An introduction:

The fate of a cell describes what it will become in the course of normal
development. The fate of a particular cell can be discovered by labelling that cell and
observing what structures it becomes a part of. When the fate of all cells of an embryo
has been discovered, we can build a fate map, which is a diagram of that organism at an
early stage of development that indicates the fate of each cell or region at a later stage of
development.

The developmental potential, or potency, of a cell describes the range of different cell
types it CAN become. The zygote and its very early descendents are totipotent - these
cells have the potential to develop into a complete organism. Totipotency is common in
plants, but is uncommon in animals after the 2-4 cell stage. As development proceeds, the
developmental potential of individual cells decreases until their fate is determined.

The determination of different cell types (cell fates) involves progressive restrictions in
their developmental potentials. When a cell “chooses” a particular fate, it is said to be
determined, although it still "looks" just like its undetermined neighbors. Determination
implies a stable change - the fate of determined cells does not change.

Differentiation follows determination, as the cell elaborates a cell-specific developmental

program. gene expression that responds to signals or triggers; a means of gene regulation,
effects of certain hormones on protein biosynthesis.Differentiation results in the presence
of cell types that have clear-cut identities, such as muscle cells, nerve cells, and skin
cells.
Differentiation results from differential gene expression: The specific components of a
given cell provides its special characteristics. These components are either synthesized by
proteins, or are themselves proteins. By expressing different subsets of genes, two cells
contain different subsets of gene products (proteins). Differential gene expression is
responsible for the morphology of different cells. All cells within an organism have the
same DNA, but not all genes are expressed. An epithelial cell will express only genes
specific to skin, whereas a neuron will express genes necessary for its development.

How can we observe that cells from two tissues express different genes? There are two
blots: the Southern blot shows that tissues A and B both contain a particular gene.
However, the Northern blots shows that only tissue A contains RNA transcribed from
that particular gene.
Differential gene expression is not a result of differential loss of the genetic
material:

DNA, except in the case of the immune system. That is, genetic information is not lost as
cells become determined and begin to differentiate. Do All Cells Really Contain the
Same DNA?

Several lines of evidence support the proposal that all of the cells within a multicellular
organism contain the same genome. For instance, although you started as a single cell
with a half-genome from each parent, that single cell quickly divided and new cells began
to differentiate, or become different from each other. While this process of differentiation
established a wide variety of cell types (e.g., skin, liver, muscle, etc.), it was not
accompanied by any permanent loss of genetic material. This is demonstrated by the fact
that fully differentiated cell types are still capable, within the right environment, of giving
rise to an entire new animal.

Experiment on frog and then Dolly:

This capability was first shown by way of an experiment in which the nucleus of an adult
frog skin cell was transplanted into an enucleated donor embryo, eventually leading to the
development of a cloned adult frog . Later, the intact complete genome of a differentiated
cell was used in the cloning of the famous sheep Dolly (Figure 1), showing that in
mammals, genes are not lost during development, so they must therefore be regulated.

In fact, even the nuclei of adult cells contain ALL

of the information needed for the construction of an
entire organism, if provided with the proper
cytoplasmic components. The cloning of Dolly
from an adult cell is a major breakthrough, not only
because of potential biotechnological applications,
but because of the importance of this result for basic
science: the result is the most convincing evidence
for the theory of differential gene expression.

In order to clone Dolly, udder cells were removed

from a Finn Dorset ewe and starved for one week to
cause G0 arrest. Nuclei from arrested Finn Dorset udder cells were fused with enucleated
eggs from a Scottish Blackface ewe, and then stimulated to re-enter the cell cycle. After a
few rounds of cell division, the embryo was transplanted into a surrogate Scottish
Blackface mother. The sheep that was born was genetically identical to the Finn Dorset
ewe, which was the source of the nucleus.

Transplantation of imaginal discs in insects and the cloning of whole plants from
individual cells strengthens the conclusion that genetic information is not lost as cells
become determined and begin to differentiate.

While differentiation results in specific cell types, morphogenesis is the process whereby
the shape (morph) of the embryo is generated (genesis). Morphogenesis in both plants &
animals involves regulated patterns of cell division and cell elongation that leads to
changes in cell shape. Cell movement also plays a critical important role in animal
morphogenesis.

Today, researchers understand that the specialized, differentiated cell types of the adult
body contain a genome as complete as any embryo's. This fascinating
demonstration has led to the proposal that changes in gene expression, rather than
losses of genetic material, play a key role in guiding and maintaining cell
differentiation.
Cell-Extrinsic Regulation of Gene Expression and differentiation:

Gene expression is regulated by factors both extrinsic and intrinsic to the cell. Cell-
extrinsic factors that regulate expression include environmental cues, such as small
molecules, secreted proteins, temperature, and oxygen. These cues can originate from
other cells within the organism, or they can come from the organism's environment.
Within the organism, cells communicate with each other by sending and receiving
secreted proteins, also known as growth factors, morphogens, cytokines, or signaling
molecules. Receipt of these signaling molecules triggers intercellular signaling cascades
that ultimately cause semipermanent changes in transcription or expression of genes.
Such changes in gene expression can include turning genes completely on or off, or just
slightly tweaking the level of transcript produced. This process is thought to regulate a
vast number of cell behaviors, including cell fate decisions during embryogenesis, cell
function, and chemotaxis.

In addition, gene expression changes can lead to changes in an entire organism, such as
molting in insects. In Drosophila, for example, the molting process is regulated by levels
of a hormone called ecdysone. This hormone acts as a signal, triggering a cascade of
events and leading to changes in gene expression. Not surprisingly, the genes that are
expressed in response to ecdysone are also the genes that are involved in the molting
process. Thus, ecdysone acts on the organism level as a cell-extrinsic factor to bring
about physiologically meaningful changes in gene expression.

What is also interesting is that scientists can learn more about a physiological process like
metamorphosis by studying how gene expression patterns change over time. For
example, although researchers were aware that ecdysone results in a decrease of
transcription from some loci, such as those involved in the glycolytic pathway,
microarray data suggest that ecdysone-induced metamorphosis also downregulates genes
involved with fatty acid oxidation, amino acid metabolism, oxidative phosphorylation,
and other pathways. This suggests that there is a more global repression of metabolic
activity during molting (Figure 2). Specifically, during metamorphosis, the larval muscle
cells are degraded, and muscle-specific genes are downregulated (Figure 2B).
Simultaneously, the development of the nervous system begins, and the genes involved in
neuronal differentiation are induced (Figure 2C).
Figure 2: Microarray data collected at different times during metamorphosis reveals the
effects of the ecdysone pulse on many downstream genetic pathways.(A) Changes in
ecdysone levels affect the glycolytic pathway. Levels of a number of enzymes involved
in this pathway are decreased as a result of the ecdysone pulse; these enzymes are listed
in red next to the reactions they catalyze. (B) This array shows expression changes in
various structural and regulatory genes involved in muscle formation (myogenesis) in
response to the ecdysone pulse. (C) This array shows how the ecdysone pulse alters
expression of multiple genes involved in central nervous system restructuring, apoptosis,
and cellular differentiation during metamorphosis. In both of the microarrays, red means
that the gene was downregulated, while green means that the gene was upregulated.
Expression levels were measured at various points before and after pupal formation (PF).
(BPF = before pupal formation; APF = after pupal formation)
Cell-Intrinsic Regulation of Gene Expression and differentiation:

Although differentiation is not thought to occur by permanent loss of genetic material,

DNA can be modified in a way that affects gene expression. For instance, DNA and its
associated histone proteins (together known as chromatin) can be chemically modified by
a cell's own machinery. Chromatin modification can affect gene expression by changing
the accessibility of genes to transcription factors, in either a positive or a negative
manner. Two major classes of such chemical modifications include DNA methylation
and histone modification (methylation and/or acetylation). These changes are often
described as epigenetic because they do not act to alter the primary DNA sequence but
instead act at a level just above the DNA sequence. Although DNA methylation and
histone modification are not genetic, cells have mechanisms to copy this epigenetic
information during their division so that their daughter cells contain the same regulatory
data.

Figure 3: Epigenetic gene regulation

during mammalian
development.This figure depicts key
developmental events together with
global epigenetic modifications and
gene expression patterns. Very early
in development, DNA methylation is
erased. In addition, pluripotency-
associated genes begin to be
expressed, and developmental genes
are repressed by the PcG protein
system and H3K27 methylation.
During the differentiation of
pluripotent cells such as embryonic stem (ES) cells, pluripotency-associated genes are
repressed, potentially permanently, as a result of DNA methylation. At the same time,
developmental genes begin to be expressed, and there is an increase in H3K4
methylation. During the early development of primordial germ cells (PGCs), DNA
methylation and repressive histone modifications (such as H3K9 methylation) are also
erased. Pluripotency-associated genes are re-expressed during a time window that allows
embryonic germ cells to be derived in culture. Imprinted genes are demethylated during
this period, and developmental genes are expressed afterwards. Flexible histone marks
such as H3K27 methylation enable developmental genes to be silenced for a short time in
pluripotent cells. By contrast, DNA methylation enables the stable silencing of imprinted
genes, transposons, and some pluripotency-associated genes. Copyright 2007 Nature
Publishing Group, Reik, W., Stability and flexibility of epigenetic gene regulation in
mammalian development, Nature 447, 425–432
Changes in chromatin modification play an important role in regulating gene expression
during developmental cell-type specification as well. For example, chromatin-modifying
proteins play an essential role in muscle cell differentiation via interactions with key
muscle-promoting transcription factors MyoD and MEF. That is, these factors are
thought to help recruit chromatin modifying factors, such as histone acetyltransferases
and deacetylases. In so doing, MyoD and MEF alter access to their target sites upstream
of muscle differentiation genes. For instance, MyoD binds histone acetyltransferases
p300 and PCAF, and this activity is essential for muscle cell differentiation. This
example provides evidence for a link among chromatin modifications, transcription
factors, and, ultimately, cell-fate-specific changes in gene expression.

Chromatin modification can be stable over the life of an organism, thereby effectively
permanently influencing gene expression. However, that is not to say that chromatin
modification is irreversible. For instance, chromatin can become mismodified in certain
cancers suggesting that, although important, the change is not permanent. Moreover,
chromatin modifications are usually erased and reset during the production of gametes,
such that the adult program of intrinsic cues is replaced with a program more suited to
embryonic development.

In fact, embryonic cell types are known to contain a unique set of chromatin
modifications that are different from those found in adult cell types. This has led to the
tantalizing proposal that chromatin modification helps lock in changes in gene expression
that are required during development. The permanent silencing of the genes involved
only in embryogenesis could then drive the development of cells toward more mature cell
types. By blocking accessibility of transcription machinery, for example, chromatin
modification could prevent the need for continued repression through active binding of a
repressive transcription factor. Alternatively, the genes required for an adult cell type
might contain chromatin modifications (especially histone acetylation) that cause the
DNA to become open and, therefore, more accessible to the transcription machinery.

Interestingly, embryonic cell types have been found to contain a signature chromatin
modification in the regions that regulate the expression of genes involved in early
embryonic development.Such regions were found to contain chromatin modifications
with both silencing and promoting characteristics. The finding of these bivalent (two-
directional) markers in association with genes important for embryonic development has
led to the belief that embryonic cells exist in a special epigenetic state, wherein they can
choose to remain embryonic (as in an embryonic stem cell) or to differentiate (as in
normal development), and bivalent domains provide a means by which to quickly choose
between the two options.

In Short:

Together, these lines of evidence have led to an emerging hypothesis that cell-cell
signaling and epigenetic changes converge to guide cell differentiation(differential gene
expression) decisions both during development and beyond.
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