BIO 185: Topics in Biology – Fall 2003
Developmental Biology – Outline for Section 2
In the following sections we will begin our study of developmental biology in earnest. We will
first investigate the very early stages of development, those that give us the most basic organization of
the embryo. This organization includes the differentiation of cells into embryo and non-embryonic
components, the three layers of the gastrula stage embryo that govern all future cell differentiation, and
the formation of directional axes in the embryo – what will be front and rear, what will be top and
bottom. Cell fates and embryo organization through this developmental point are amazingly similar
across a wide variety of species. A wise man once told me, “The most important event to occur in your
entire life was gastrulation.” Consider yourselves wonders of nature, baby – it is truly amazing that any
of us have got this far!
II. Early Development: Early development is the critical period that determines the fate of most
conceived embryos. A remarkably high percentage of fertilized eggs in mammals (particularly those of
humans) do not produce viable offspring. The main reason for this is that extended development of misformed embryos is too taxing an energy demand on the mother. In most cases, these embryos are reabsorbed
and their components reused as soon as the “fatal flaw” is detected. Some flaws escape detection due to their
late onset or their low impact in the developing embryo, and because the mother provides much of the
essential metabolism of the early embryo. Thus, inborn errors of metabolism are the most prevalent genetic
disorders found in infants. It is easy to theorize why the reliance on large numbers of offspring for species
survival tends toward simpler organisms – not those as complicated as ourselves.
The “Big Idea” of cell
differentiation is that a given cell’s fate choices are determined by its current position in the embryo, the
soluble and insoluble environments around it, and the history of its predecessors that got it to that point. The
restriction of a cell’s choices is an event called commitment. It has been shown experimentally that this
happens in two stages. Specification is a reversible ability to differentiate down the committed path even if
taken out of the embryo and put in a “neutral” environment. Determination is an irreversible ability to
complete differentiation even when placed in a “non-neutral” area of the embryo.
A. Differentiation, Commitment, Specification and Determination:
1. Receptor Summation, Morphogens and Morphogenetic Fields (p. 63)
a. Think of all cells on the neuronal model you’ve already learned – summation of inputs.
b. Cell fate is largely determined by immediate neighbors and matrix molecules.
c. Soluble morphogen gradients add to the summed signals a cell receives.
d. Cells in a given region tend to commit to related fates.
2. Autonomous Specification (p. 56)
a. Mostly invertebrates.
b. The cells of the earliest divisions have restricted fates based on cytosolic restrictions.
c. A cell killed at the 4- or 8-cell stage will cost the embryo all of its descendents.
3. Conditional Specification (p. 58)
a. Mostly true for all invertebrate cells. Invertebrates also use it.
b. Cells have restricted fates based on environmental restrictions.
c. A change in environment will produce a change in fate.
d. Advantage is that if a cell is lost, others can take its place.
4. Synctitial Specification (p. 69)
a. Mostly insects.
b. Multiple partial divisions produce a cell with many nuclei.
c. The cytosol is restricted into many subdomains.
d. In Drosophila, a bicoid (anterior) and nanos (posterior) double gradient contributes to cell
fates all along the egg cell prior to any separations of membranes.
5. Stem Cells and Commitment (p. 68)
a. Stem cell division produces one committed daughter and one stem cell.
b. Stem cells can have increasing levels of commitment – down to just a single cell type.
B. Mechanisms of Differential Gene Expression
1. As I mentioned before, the study of developmental biology is journey into the “Dominance of
Phenotype”. The genotype may determine the choice of traits but it is their expression that
dominates this field. So how do we get so many different kinds of cells, each with its different
complement of gene products expressed? This area of research gets a lot of attention!
2. Control of Gene Expression at the Level of mRNA Transcription (p. 107)
a. DNA Anatomy Governs Access by Transcription Machinery - “Expressibility”
1. Chromatin Structure – Half DNA, Half Protein by Weight.
a. Heterochromatin
b. Euchromatin
c. The “default-state” is inaccessible!
2. Gene Structure: Exons and Introns.
a. You already know the basics here – sequences that exit the nucleus (exons)
vs. those that remain inside (introns).
b. We’ll talk about what’s really true as time goes by…
3. Gene Structure: Untranslated Regions (UTRs), Promoters and Enhancers,
Transcription and Translation Start-Sites, TATA-boxes and Termination Sequences.
a. DNA sequences around a gene that do not themselves get expressed, but
dictate when and where that gene gets expressed.
b. 5’ and 3’ UTRs have lots of information in them.
c. The promoter is the direct control found in 3’ UTR
d. Enhancers can be anywhere – seem to like the first intron.
e. The other stuff…
b. Transcription Factors Determine Specificity
1. Basal Transcription Factors set up the transcriptional machine: RNA Polymerase.
a. It takes at least six proteins to get RNA polymerase to bind to DNA.
b. Transcription Factor IID binds the TATA-box
2. Tissue-Specific Transcription Factors
a. The real source of differentiation
3. Transcription Factor Cascades
a. Increasing expression of tissue-specific factors, driven by those expressed
previously, leads to a lock-down of phenotype.
4. Silencers Give Negative Regulation
a. Transcription inactivation – can be cis- or trans-acting
c. Methylation and Acetylation and Control of Transcription (p. 121)
1. Promoter Methylation Gives Stable Gene Inactivation
a. 5-methylcytosine in Vertebrates
b. Is This Why We Can’t Grow New Limbs?
2. Chromatin Methylation Gives Stable Cell Differentiation
a. The Methylation-Acetylation Switch
b. Protein Interactions with Methylated DNA
c. Methylation and Cloning
3. Insulators Keep Heavily Used Enhancers from Activating Other Genes
4. Compensation for X Chromosome Dosage in Males and Females
a. Male Flies Acetylate Their One X Chromosome
b. Female Mammals Methylate Their Second X Chromosome
c. Reactivation in Germ Cells Prior to Meiosis
d. Exceptions to Every Rule (the interested should read further)
3. Control of Expression at the Level of RNA Processing and Translation (p. 127)
a. RNA Processing in the Nucleus
1. The Basic Steps
a. Primary RNA transcripts are made into mRNA by removal of
their introns in the nucleus.
b. mRNA transcripts are then transported from the nucleus to the
ribosomal complexes in the cytosol through the nuclear pore.
2. Nuclear RNA Selection
a. More primary transcripts are made than are allowed to become
mRNA.
b. In one case, the exons go to the cytosol to be degraded while
the introns assist in nucleolus construction.
3. Differential mRNA Splicing
a. Different cells make different proteins out of the same transcript by splicing
in different exons (sometimes introns!).
b. Splice sites in the 5’ and 3’ end of introns can be recognized differently in
different cells.
c. Splicing isoforms are protein families made from one gene and can even
occur in the same cell at the same time.
d. One Drosophila gene has the theoretical ability to produce 38,016 proteins
– more than three times the total number of fly genes!
b. RNA and Protein Processing in the Cytosol
1. Differential mRNA Longevity
a. The length of the poly(A) tail determines longevity
b. Different transcript isoforms have different longevity
2. Selective inhibition of mRNA Translation
a. Stored maternal RNAs are found in the egg cytosol
b. 5’ caps and poly(A) tails
c. Amphibian maskin makes “inactive plasmids”
d. Protein inhibitors – smaug and nanos in Drosophila
e. Antisense RNAs – small regulatory RNAs
1. RNA regulation is an important emerging area of research!
3. Differential mRNA Localization
a. This is also a critical phenomenon in oocytes
b. RNAs are stored in different regions of the egg and end up in different
daughter cells because of it
4. Post-Translational Modification
a. Trafficking sequences that direct destination
b. The pre-pro-protein phenomenon
c. Subunit assembly
d. Co-factors
e. Acectylation, methylation, phosphorylation, etc.