nature of many inductive interactions.
• To continue the above example, once the lens has
formed, it induces other tissues.
• One of these responding tissues is the optic vesicle
itself; thus, the inducer becomes the induced.
– Under the influence of factors secreted by the lens, the
optic vesicle becomes the optic cup, and the wall of the
optic cup differentiates into two layers: the pigmented
retina and the neural retina.
• Such interactions are called reciprocal inductions.
Instructive and Permissive Interactions
• Howard Holtzer (1968) distinguished two major modes of inductive
interaction.
• In instructive interaction, a signal from the inducing cell is necessary for
initiating new gene expression in the responding cell.
– Without the inducing cell, the responding cell is not capable of differentiating in
that particular way.
– For example, one instructive interaction is when a Xenopus optic vesicle
experimentally placed under a new region of head ectoderm causes that region
of the ectoderm to form a lens.
• The second type of inductive interaction is permissive interaction.
– Here, the responding tissue has already been specified and needs only an
environment that allows the expression of these traits.
– For instance, many tissues need an extracellular matrix to develop. The
extracellular matrix does not alter the type of cell that is produced, but it enables
what has already been determined to be expressed.
– A dramatic example of permissive interactions at work comes from the
regenerative medicine field, in which an extracellular matrix scaffold can
promote the differentiation and rebuilding of a beating heart
 Epithelial - mesenchymal interactions
• Some of the best-studied cases of induction involve the interactions
of sheets of epithelial cells with adjacent mesenchymal cells.
• All organs consist of an epithelium and an associated mesenchyme, so these
interactions are among the most important phenomena in nature.

Regional Specificity of Induction

• The first of these properties is the regional specificity of induction.
• Skin is composed of two main tissues: an outer epidermis (an epithelial
tissue derived from ectoderm) and a dermis (a mesenchymal tissue derived
from mesoderm).
 – The chick epidermis secretes proteins that signal the underlying dermal cells to
form condensations, and the condensed dermal mesenchyme responds by
secreting factors that cause the epidermis to form regionally specific cutaneous
structures
– These structures can be the broad feathers of the wing, the narrow feathers of
the thigh, or the scales and claws of the feet
• The dermal mesenchyme is responsible for the regional specificity of
induction in the competent epidermal epithelium.
Genetic Specificity of Induction
• The second property of epithelial-
mesenchymal interactions is the
genetic specificity of induction.
whereas the mesenchyme may
instruct the epithelium as to what
sets of genes to activate, the
responding epithelium can comply
with these instructions only so far as
its genome permits.
– This property was discovered
through experiments involving the
transplantation of tissues from one
species to another
• The mesenchymal cells instructed the
ectoderm to make a mouth, but the
ectoderm responded by making the
only kind of mouth it "knew" how to
make, no matter how inappropriate.
 Paracrine Factors: Inducer Molecules
• When membrane proteins on one cell surface interact with receptor proteins
on adjacent cell surfaces (as seen with cadherins), the event is called a
juxtacrine interaction (since the rnembranes are juxtaposed).
• When proteins synthesized by one cell can diffuse over small distances to
induce changes in neighboring cells, the event is called a paracrine
interaction.
– Paracrine factors are diffusible molecules that work in a range of about 15 cell
diameters, or about 40-200 m
• A specific type of paracrine interaction is the autocrine interaction.
– Autocrine interactions occur when the same cells that secrete the paracrine factors
also respond to them.
• Many paracrine factors can be grouped into one of four major families on
the basis of their structure:
1. The fibroblast growth factor (FGF) family
2. The Hedgehog family
3. The Wnt family
4. The TGF-β superfamily, encompassing the TGF-B family, the activin family, the
bone morphogenetic proteins (BMPs), the Nodal proteins, the Vg1 family, and several other
related proteins
Signal transduction cascades: The response to inducers
• Paracrine factors function by binding to a receptor that initiates a series of
enzymatic reactions within the cell.
– These enzymatic reactions have as their end point either the regulation of
transcription factors (such that different genes are expressed in the cells
reacting to these paracrine factors) and/or the regulation of the cytoskeleton
(such that the cells responding to the paracrine factors alter their shape or are
permitted to migrate).
• These pathways of responses to the paracrine factor often have several end
points and are called signal transduction cascades.
• The major signal transduction pathways all appear to be variations on a
common and rather elegant theme, exemplified in FIGURE 4.24.
– Each receptor spans the cell membrane and has an extracellular region, a
transmembrane region, and a cytoplasmic region.
– When a paracrine factor binds to its receptor's extracellular domain, the
paracrine factor induces a conformational change in the receptor's structure.
– This shape change is transmitted through the membrane and alters the shape of
the receptor's cytoplasmic domain, giving that domain the ability to activate
cytoplasmic proteins.
• Often such a conformational change
following the binding of a paracrine
factor confers enzymatic activity on
the domain, usually a kinase activity
that can use ATP to phosphorylate
specific tyrosine residues of
particular proteins.
• Thus, this type of receptor is often
called a receptor tyrosine kinase
(RTK).
– The active receptor can now catalyze
reactions that phosphorylate other
proteins, and this phosphorylation in
turn activates their latent activities.
– Eventually, the cascade of
phosphorylation activates a dormant
transcription factor or a set of
cytoskeletal proteins.
 Juxtacrine Signaling for Cell Identity
• In juxtacrine interactions, proteins from the inducing cell interact with
receptor proteins of adjacent responding cells without diffusing from
the cell producing it.
• Three of the most widely used families of juxtacrine factors are the Notch
proteins (which bind to a family of ligands exemplified by the Delta
protein); cell adhesion molecules such as cadherins; and the eph receptors
and their ephrin ligands.
• When an ephrin on one cell binds with the eph receptor on an adjacent cell,
signals are sent to each of the two cells
• These signals are often those of either attraction or repulsion, and ephrins
are often seen where cells are being told where to migrate or where
boundaries are forming.
• The ephrins and the eph receptors functioning in the formation of blood
vessels, neurons, and somites.