In homeotic transformation, a normal body part is replaced by a body part which is regularly found in other regions.
| Example | Overview |
|---|---|
| Antennapedia | Antennapedia mutants of Drosophia have antennae replaced by legs. |
| Ultrabithorax | Ultrabithorax (Ubx) mutants of Drosophila have halteres (T3) replaced by wings (T2), imparting four total wings. |
| Invertebrate | Vertebrate |
| Nematode | Xenopus |
| Drosophila | Chicken |
| Sea Urchin | Zebrafish |
| Mouse |
Different model organisms are used to study development, chosen for their: length of embryonic development: length of life cycle; size of organism; ease of lab growth; size of genome; number of chromosomes; and experimental techniques available for that organism. Embryos that develop internally are difficult to see and manipulate, as they embed into the mother’s uterus. Large embryos are easier to directly manipulate (ie, tissue transplantation). Large adult organisms are space- and money-consuming versus smaller organisms, which can be easier to analyze and in large numbers.
| Organism | Pros | Cons | Tools | Notes |
| Drosophila | Small organisms. Large litters. Fast development External development |
Genetic screens. Other excellent tools. |
||
|---|---|---|---|---|
| Mouse | Mammal. | Internal development. Small litter. Relative large. |
Many excellent tools. | |
| Xenopus | Very large embryos. External development. |
Tetraploid. | Few genetic tools. | Genetic tools are being developed for diploid frog species. |
| Zebrafish | Vertebrate. Large embryos. External development. Many progeny. |
Excellent genetic tools. | ||
In Xenopus, the Nieuwkoop Center is the dorsal- and vegetal-most region. It gives rise to the Primary Organizer (aka Spemann Organizer or Spemann-Mangold Organizer), which is the region known as the dorsal lip of the blastopore (DLB). Spemann and Mangold’s experiments found that the DLB dorsalizes surrounding tissue, thus forming (along with the SEP) the dorsal-ventral axis. In addition to dorsalizing surrounding tissue, the Primary Organizer: fates overlying ectoderm as neural plate tissue; and is determined to be notochord tissue. Dorsalized tissue gives rise to somites and pronephric tubules.
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The DLB uses induction (interaction with adjacent cells) via secreted diffusible signals. A cell that can be induced is competent; embryonic tissues are only competent during gastrulation. The use of diffusible substances was proven when dorsal lip tissue and ectoderm were cultured together, but separated by a filter with a 0.5µm pore; the ectoderm was induced into neural tissue, despite no cell processes seen to pass through the filter. Dr. DeRobertis identified genes expressed only in the organizer via differential screening of Xenopus dorsal lips. Direct purification was ineffective because the hypersensitive ectoderm overlying the chordamesoderm was induced by even unnatural substances. Organizer-specific gene products are divided into two groups:
| Factor | Overview |
| Transcription | Three homeodomain proteins: Lim1, Gooseceoid and Xnot. Also, HNF3β. |
|---|---|
| Secreted | The noggin, follistatin, chordin and frzb gene products induce the neural plate by antagonizing the ventralizing and mesodermalizing properties of BMP-4 and Wnt-8. These genes can induce a second axis when their mRNA is injected into an early embryo. |

The primary organizer arises in the dorsal marginal zone via induction by the Nieuwkoop center. The Nieuwkoop center arises in the dorsal vegetal zone due to a gradient of nodal-related proteins (for frogs, Xenopus nodal-related or Xnr). The marginal zone involutes at the DLB during gastrulation to give rise to the mesoderm.
Notice that this figure (multi-cellular) differs from the one immediately above (single-cell) in that the dorsal-ventral axis is now horizontal.

The first signal (Veg1) is a vegetal-localized maternal mRNA that encodes a TGF-β. Injection of Veg1 mRNA rescues irradiated embryos, and at high levels induces dorsal mesoderm. VegT is another vegetal-localized Xenopus mRNA. VegT encodes a T domain protein required for endoderm formation and transcription of mesoderm-inducing signals. VegT-ablated embryos form mesoderm and ectoderm but not endoderm, and cannot induce animal caps to form mesoderm.
The second signal (β-catenin) differentiates the dorsal region from the ventral region at an early stage. β-catenin was identified when cortical rotation was noted to cause a high concentration of β-catenin to appear near the Nieuwkoop Center. When activated by Wnt signaling, β-catenin links E-cadherin to the actin cytoskeleton and is a transcription factor. As a result, the Nieuwkoop Center contains higher levels of Veg1, VegT and β-catenin to produce a signal inducing dorsal mesoderm.
Xenopus nodal related molecules (Xnr) are five TGF-β-like signals with overlapping and similar function. VegT and TCF/LEF (requiring β-catenin as a cofactor) overlap, establishing a Xnr gradient along the D/V axis. High [Xnr] induces dorsal mesoderm, while low [Xnr] induces ventral mesoderm. Ablating and increasing Xnr activity (using Cerberus, a head inducer and Xnr inhibitor) indicates that Xnr is necessary and sufficient for inducing dorsal and ventral mesoderm at the blastula stage.
The maternal mRNAs VegT and Veg1 are vegetal-localized. β-catenin accumulates dorsally via cortical rotation. This causes a perfect storm at the vegetal- and dorsal-most position of Veg1, VegT, TCR/LEF and the cofactor β-catenin. From this vegetal- and dorsal-most position arises a dorsal to ventral gradient of Xnr activity. The Xnr gradient is encoded by the zygotic genome. High [Xnr] induce dorsal mesoderm, and low [Xnr] induce ventral mesoderm.
The Spemann Organizer emits the third signal to dorsalize adjacent mesoderm. This signal consists of: Noggin, Chordin and Follistatin, which bind and inhibit the ventralizing growth factors BMP-4 and Frzb. Frzb antagonizes Wnt-8. Noggin was identified when injection of Noggin mRNA dorsalized and partially rescued irradiated embryos. Chordin and Frzb were identified during a differential screen for genes expressed only in the DLB. Injection of either Noggin or Chordin mRNA into a four cell stage embryo induces a second axis. The Spemann Organizer exclusively encodes transcriptional activators for BMP-4 and Wnt-8 antagonists, including: three homeobox genes, Goosecoid, Lim1 and Xnot; the fork head protein, HNF3-β.
This is similar to the the Drosophila Dpp (BMP-4 homolog) activity morphogen gradient, which is highest at the dorsal region and lowest at the ventral region where Sog (Chordin homolog) binds and inactivates Dpp to allow Dorsal protein expression. BMP-4 is a Dpp homolog and Chordin is a Sog homolog. These Xenopus genes can be interchanged with their Drosophila homologs. However, since the dorsal-ventral axis (as well as the heart location) was inverted in an ancestor of vertebrates, Dpp promotes dorsal formation in Drosophila and its homolog BMP-4 promotes ventral formation in Xenopus (accordingly, the opposite goes for Chordin and Sog). Wnt-8 is a homolog of Drosophila’s Wingless.
Methods to identify genes for early Xenopus embryo D/V and A/P patterning include: differential screening (aka subtractive hybridization) to identify genes expressed at specific times and places, as with the egg vegetal pole and early gastrula organizer tissue; testing Xenopus homologs of mammalian cell signaling genes for ability to induce mesoderm in isolated animal caps; and testing cloned mRNAs for ability, when injected, to induce a new axis. After identifying relevant genes, their role was assessed by injecting into the one- or two-cell embryo the corresponding mRNA, antisense DNA olignucloetides, RNAi or dominant negative or active DNA construct of the gene. After this injection, the embryo is examined whether it does or does not form an axis (dorsalize).
| Step | Overview |
| Step 1 | Niuewkoop found that marginal zone cells from an early blastula (before 64 cell stage) did not form mesoderm when isolated and cultured. However, marginal zone cells from a blastula after the 64 cell stage did form mesoderm. |
|---|---|
| Step 2 | Nieuwkoop removed the marginal zone and recombined dye-marked animal and vegetal caps. Dorsal mesoderm arose from animal cap cells nearest the vegetal cap, and from vegetal cells opposite the SEP. |
| Step 3 | Other biologists combined the animal cap with different vegetal blastomere cells. Dorsal vegetal blastomere cells induced dorsal mesoderm; ventral vegetal blastomere cells induced ventral mesoderm. Also, dorsal mesoderm induced ventral mesoderm to become lateral mesoderm. Thus, signaling must be involved in dorsal and central cell fates. |
| Step 4 | Gimlich and Gerhart found that fertilized eggs did not form a D/V axis when irradiated at the vegetal pole, but could be restored by a single dyed vegetal- and dorsal-most cell (though this cell was not itself dorsal mesoderm). Thus, this vegetal- and dorsal-most structure must induce other regions to become dorsal mesoderm. This vegetal-most and dorsal-most region first induces the primary organizer (which then induces other tissues) and was called the Nieuwkoop center. |
| Step 5 | To determine which part of the embryo acts to organize the mesoderm into dorsal structure and to induce neural tube formation, Spemann and Mangold transplanted the dorsal lip of the blastopore of an early gastrula from a light-colored newt into an early gastrula of a dark-colored newt. The donor tissue formed a second embryonic axis. The notochord of this second embronic axis was composed entirely of graft (donor) tissue, while the neural tube and somites were composed only partly of graft (donor) tissue and the kidney tubules and gut of the new axis were composed entirely of host tissue. Spemann and Mangold concluded that the graft tissue induced a new embryonic axis. This structure is named Primary organizer. |
| Factor | Overview |
|---|---|
| CDK | |
| Cyclin | |
| Cytoskeleton | Includes microtubules and microfibers. Microtubules inhibited by colchicine and nocodazole (inhibit chromosome segregation); and microfilaments inhibited by cytochalasin (inhibits cytokinesis). |
At the 8-cell stage, the mammalian embryo undergoes compaction where the spherical and loose blastomeres nestle tight together to establish new cell junctions and form a blastocyst. The blastocyst has an outer trophoblast layer (responsible for implantation into the uterine wall) and an inner cell mass placed eccentrically within the blastocoel. The inner cell mass gives rise to the embryonic epiblast (from which the embryo arises), the overlying amniotic ectoderm (separated from the epiblast by the amniotic cavity) and the underlying hypoblast. The mammalian blastocyst is analogous in structure to the yolky bird embryo, without the yolk.

Intrinsic (aka cytoplasmic) and extrinsic determinants coexist, as shown by two (respective) urchin blastula experiments. Removing the progenitor cell of mesoderm from an urchin blastula results in a mesoderm-lacking larva. However, sagittally halving an entire blastula will result in a normal larva. The phenom of extrinsic determinants is known as regulative development.

The end result of gastrulation is the transformation of the blastula, which consists of a ball or disc of relatively undifferentiated cells into an embryo that contains three germ layers.
The mode of gastrulation depends on the distribution of yolk, but all different types of gastrulation are related to each other in that they are different ways for cells on the outside to get inside (via different types of rearrangement and movement) to form the three germ layers. The cytoskeleton (microfilaments and microtubules) and extracellular matrix play a critical role in providing the motive force and the cues for gastrulation. The position at which gastrulation occurs is determined by local production of a signal that activates small GTPases like Rho, which reorganize the cytoskeleton locally.
During gastrulation, the blastula transforms and the cells begin to manifest their different fates. By the end of gastrulation, three different germ layers have formed: ectoderm (outer); mesoderm (middle); and endoderm (inside). Different cell types arise from these germ layers.
In invagination, the epithelium buckles inward like a finger poking into a soft ballon, thus forming an invagination. More technically, groups of contiguous epithelial cells actively constrict at their apical pole by contraction of the band of actin microfilaments located there. Thus, the epithelial sheet folds in forming a tubular (or vesicular) endoderm with its apical surface facing a lumen.
If invagination happens passively, for example in the wake of a neighboring population of cells that actively invaginates, it is called involution. This movement can also be seen in sea urchin embryos. Most morphogenetic movements in which cells withdraw from the surface to form inner tubular structures are achieved by a combination of invagination and involution.
In ingression, tight and adherens junctions are lost, epithelial cells become mesenchymal and this mesenchyme reforms a polarized epithelium. This occurs in higher vertebrates, including birds and mammals. Birds form a disc-shaped blastula whose cells migrate toward the midline when gastrulation begins. These cells pile up to form a visible structure called the primitive streak. The primitive streak ingresses inward; ingressed cells spread out laterally and reorganize into an epithelium (endoderm) that gradually spreads around the yolk.
Epithelia change in length and width by convergent extension and individual cells slide past each other. Cells that start out positioned beside each other in one row intercalate. Thereby, the shape of an epithelium that was wide and short before the convergent extension changes to narrow and long afterwards. More technically, a cell layer elongates in one axis via intercalation (interdigitation) of cells along a perpendicular axis. Two types of convergent extension are meso lateral intercalation and radial intercalation.
Cellular intercalation during convergent extension involves degradation and reformation of tight and adherens junctions. Many organisms, including amphibians like Xenopus, use convergent extension to convert the embryo from a sphere to an elongated rod more like the final shape of the mature organism.
Epiboly is the process in which the layer of cells spread out and expand to cover the yolk or yolk-filled cells (in fish and amphibians) at the vegetal pole. This spreading of the cells occurs through an increase in area due to a flattening of individual cells and an intercalation of cells.
| Endoderm | Epithelial lining of respiratory tract and GI tract. | ||||||
|---|---|---|---|---|---|---|---|
| Mesoderm |
There are dorsal/ventral differences in what the mesoderm gives rise to. This is induced by differences in dorsal and ventral endoderm. Organizer cells self-diffrentiate into dorsal mesoderm (notochord), organizer cells dorsalize adjacent mesoderm to for paraxial mesoderm (somites) and organizer cells secrete dorsalizing signals (noggin, chordin, nodal-related, etc) to induce the neural plate. The cardiovascular system, reproductive/excretory organs, connective tissues, vessels and skeleton. In mnemonic form: mesothelium (peritoneal, pleural, pericardial), muscle (striated, smooth, cardiac), spleen, soft tissues, serous linings, sarcoma, somite, osseous tissue, outer layer of suprarenal gland (cortex), ovaries, dura mater, dducts of genitalia, endothelium, renal (kidney), microglia, mesenchyme, male gonad (MMSSSSSOOODDERMMM). |
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| Ectoderm |
The surface of the ectoderm and its neural plate give rise to different tissues.
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Note that all three germ layers are derived from the epiblast. Furthermore, epithelium is derived from all three germ layers: endoderm (epithelial lining inside viscera); mesoderm (mesothelial lining outside of viscera); and ectoderm (skin epithelium).
| D/V Axis | The DLB dorsalizes surrounding tissue, thus forming (along with the SEP) the dorsal-ventral axis. In addition to dorsalizing surrounding tissue, the primary organizer: fates overlying ectoderm as neural plate tissue; and is determined to be notochord tissue. Dorsalized tissue gives rise to somites and pronephric tubules. |
|---|---|
| A/P Axis | By inducing neurectoderm, it makes ectodermal cells competent to receive patterning signals from the non-organizer mesoderm and thereby enable the formation of a complete and stable AP pattern along the trunk |
| Experiments Demonstrating Role | |
| 1 | Marginal zone cells do not form mesoderm when isolated and cultured until after the 64-cell stage. |
|---|---|
| 2 | Removing the marginal zone and recombining animal and vegetal caps, dorsal mesoderm arises from animal cap cells nearest the vegetal cap, and vegetal cells opposite the SEP. |
| 3 | Recombining animal caps with various vegetal blastomeres: dorsal vegetal blastomere cells induced dorsal mesoderm; ventral vegetal blastomere cells induced ventral mesoderm. Also, dorsal mesoderm induced ventral mesoderm to become lateral mesoderm. Thus, signaling must be involved in dorsal and central cell fates. |
| 4 | Fertilized eggs did not form a D/V axis when irradiated at the vegetal pole, but could be restored by a single vegetal- and dorsal-most cell. Thus, this vegetal- and dorsal-most structure must induce other regions to become dorsal mesoderm. This vegetal-most and dorsal-most region first induces the primary organizer (which then induces other tissues) and was called the Nieuwkoop center. |
| 5 | To determine which part of the embryo acts to organize the mesoderm into dorsal structure and to induce neural tube formation, the dorsal lip of the blastopore of an early gastrula from a light-colored newt was transplanted into an early gastrula of a dark-colored newt. The donor tissue formed a second embryonic axis. The notochord of this second embronic axis was composed entirely of graft (donor) tissue, while the neural tube and somites were composed only partly of graft (donor) tissue and the kidney tubules and gut of the new axis were composed entirely of host tissue. Spemann and Mangold concluded that the graft tissue induced a new embryonic axis. This structure is named Primary organizer. |
The Nieuwkoop Center is the dorsal- and vegetal-most cell of the early blastula. It gives rise to the Spemann Organizer, which is the dorsal lip of the blastopore. The Spemann Organizer has a dorsalizing effect, and together with the Sperm Entry Point (SEP) gives rise to the dorsal/ventral axis.
The first signals are the vegetal maternal mRNAs Veg1 and VegT. The second signal is the dorsal-most protein β-catenin, which accumulates via cortical rotation. This induces formation of the Spemann Organizer and the Nieuwkoop Center. The Spemann Organizer is responsible for the third signal by expressing Noggin, Chordin and Follistatin, which bind and inhibit the ventralizing factors BMP-4 and Frzb.
Drosophila Dpp is homologous to BMP-4. Dpp activity is highest at the dorsal region. Drosophila Sog is homologous to Chordin. [Sog] is highest at the ventral region, where it binds and inactivates Dpp. These Drosophila genes can be replaced by their Xenopus homologs, but their activity along the dorsal-ventral axis is inverted. This switching occurred in a vertebrate ancestor. Also, Drosophila Wingless is homologous to Wnt-8.
Development of placodes in the epithelium involves multiple inductive interactions. In the case of the sensory placodes, the neural tissue induces placode formation. In the case of ectodermal appendages, the mesenchyme is a source of inductive signals. In all cases, there is reciprocal signaling between the epithelium and the mesenchyme. In addition to positive signals that induce placode formation (Shh, Wnts, FGFs, BMP antagonists), there are negative signals (such as BMPs) that are important for allowing spacing of ectodermal appendages like teeth and hair follicles.
The developing brain induces the overlying ectoderm to develop into sensory organs. The neural crest arises at the posterior border of the neural plate and the epidermis; ectodermal placodes arise at the anterior border of the neural plate and the epidermis. VIa invagination, ectodermal places then develop into ganglia (nerve bundles) and parts of the ear, eye and nose (sensory organs of the head).
Epithelial placodes do not properly develop in Individuals with ectodermal dysplasia, thus retarding development of ectodermal appendages. Mice and humans with ectodermal dysplasia have little or no hair, fewer and smaller teeth, few or no sweat glands and small nails. Cloning of mutated genes in ectodermal dysplasia patients led to the discovery of a secreted factor called ectodysplasin-A (EDA) and its receptor (EDAR). EDA is expressed throughout the epidermis, and EDAR is induced by signals from the mesenchyme (dermis). Islands of EDAR expression are induced by further signals to grow downward into the mesoderm and form placodes.
Epidermal ectoderm gives rise to teeth, hair, nails, mammary glands, scales and feathers. Via epithelio-mesenchymal interaction, underlying mesenchyme determines which structures are formed from the epidermis. For example, if chicken thigh mesoderm is grafted beneath wing ectoderm, then the wing ectoderm will form thigh feathers rather than wing feathers. Epithelio-mesenchymal interaction occurs in three steps:
| Process | Overview |
| Initiation | Signals provide positional information so that organs form in the correct place. For example, secreted signals control initiation of tooth development so that the right number of teeth develop and with proper spacing. |
|---|---|
| Morphogenesis | Epithelial and mesenchymal cells interact to form a rudiment, for example a tooth bud or hair follicle. |
| Differentiation | Cells differentiate to form specific structures. For example: tooth bud epithelial cells differentiate into enamel-producing cells; and hair follicle epithelial cells differentiate into hair-producing cells. |
In birds and mammals, the endoderm is a disk that invaginates, starting at its anterior and posterior ends, to form a closed epithelial cylinder surrounded by a thin layer of splanchnic mesoderm. The splanchnic mesoderm later becomes smooth muscle. The endoderm gives rise to the pancreas, liver and lungs via branching of endodermal tubes. Regional morphological differences amongst epithelial cells demarcates the three endodermal segments, each of which evaginate:
| Segment | Overview |
| Foregut | The most anterior region of the foregut broadens and becomes the pharynx. The lateral sides evaginate, forming pharyngeal pouches which give rise to: gill slits (fish and amphibians) or part of the jaw, ear and neck (reptiles, birds and mammals). The esophagus forms as a dorsal extension of the pharynx. At its posterior end, the esophagus widens into the stomach. At its anterior end, the esophagus forms a lung bud (aka tracheal bud) that gives rise to lungs in a manner similar to hepatic (liver) and pancreatic development. |
|---|---|
| Midgut | The midgut becomes the small intestine. Epithelium develops finger-like outgrowths called villi. Villi hugely expand the gut’s surface area, thus aiding nutrient absorption. Between villi, the epithelium sinks to form crypts. The foregut and hindgut also form crypts, but lack villi. Undifferentiated endodermal stem cells proliferate at the neck of each crypt (the proliferation zone). Enterocytes (absorptive cells) migrate into the villi as they differentiate. Gland cells migrate deeper into the crypt as they differentiate. This polarized pattern is maintained throughout life. In the anterior of the midgut, hepatic and pancreatic buds arise; these will form the liver and pancreas, respectively. |
Regulation of the constant rapid division in the intestine is import to avoid cancer. Intestinal cell differentiation depends on Cdx2 expression. If cells do not differentiate correctly, they continue to proliferate. As expected, Cdx2+/- knockout mice develop colon tumors at a high rate. Defects in the APC gene (encoding adenomatous polyposis coli or APC) are the most common cause of human colorectal cancer. APC targets β-catenin for degradation; β-catenin interacts with TCF/LEF factors in the Wnt signaling pathway, which maintains stem cell proliferation. APC defects reduce β-catenin degradation, causing excessive Wnt signaling and thus overabundant proliferation. Similarly, colorectal cancers sometimes arise from mutations that stabilize β-catenin or increase TCL/LEF factor levels.
Development of endodermal organs is dependent on interaction between the endoderm and the surrounding mesoderm. Endodermal tissue cultured in vitro does not differentiate without its surrounding mesoderm; endodermal tissue co-cultured in vitro with splanchnic mesoderm undergoes organ-specific differentiation. Furthermore, organ development depended on the position of the mesoderm — not the endoderm — along the antero-posterior axis. For example, tracheal bud endoderm cultured with mesoderm from different regins differentiates according to location from where mesoderm derived. Mesoderm fromnear liver leads to liver-like tubues in the tracheal bud. Mesoderm outside the immediate splanchnic layer also instructs the endoderm.
For example, as we will discuss in more detail below, signals from the notochord (dorsal of the endoderm) and the heart primordium (antero-ventral of the endoderm) play an essential role in the specification of the pancreas and liver, respectively. Inductive signals also pass from the endoderm to the mesoderm. In other words, signaling between the mesoderm and endoderm is reciprocal. Thus, endoderm co-cultured with somitic mesoderm (which normally forms muscle and bone) will induce the mesoderm to become smooth muscle.
Hedgehog, TGFβ and FGF are families of regulatory genes involved in endo-mesodermal interactions and are critical for region-specific endodermal differentiation.
| Genes | Source | Overview |
| Ssh | Notochord | Hedgehog genes (Shh and Ihh) are expressed in the endoderm and are regulated by signals from the surrounding mesoderm. Ssh-/- mice have overall smaller guts, and regional abnormalities as well: stomach epithelium (specialized crypts with acid-producing cells) is replaced by intestine-like epithelium (villi containing absorptive cells). FGF and TGFβ genes repress Shh expression in the region of dorsal endoderm that gives rise to the posterior stomach, spleen and pancreas. In regions of the endoderm where Ssh is not repressed, it upreguates BMP expression in the splanchnic mesoderm. |
|---|---|---|
| TGFβ | Notochord | Loss of notochord-derived TGFβs allows ectopic posterior Ssh expression in the dorsal endoderm: the spleen and pancreas are reduced or absent. |
| FGF | Cardiac | FGF signaling from the cardiac mesoderm (aka heart) is critical for liver formation. In contrast, signals from the notochord (such as Shh) suppress liver formation. Thus, placing notochord tissue next to ventral endoderm results in absence of a liver. Liver formation is monitored via albumin, a marker of liver tissue that is expressed even before the liver bud forms. |
| BMP | Splanchnic Mesoderm |
BMPs are required in the splanchnic mesoderm for proliferation and differentiation as smooth muscle. |

| Layer | Vertebrates | Insects | Overview | ||||||
| Ectoderm | Gut, Liver, Lungs |
Gut | The ectoderm gives rise to the skin and its differentiated structures: hair, nails, feathers, scales, mammary glands and teeth. Ectodermal placodes give rise to the eye, ear and nose. Much of this organogenesis requires interaction between the ectoderm and the underlying mesoderm, referred to as epithelio-mesenchymal interactions. | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Mesoderm | Muscle, Heart, Blood, Skeleton, Kidney |
Muscle, Heart, Blood |
In amphibians, signals from the vegetal portion of the egg establish mesoderm; various growth factors play a role in signaling to the marginal zone cells to cause them to become mesoderm precursors. For example, we discussed the role of Xnr (Xenopus nodal-related) in mesoderm formation. Expression of nodal-related is also required for proper function of the node in birds and mammals, specifically for induction of axial mesoderm. We have seen that, in vertebrates, the most dorsal mesoderm forms the notochord, and that BMP inhibitors such as chordin and noggin are required for notochord formation. |
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| Endoderm | Nervous System, Skin |
Nervous System, Cuticle |
After gastrulation, the endoderm is the innermost germlayer.
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The mesodermal layer of the early embryo forms as a result of gastrulation. This mesodermal layer of cells initially constitutes an epithelium; after gastrulation the cells of this epithelium lose their close association with each other (undergo an epithelial-mesenchymal transformation).
| Mesoderm | Position | Overview |
|---|---|---|
| Axial Mesoderm | Most Dorsal | Forms the notochord. |
| Paraxial Mesoderm | Along Dorsal | Positioned on either side of the axial mesoderm. Gives rise to somites. |
| Intermediate Mesoderm | More Lateral | A mesenchyme that forms the ducts that will form the kidney and internal sexual organs. |
| Lateral Mesoderm | Most Lateral | Extends from either side of the embryo to the ventral midline. Gives rise to blood, blood vessels, smooth muscle and heart. |
Hensen’s Node is present in birds and mammals. The Spemann Organizer is present in Xenopus. The Node establishes l
For example, we learned that the mesoderm that comes to occupy the most dorsal position in the embryo, the dorsal mesoderm, will become the notochord. Mesoderm that occupies more ventral positions go on to become other derivatives. For example, we also saw that the endoderm becomes surrounded by mesoderm, and that mesoderm is a more ventral type (the splanchnic mesoderm).
| Axial | It gives rise to the notochordal process which later becomes the notochord. |
|---|---|
| Paraxial | On either side of the neural tube lie bands of paraxial mesoderm. Paraxial mesoderm gives rise to somites. Somites form the vertebral column, dermis and skeletal muscle. Paraxial mesoderm also gives rise to branchial arches, which develop into facial muscle and cartilage. Paraxial mesoderm is exposed to BMP antagonists, but at a lesser concentration than dorsal axial mesoderm. Posterior paraxial mesoderm expresses high levels of FGF, thus keeping it in a proliferative and undifferentiated state. As the primitive streak regresses posteriorly, cells further from the node are no longer under the influence of FGF. Outside the reach of FGF, the paraxial mesoderm cells begin to compartmentalize into somites. Cells within an individual somite become compacted (which involves an increase in cadherin expression). These changes in cell adhesion cause the newly forming somite to separate from the rest of the paraxial mesoderm. |
| Intermediate | Intermediate mesoderm is located between the paraxial mesoderm and the lateral plate. It develops into the part of the urogenital system (kidneys and gonads). |
| Lateral Plate | This is ventral mesoderm and gives rise to limbs. |
| Discovery | |
| Transplant | Transplanting a small group of cells from a region that will eventually form a somite boundary, into a region of unsegmented paraxial mesoderm that normally would not be part of a boundary. |
|---|---|
| Result | Transplanted cells instruct the cells anterior to them to undergo a mesenchymal-epithelial transition and to separate from the unsegmented mesoderm. |
| Boundaries are signaling centers, and the somite boundary instructs neighboring cells to undergo a mesenchymal-epithelial transition. Nonboundary cells can acquire this ability to induce boundary formation if the Notch pathway is activated in them, for example, by introducing an activated Notch receptor. | |
| Mutations in Notch signaling lead to defects in somite formation. For example, mice lacking the Notch ligand Delta-like 3 (Dll3) have serious vertebral and rib defects. As we will see below, these structures are derived from somites. In Dll3-/- mice, somite formation is irregular and delayed. As a result the structures that form from the somites are abnormal. | |
Notch controls somite size and segmentation in a negative feedback pathway. The Notch pathway establishes an oscillating pattern in somites, and one cycle of the oscillation corresponds to the budding off of one somite from the unsegmented paraxial mesoderm. Notch signaling activates a transcription factor (RBJ) that activates the expression of Hes.
Hes is a transcriptional repressor that has two functions. First, it represses expression of itself. This limits the duration of the Notch response. Second, Hes represses expression of an inhibitor of the Notch receptor, lunatic fringe (Lfng). Thus, this activity of Hes would serve to activate the Notch pathway. The oscillations are created because Hes has a very short half-life, leading to transient repression of Notch.
When the somite first separates from the presomitic mesoderm, it can give rise to any somite-derived structure. As the somite matures, its various regions become committed to forming certain cell types.
| Somite | Region | Overview | ||||
| Sclerotome | Medial | Ventral-medial cells are farthest from the back but closest to the neural tube. These undergo mitosis and an epithelial-mesenchymal transition. They eventually become chondrocytes (cartilage cells) of the vertebrae and most (if not all) of each rib. The sclerotome is induced by paracrine factors, especially Shh, secreted from the notochord and neural tube floor plate. If any source of Shh is transplanted next to other regions of the somite, they too will become sclerotome cells. Sclerotome cells express Pax1, which induces them to differentiate into cartilage; also, pax1 is necessary for formation of the vertebrae. Sclerotome cells also express I-mf, an inhibitor of the myogenic bHLH family of transcription factors that initiate muscle formation. | ||||
|---|---|---|---|---|---|---|
| Dermamyotome | Lateral |
Cells in the two lateral portions of the epithelium (closest and farthest from the neural tube) give rise to dermamyotome, a double-layered structure composed of myotome in the lower layer and dermatome in in the upper layer.
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| Streak | Cells ingress into the streak via an epithelial→mesenchymal transition. |
|---|---|
| Somites | Somites go mesenchymal→epithelial to separate from the unsegmented mesoderm. |
| Sclerotome | Sclerotome goes epithelial→mesenchymal to generate chondrocytes of the vertebrae and most (if not all) of the ribs. |
| Dermatome | Dermatome goes epithelial→mesenchymal to generate mesenchymal connective tissue of the back dermis. |
An axon often has to navigate great distance to reach its target cell (ie, another neuron or muscle fiber) and establish the synaptic connection. This process is axonal pathfinding. The axon does not navigate its natural pathway due to any single cue, but via combinations of signals. This redundancy makes axonal pathfinding extremely complex. Axonal pathfinding is extremely specific: a particular axon always contacts the same (or at least very similar) set of neurons or muscles.
Neurons have an intrinsic polarity that is always the same for a specific type of neuron. At one end of this polarity, a localized increase in cell membrane activity occurs (with ruffles, aka lamellipodium often visible) and fine filopodia of the cell cytoplasm extend and withdraw. The structure of filopodia is maintained by microfilaments, while axonal strucure is maintained by microtubules. Eventually, a filopodium forms a growth cone, an actively motile region at the far end.
The growth cone travels based on cues from a substrate called the extracellular matrix (ECM). The ECM contains laminin, collagen and fibronectin (the first being the most important) that adhere to cadherins and integrins in the growth cone membrane. Also, the ECM contains unique molecules (ie, nerve growth factor and retinoic acid) that guide the growth cone, sometimes across a gradient and other times along a narrow path. These unique molecules are deposited: by tissues over which the axons grow (ie, epithelia, somites and blood vessels); by cells at crucial migratory points; and even by the target tissue itself.
Once the growth cone reaches its specific target (ie, muscle fibers or another neuron) it must stop growing and establish a synaptic connection. The high specificity of axonal pathfinding is determined by any of three ways:
| Method | Overview |
|---|---|
| Timing | There may a single cell (or group of cells) mature enough to form a synapse with the incoming axon. Therefore, specificity is determined by the timetable of donor and receiver neuronal maturation. |
| Chemoaffinity | The growth cone and target cell may express matching recognition molecules that restrict interactions with other cells. Once in the target region, the growth cone locates its target cell by unique molecular tags that bind to recognition molecules on the target cell. |
| Pruning | Axons may bind target cells in a somewhat non-specific manner; improper connections are recognized via neuronal activity or trophic factors produced by the target cell. Incorrect connections are eliminated via cell death or selective retraction of certain axonal branches. |
Commisural neurons are interneurons in the (usually dorsal) spinal cord that extend their axons across the midline. Commisural projects project ventrally toward the floor plate, and then cross the midline ventral to the floorplate of the spinal cord. Recombination experiments have shown that the floor plate secretes netrin, an attractive signal critical for commisural axons to migrate to the floor plate and cross the midline. In netrin-/- mutants, commisural axons fail to grow to the floor plate.
Ephrins are membrane-bound ligands that bind to membrane-bound ephrin-receptors called ephs. When an ephrin and an eph bind, a signal is generated in both cells — this means the signal is bi-directional. Ephins are repulsive signals in axon migration, with ephrin/eph signaling responsible for setting the retino-tectal topographic map. In a topographic map, the spatial organization of neurons in one region (retina) is replicated in a connected region (tectum). The retina and tectum contain inverse gradients of ephs and ephrins; axons extend from the retina to the tectum until reaching a signaling threshold (inversely proportionate to their starting point) that inhibits further navigation. Thus, axons from a retinal region with low levels eph will target a tectal region with high levels of eph. In the figure below, axons from a given retinal quadrant will target the tectal quadrant of matching color.

All in all, ephrin/eph signaling is critical for:
| Step | Overview |
| 1st Induction | Specific positions along the anterior-posterior axis of the archenteron (cells arising from the organizer to form dorsal mesoderm and endoderm) induce specific regions of the brain to form. For the developing eye, the diencephalon is induced along with its outpatching, the optic vesicle. |
| 2nd Induction | The optic vesicle induces the lens placode in the overlying head ectoderm. This is evidenced by: surgical or genetic removal of the optic vesicle cases failure of lens formation; optic vesicle transplantation causes formation of a new, ectopic lens. The optic vesicle then folds back on itself to form the optic cup: the outer optic cup layer becomes the pigmented retina; the inner optic cup layer becomes the neural retina. The lens placode also invaginates to form the lens vesicle. Axons from the neural retina travel down the optic stalk; once travelled by axons, the optic stalk becomes the optic nerve. Next, the lens cells differentiate. |
| 3rd Induction | The lens vesicle induces the overlying ectoderm to differentiate as cornea. |
A critical gene that is expressed throughout the developing eye is Pax6. Mutants of Pax6 have aniridia (no iris), small eyes and even no eyes. Pax6-/- homozygotes lack eyes and nasal cavities. Pax6 is required in the ectoderm, as shown by tissue recombination studies using Pax6+/+ and Pax6-/- ectoderm and optic cups. Also, ectopic expression of eyeless (the Drosophila homolog of Pax6) in Drosophila larvae causes ectopic eyes to develop on the legs and wings; murine Pax6 has a similar effect, showing its strong conservation.
|
Reciprocal signaling between the lung endoderm and surrounding mesenchyme controls the pattern of bronchial (lung) branching. Mesenchymal cells close to budding region produce Fgf10, which promotes proliferation of bronchioli. The tracheal bud does not branch in Fgf-/- mice, thus confirming that FGF induces cell proliferation. However, if FGF were the only signal then the bronchioli would continually grow without branching. Several mechanisms define branch points, one of which involves Shh.
Shh inhibits FGF expression, and is secreted from the tip of the bronchiolus when branching is about to occur. This leads to a high FGF concentration along a growing bronchiolus, but a low FGF concentration at its tip. As a result, the bronchiolus splits at the tip into two branches; each new branch grows toward the high FGF concentration. Shh-/- knockout mice have primitive sacs instead of lungs due to complete failure of branching.
Drosophila has a signaling mechanism similar to the aforementioned FGF/Shh system. The Drosophila respiratory system begins as a series of invaginating placodes which later future to form multiple branches. Growth of tracheal primordia is induced by binding of its FGF receptor by an FGF homolog called branchless. The tip of the tracheal primordium expresses sprouty, which diffuses and inhibits FGF-stimulated proliferation in basal cells. This causes a T-shaped expansion of the tracheal primordium tip.
Similar to the tracheal and pancreatic buds and their branches, the hepatic (liver) bud is an evagination of the endoderm which branches profusely to form the liver.
Similar to the tracheal and hepatic buds and their branches, the peancreatic bud is an evagination of the endoderm which branches profusely to form the liver. This branched endodermal endothelium differentiates into two types of glandular tissue: exocrine glands, which produce essential digestive enzymes that are secreted into the small intestine; and endocrine glands (aka islet of Langerhans or islets) that produce the hormones insulin and glucagon.
The brain develops from the neural tube. Before even fully developing at the posterior, the neural tube (initially straight) begins to form bulges at the anterior that will give rise to the brain. First, three primary vesicles are formed; starting at the most anterior, these are the forebrain (prosencephalon), midbrain (mesencephalon) and hindbrain (rhombencephalon). Many transcription factors confer identity upon the mammalian brain, including Hox genes.
| Primary Vesicle | Overview |
| Rhombencephalon |
The anterior of the rhombencephalon is the metencephalon, which gives rise to the cerebellum and pons; the posterior is the myelencephalon, which gives rise to the medulla oblongata. Unlike the rest of the brain, the rhombencephalon segments into totally separate and morphologically distinct rhombomeres. There are seven rhombomeres, and also seven Hox genes whose regions of expression end at the anterior end of each rhombomere.
The rhombencephalon of a knockout for any of these seven Hox genes develops normally anterior to the range of expression of that Hox gene; however, rhombomeres within the range of expression of that Hox gene develop abnormally. This suggests that Hox genes play a role in rhombomere identity, just as they control vertebral identity in the trunk. |
|---|---|
| Mesencephalon | The mesencephalon does not subdivide. |
| Prosencephalon |
The prosencephalon subdivides to form the telencephalon (at the anterior) and the diencephalon (at the posterior). The telencephacon gives rise to the cerebral hemispheres; the diencephalon evaginates to form much of the eye in addition to the thalamic and hypothalamic brain regions. Subdivision of the prosencephalon is managed by spatially localized expression of transcription factors. However, the mechanism of subdivision is still vague due to difficulty knocking out relevant genes, and because the segments are not clearly distinct. Outgrowing neurons mark off groups of cells that do not intermix, suggesting there are three or four subdivision (neuromeres or prosomeres) in the telencephalon and diencephalon. There are at least 25 homeobox genes expressed in restricted regions of the forebrain, also implying that the forebrain is divided into functional units. These genes (ie, Emx, Otx and Dlx) often have overlapping expression regions and are homologous to genes (ie, ems, otd, Dll) expressed in the embryonic fly head semental patterns. |
Expression of vertebrate Sonic hedgehog protein is extremely localized to the notochord and spinal cord floorplate. The floorplate forms where Sonic hedgehog levels are highest, and motor neurons form where Sonic hedgehog levels are lower; this suggests that a notochord-releaseed Sonic hedgehog protein gradient patterns at least the ventral portion of the neural tube. Addition of cells producing Sonic hedgehog has a similar effect as adding an additional notochord: an ectopic floorplate and motor neurons.
The role of Sonic hedgehog was confirmed via Shh-/- knockout mice. Loss-of-function homozygotes die as fetuses and exhibit severe defects consistent with Sonic hedgehog’s aforementioned inductions: the floorplate of the neural tube, with mutant fetuses exhibiting cyclopia (eye and nose primordia fused along a degenerated ventral midline); and sclerotomes, with mutant fetuses lacking vertebrae and ribs.
In humans, mutant Sonic hedgehog range in severity from mild (two front incisors fused together) to severe (holoprosencephaly, leading to cyclopia and a single front hemisphere of the brain. Different individuals with the same mutation can have different phenotypes, suggesting that modifying genes affect the severity of the phenotype. The fetus’ prenatal environment may also impact the phenotype.
Read about Sonic hedgehog in lung development, where Shh inhibits FGF expression and FGF induces cell proliferation.
| Apical Ectodermal Ridge | |
| The Apical Ectodermal Ridge (AER) controls identity along the proximal/distal axis. The AER is a ridge of thickened ectoderm that forms along the entire edge of the limb bud at the dorsal/ventral boundary. This thickened ridge is analogous to ectodermal placodes in that each are areas of thickened ectoderm created by cell shape changes and they each signal to the underlying mesoderm. The mesoderm underlying the AER is called the Progress Zone. | |
| Experiment | Overview |
|---|---|
| Removal | The AER was removed from the limb at various times. This resulted in limb truncations. Thus, the AER signals the underlying mesenchyme to allow proximal/distal outgrowth. Late removes results in only the most distal elements (ie, digits) missing; early removal results in more proximal elements also missing. Thus, proximal-distal patterning occurs progressively over time with proximal elements forming first. |
| Hybridization | In situ hybridization was used to determine what factors are expressed by the AER. Among those factors were FGF-4 and -8. To test if these are the factors responsible for AER’s proximal-distal patterning activity, implantation of beads was performed in embryos stripped of their AER. |
| Implantation | The AER was removed and beads soaked in FGF-8 were implanted. The implanted beads were nearly as effective as the AER itself. Thus, the AER is clearly a signaling center that secretes FGFs to induce underlying mesenchyme. |
| Zone of Polarizing Activity | |
| The Zone of Polarizing Activity (aka ZPA or Polarizing Region) controls identity along the anterior/posterior axis (and thus digit identity). It is a mesenchyme located at the posterior end of the limb bud. Digit 1 is most anterior numeration proceeds posteriorly. | |
| Experiment | Overview |
|---|---|
| Transplantation | A ZPA was grafted to an ectopic anterior position. This caused formation of a new anterior/posterior axis. This is similar to the grafting of the frog embryo DBL to an ectopic position to induce a new dorsal/ventral axis with a new neural tube and complete set of structures. The interpretation for the ZPA results is the same as in the DBL results: the grafted tissue must be a source of a secreted signal that acts upon neighboring cell. |
| Hybridization | In situ hybridization identified Shh as the potential signal secreted by the ZPA. |
| Implantation | Implanting a bead soaked with Shh at the anterior end of the limb will cause the limb to form with two anterio-posterior axes as though it were a reflection of itself. |
| Formation of structures along the anterio-posterior axis is dependent on the concentration of Shh. Naturally, the [Shh] is highest posteriorly where the ZPA is located. Adding a source of Shh at the anterior end will form a concentration gradient that is high anteriorly and posteriorly and intermediate in the middle. Mutations that lead to ectopic Shh are the most frequent cause of limb/digit duplication. | |
| Progress Zone, Part I | |
| The Progress Zone controls identity along the proximo-distal axis. The Progress Zone is the limb mesenchyme directly underneath the AER. The proximal/distal fate of a cell is determined by the amount of time it spends in the Progress Zone. Outgrowth of the limb is proximal→distal, meaning proximal structures develop first and distal structures last. | |
| In the early limb bud most mesenchymal cells are in the Progress Zone. However, as cells divide and the limb grows, more and more cells are found outside of the Progress Zone. They only begin to differentiate once outside the Progress Zone. This is similar to the nervous system, where progenitor cells only differentiate after leaving the ventricular proliferative zone. | |
| Experiment | Overview |
|---|---|
| Labeling | Different cells are labeled with different markers. This reveals that as development proceeds, cells in the Progress Zone proliferate. As they proliferate, some cells are pushed out of the Progress Zone. Cells pushed out first become proximal structures. As limb development proceeds, cells i the Progress Zone continue to proliferate and additional cells are pushed out. |
| Progress Zone, Part II | |
| Since the amount of time spent in the Progress Zone fates a cell along the proximal/distal axis, the labeling experiment explains why removing the AER at an early stage leads to greater limb truncations. | |
| Transplantation | An early Progress Zone was transplanted onto a late limb bud. Many cells had already left the host’s late Progress Zone. Grafting a new Progress Zone onto the tip of the limb caused a new population of cells to proliferate and leave the Progress Zone as the host cells had. The result is duplication of structures. |
|---|---|
| Transplantation | An early limb bud Progress Zone was removed and replaced with a late limb bud Progress Zone. Only the most proximal structures had time to leave the host Progress Zone. The donor Progress Zone was only left with the most distally determined cells. This resulted in a loss of intermediate limb elements. |
We have seen that the ZPA produces Shh and controls A/P identity.
The PZ and AER control P/D outgrowth.
The PZ produces FGF10 and the AER produces FGF8.
The new concept I want to introduce is that these signaling centers interact to maintain each other. For example, in addition to controlling A/P identity, Shh also acts on the PZ to to maintain its survival.
Similarly, the FGF10 produced by the PZ maintains the AER.
Finally, the FGF8 produced by the AER acts on both the PZ and the ZPA to maintain these structures.
1. Removal of AER stops formation of distal structures
2. Removal of AER causes loss of ZPA activity
3. Replacement of PZ mesoderm with flank
mesoderm causes degeneration of AER
4. Removal of ZPA causes loss of formation of distal structures (i.e. PZ activity and AER activity)
There are some experiments that tell us that the PZ, AER, and ZPA interact to maintain each other.
For example, we have seen that removal of AER blocks formation of distal structures. This suggests it is required to maintain the PZ.
Next, removal of the Aer also causes a loss of ZPA activity. Shh expression is lost. This shows the AER is required to maintain the ZPA.
The role of the PZ on maintaining the AER can be seen if we replace the PZ mesoderm with other flank mesoderm. This other mesoderm is unable to maintain the AER.
Finally, removal of the ZPA causes a loss in the formation of distal structures.
To review, as I mentioned earlier, the limb bud consists of mesenchymal cells arising from the lateral plate mesoderm, and an epithelial covering coming from the ectoderm. It is at this early stage of development, before any cell differentiation takes place, that different parts of the limb bud begin to produce signals that control development along the P/D and A/P axes. The basic point here is that these signaling sends transmit information to cells in the limb bud at an early stage of development, and it isn’t until much later that cells start to differentiate into different skeletal elements at specific locations, depending on the signals they received earlier.
Hox genes are expressed along the anterio-posterior axis. Hindlimbs and forelimbs appear at different places along the anterio-posterior axis. Furthermore, hindlimbs and forelimbs have different identity. Hox gene expression is responsible for this, as it induces various Tbx genes which the mesodermal mesenchyme conferring regional specificity to the overlying ectoderm.
Evidence for existence of a “prepattern”: digits can form in absence of polarizing activity
A final feature I want to mention to you is that the ability of the limb mesenchyme to form segmented structures is instrinsic to the limb bud cells themselves. If we take the cells, diserse them so that we no longer have any gradients of FGF or Shh, and then put them back into an ectodermal limb jacket, a disorganized limb will grow out, but what is striking is that it has recognizable digits composed on individual bones. So the e ability to form a repeated segmental structure is present and doesn’t involve gradients of the patterning molecules we already discussed. This is somewhat reminiscient of the situation with the somites, where we saw the somite formation occurs due to an oscillation of a negative feedback pathway.
Picture 7
Generating Periodic Structures
Reaction-diffusion mechanisms: a form of lateral inhibition established by negative feedback loops.
Observations of this sort have led to the theory that reaction-diffusion mechanisms are involved. These are related to the negative feedback pathway we discussed for somite formation.
The difference is in the reaction diffusion mechanism, the activator protein that gets induced is stable, but it forms a concentration gradient.
Forelimb vs Hindlimb is determined by Tbx = T box (DNA binding domain) transcription factor. Tbx5 determines wing bud and Tbx4 determines leg bud. In the previous slide, we saw that the mesoderm differentiates according to its own developmental program, which was to make leg structures. The positional signals for regional identity must be present in the mesoderm. This implies that there is differential gene expression in wing vs leg.
Whether a hindlimb or forelimb develops is determined very early, by the time a limb bud is evident. The identity will be under the control of Hox genes, since limb identity depends on where on the AP axis the limb bud develops.
Limb identity is determined by the ability of Hox genes to activate the expression of Tbx genes. These are transcription factors. The Tbx genes that control limb identity are Tbx4 and Tbx5.
Now we’ll look at some experiments that demonstrate that Tbx genes control limb identity.
One way to look at this is to induce an ectopic limb to see what type of limb develops, either forelimb or hindlimb, and then to correlate that with the expression of Tbx4 or Tbx5.
In this experiment, a limb bud can be induced in the lateral plate mesoderm by implantation of a bead soaked in FGF. In this case, the bead is implanted in a location where Tbx5 is induced, and the limb develops as a wing.
However, infecting lateral mesoderm with a virus that causes overexpression of Tbx4 will override the normal course of development by altering expression patterns of Tbx genes. Tbx4 is overexpressed in the flank mesoderm by introducing a vector containing a Tbx4 gene. The limb but that now deelops expressed high levels of Tbx4, the gene normally expressed in hindlimb bud. The wing bud now develops into a leg instead of a wing.
We have seen that the PZ controls P-D identity. This must involve differential gene expression. We have already seen that Hox genes control identity along the A/P axis of the embryo and the positioning of the limb buds. They also control identity along the P/D and A/P axis in the limb.
The expression patterns change during development. However, if we look at the expression of Hoxa9 through Hoxa13 in an early limb bud, we can see a colinearity of expression, with the most distal regions expressing the most members of the complex.
Evidence that Hox genes are involved in P/D patterning comes from looking at the phenotypes of mice in which Hox genes are knocked out. For example, were is a normal mouse forelimb. In this mutant, all of the Hox11 genes (hoxa11, d11,etc) are defective. As a result of having no normal Hox11, the foreleg (radius and ulna are almost completely missing).
What we don’t see are homeotic transformations.
Here is an example of a Hox mutation in humans. As we saw in the previous slide, Hoxa13 is expressed in the most distal cells in the limb. In people lacking hoxa13, it is the most distal elements, the digits, that are affected. The types of malformations are complicated and not understood on a molecular level.
What is important is not the type of malformation, but rather the type of structure that is affected by a particular Hox mutation. So, the Hox genes that show the most distally restricted expression affect the most distal limb elements. Hox genes like Hoxd11 that show a more proximal range of expression affect more proximal structures.
Maternal effect genes are transcribed, and their mRNA translocated into the egg, during oogenesis. Maternal effect genes acts before any zygotic genes, which are encoded by the embryonic genome itself. The maternal phenotype determines the zygotic phenotype. Thus, a MEG+/- female will have all normal children even if the child’s phenotype is MEG-/- (due to mating with a MEG+/- male or MEG-/-). However, a MEG-/- female will be unable to have normal children because embryonic development will be defective. There are forty maternal effect genes in Drosophila, including:
| Region | Description | Maternal Effect Genes |
| Acron | Part of the head. | torso |
|---|---|---|
| Anterior | Head and thorax. | bicoid (bcd) |
| Posterior | Abdomen | nanos |
| Telson | Tail region. | torso |
A spacially restricted ligand activates the Torso RTK, which then initiates a phosphorylation cascade — involving Ras, Raf-1, MAP kinase kinase (MAPKK, aka MEK) and then MAP kinase (MAPK) — that inactivates transcriptional repressors at the two poles of the embryo. This is critical for terminal formation. Where RTK is most activated, huckebein and tailless transcription is activated; extending to where activation is reduced, tailless transcription (encoding tailless) is still activated.

Sex-lethal is a sequence-specific RNA binding protein that recognizes a specific UGUUUUUUU element in its target RNAs. It has a Β1,2,3 & 4 domains as well as RNA recognition motifs RRM1 and RRM2. The presence or absence of Sxl in an early embryo will determine whether it develops as a male or a female.
| Early Female Embryo | Late Female Embryo | |
| There is transcription from the Sxl PE promoter. An mRNA is encoded starting at the E1 exon. A functional Sxl protein is expressed. | The PL promoter is activated. Its ORF is different than PE and L3 now has a premature stop codon. However, Sxlearly binds near L3 to block U2Af from binding the 3′ splice site. Thus L3 (and its stop codon) is skipped in females. Functional Sxl is expressed. | |
| Early Male Embryo | Late Male Embryo | |
| No transcription from PE. No Sxl expressed. | The PL promoter is activated. There is no Sxlearly, so the stop codon in L3 leads to expression of a truncated and inactive Sxl. | |

The female produced Sex-lethal protein also regulates splicing of Transformer (Tra), the next gene downstream in the Sexual Differentiation Pathway.
An exon in Tra pre-mRNA has two 3’ splice sites. U2AF has higher affinity for the primary upstream 3’ splice site, so splicing occurs there. However, this polypyrimidine tract also contains a high affinity Sxl binding element allowing Sxl to bind if it is present.
Gametogenesis is the development of germ cells into gametes. Gametes are large nonmotile oocytes in females, and small motile sperm in males. Gametogenesis occurs in the gonads: ovaries in females and testes in males. The two main differences between oogenesis and spermatogenesis: prophase arrest; and unequal division.
| Step | Start | Result | Overview |
|---|---|---|---|
| Germ Cell | Germ Cell | Germ cells originate in the earliest embryonic cell divisions and remain distinct. | |
| Mitosis 1 | Germ Cell | 2N Gamete | Germ cells migrate to newly formed gonads and proliferate mitotically into diploid gametes. |
| Mitosis 2 | 2N Gamete | 1° Gamete | Diploid gametes divide mitotically into diploid primary oocytes and primary spermatocytes. |
| Meiosis | 1° Gamete | 1N Gamete | Meiosis reduces the chromosomes to haploidicity. |

| Meiosis 1 | Primary spermatocytes undergo the first meiotic division into haploid secondary spermatocytes. |
|---|---|
| Meiosis 2 | Secondary spermatocytes under the second meiotic division into four haploid spermatids per primary spermatocyte. |
| spermatogonium |
|---|
| ↓ |
| proliferation |
| ↓ |
| 1° spermatocyte |
| ↓ |
| meiosis I |
| ↓ |
| 2° spermatocyte |
| ↓ |
| meiosis II |
| ↓ |
| spermatid |
| ↓ |
| differentiation |
| ↓ |
| sperm |
In spermatogenesis: microtubule-based flagellum are built (for motility); ribosomes and mRNA are lost; and the nucleus is condensed (to stop transcription).
Mammalian spermatocytes are connected by cross-bridges of cytoplasm whilst dividing. This is due to asymmetry of sex chromosomes in males. Half of secondary spermatocytes receive an X chromosome, and the other half receive a Y chromosome.
However, some gene products essential for spermatocyte development are found only on the X chromosome. Cytoplasmic contact allows all 4 secondary spermatocytes to share X chromosome gene products.
| Arrest | Oogenesis begins the first meiotic division but is arrested in prophase for days, months or years. |
|---|---|
| Growth | As Prophase 1 arrest ends, the primary oocyte uptakes yolk from blood and synthesizes proteins, maternal mRNAs, ribosomes, organelles and localized cytoplasmic determinants. This stocks all RNA needed for the first embryonic divisions, and all the embryo’s nutrients until the placenta forms or it self-feeds. |
| Meiosis 1 | The primary oocyte divides meiotically such that one daughter cell receives most cytoplasm (the secondary oocyte) and the other daughter cell receives almost none (1st polar body). |
| Arrest | In many species, the 2nd meiotic division does not occur until the egg is fertilized. |
| Meiosis 2 | The secondary oocyte undergoes a second asymmetrical meiosis divides to produce a large haploid ootid and a 2nd polar body. |
| Mature | The polar bodies degenerate. The large haploid ootid is a mature egg. |

The egg must provide a nucleus (genetic informatino), specific regulatory molecules (mRNAs, cytoplasmic determinants) that interact with nuclei, and building materials for development (protein, carbon source) until the embryo’s feeding or placental stage. The volume of the egg can range from 103 (mammals, sea urchin) to 106 (amphibian) to 1011 (ostrich egg) times larger than a somatic cell. A normal-size oogonium gives rise to such an enormous ova by conserving cytoplasm during meiosis and also undergoing a massive growth phase. Except for gas and limited ion and water exchange, the egg is a closed system. Thus, embryogenesis uses only macromolecules from within the egg itself (formed during oogenesis) until the embryo is developed enough to feed itself or can draw from the mother via a placenta. Common features of oogenesis are: the uptake of yolk from a source outside the oocyte; a high level of transcription of mRNA; and the presence of follicle cells. Features specific to oogenesis in only some organisms are: nurse cells; and DNA amplification. The components of the egg that must be synthesized during oogenesis are:
| Component | Source | Overview | ||||||
| Egg Shell | Follicle cells (insects, mammals) Oviduct (birds) | The egg shell — or egg membrane or vitelline membrane — is synthesized by follicle cells (the cells surrounding the egg) in most organisms and by cells of the oviduct in birds. In some insects, including Drosophila, follicle cells contain amplified quantities of egg shell genes — thus, there are hundreds as opposed to just two copies of the genes required for egg shell formation. Amplification allows faster synthesis and assembly of the egg shell. | ||||||
|---|---|---|---|---|---|---|---|---|
| Yolk | Vertebrate liver secretion. Insect fat body secretion. |
Yolk is a heterogeneous mix of phospholipoproteins that serves as an energy- and carbon-source. It is synthesized in the vertebrate liver and insect fat body, transported through blood and uptaken by the egg to form membrane-enclosed yolk platelets. The amount of yolk in an egg has tremendous inter-species variability: primitive mammals contain massive amounts of yolk; placental mammalian eggs contain very little yolk. | ||||||
| Cytoplasm |
Fertilization is usually immediately followed by rapid cell division that requires quick synthesis of DNA, mitotic spindles and cleavage rings. Thus, the following are usually present in the egg cytoplasm before fertilization:
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| mRNA | Early zygotic development relies on mRNA stored in the egg, known as stored maternal mRNA. This mRNA is stable, untranslated and mostly encodes proteins required for all rapidly dividing cells, such as cytoskeletal, membrane, metabolic, histone and other proteins. However, a small fraction of these mRNAs are localized to certain regions of the cell and control embryonic polarity — these mRNAs determine which daughter cells will eventually become which body regions (examples include bcd, nos and others). |

A sperm’s role is to deliver a male’s nucleus (namely, the genetic information within) to the egg. Mature sperm lack ribosomes and mRNA; they are transcriptionally and translationally inactive.
| Component | Overview |
|---|---|
| Haploid Nucleus | The sperm nucleus is very condensed, thus reducing its size for faster swimming. The sperm nucleus contains only DNA and positively charged proteins, which are different from somatic histones — all enzymes and non-histone chromosomal proteins are removed during spermatogenesis. |
| Propulsion System | The flagellum contains an axoneme, composed of nine microtubules arranged in a circle, two microtubules in the center and dynein arms (which hydrolize ATP) accompanying the microtubules. At the nuclear-proximal end (near the ‘head’) is a cluster of mitochondria which provide metabolic energy for flagellar movement. |
| Centriole | In addition to organizing the flagellum, the sperm centriole may organize the microtubules of the mitotic spindle of the fertilized egg. This is a controversial point, but the egg may not have functional centriole, hence the presumed importance of the sperm centriole. |
| Acrosomal Vesicle | Formed from the Golgi Apparatu, the acrosomal vesicle is a membrane-bound cap on the sperm nucleus which contains digestive enzymes that allow the sperm to penetrate the outer layers of the egg and reach the egg membrane. |
Vertebrates are bilaterally symmetric about the midline for many structures, like eyes, nasal passages, and limbs. However, most internal organs (including endodermal derivatives) are arranged asymmetrically in the abdominal cavity.
For example, the heart is on the ventral side. The lung has fewer lobes on this side to provide space for the heart. Similarly, endodermal organs are invariantly placed within the abdominal cavity so there is enough space for each organ.
Left/right asymmetry is controlled early in development by the node. The node expresses Shh only on its left side. Shh then induces expression of nodal, a secreted protein. If the pattern of nodal expression is made symmetric by implanting a pellet of cells expressing Shh on the right side of the node, then organ asymmetry is lost, and organs are randomly placed in the body.
Cells in the node contain cilia that cause a directional flow of a signaling molecule involved in left/right asymmetry. Mutations in left-right dynein (LRD) cause randomization of organ placement. Dyneins are motor proteins that move along microtubules and drive cilia movement. Individuals with Kartagener’s Syndrome have immotile cilia and their handedness is thus random.
In Drosophila, the dorsal-ventral patterning system causes a ventro-lateral portion of the blastoderm layer to become committed to a neurectodermal fate. The presumptive neurectodermal cells develop from nuclei that contain moderate levels of nuclear dorsal protein. Following cellularization of the blastoderm and the onset of zygotic gene expression, these cells express Sog, an inhibitor of DPP. The neurectoderm in the Drosophila embryo consists of two lateral stripes on either side of the embryo. These stripes are separated ventrally by the presumptive mesoderm (twist-expressing cells). Following invagination and internalization of the mesoderm, the presumptive neurectoderm comes to occupy the most ventral position in the embryo.
| Proneural | Proneural clusters are groups of neuroectoderm that become competent to give rise to neuroblasts. This is due to their activation of proneural gene expression. Proneural genes a group of bHLH (basic helix-loop-helix) transcription factors encoded by the Achaete-scute complex. The requirement for the proneural genes is shown by the fact that many neuroblasts do not appear in Achaete-scute-/- embryos. |
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| Inhibition | One of the cells that has delaminated from the proneural cluster inhibits other cells of the cluster from becoming neuroblasts. This process is called lateral inhibition, and it is important for assuring that the correct number of cells become neuroblasts. |
Starting at the ventral end, the following structures comprise the spinal cord: floor plate; cell bodies of somatic motor neurons; cell bodies of commisural neurons; roof plate. The floor plate guides axons that grow into it, and the motor neurons send out axons that innervate muscles.
The notochord patterns the neural tube’s dorso-ventral axis. An additional notochord transplanted underneath a closing neural tube in the chick embryo induces an additional floorplate with adjacent motor neurons. Removing the notochord from the neural tube results in absence of a floor plate and motor neurons. Thus, the notochord induces at least the most dorsal neural tube structures. Furthermore, both the notochord and floorplate induce adjacent somite tissue into sclerotome, which gives rise to the vertebrae and ribs.
Vertebrate Sonic hedgehog protein (Shh, homolog of Drosophila Hedgehog) is localized to the notochord and floorplate of the spinal cord. Perhaps Shh is the notochord signal that patterns the neural tube in dorso-ventral axis, and that patterns the somites. Addition of cells producing Shh has a similar effect to adding an additional notochord: an ectopic floorplate and motor neurons. The floorplate differentiates where the level of ectopic Shh is highest and the motor neurons where the level is lower. This indicates that a gradient of Shh released from the notochord patterns the neural tube.
The key role of Sonic hedgehog was revealed by the phenotype of Sonic hedgehog knockout mice. Shh-/- mice die early and are extremely defective. The defects observed are consistent with a role of Shh in inductions:
| Floorplate | Shh form the notochord induces the floorplate. Shh-/- fetuses have severe ventral midline defects, i. e., the ventral midline seems to degenerate. This results in a fusion of the eye and nose primordia in the ventral midline (cyclopia). This defect is consistent with the known role of Shh in inducing the formation of the floorplate and other ventral cell types in the neural tube. |
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| Sclerotomes | Shh from the notochord and floor induces sclerotomes. Another defect is the virtual absence of the vertebrae and the ribs. Again, this is consistent with the role of Shh in giving a more ventral identity (sclerotome) to a portion of each somite. We will discuss this aspect of Shh signaling in a future lecture. |
Hox genes and head gap genes
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Conclusion: Pax6 is required in the lens ectoderm for lens induction (required for competence to respond). | ||||||||||||||||||
| A series of experiments in fetal rabbits led to the conclusion that the sex of the gonad controlled the development of all other sexual characteristics. These experiments showed: | |
| Removed | Overview |
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| Testes | Removing testes from a male fetus will cause it to develop a female phenotype without gonads. |
| Ovaries | Removing ovaries from a female fetus will cause it to develop a female phenotype without gonads. |
| Conclusion: The ground state is female. Testis are required for male differentiation. Without testis then the phenotype is female. | |
| These results led to the hypothesis that a substance produced by the male gonad causes male differentiation. We now know that the key products of the testes that allow male development of secondary sexual characteristics are hormones. | |
| Injection | Overview |
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| Testosterone | Testosterone injected into female fetuses will cause them to develop as males, except that the ovary does not differentiate into a testis and produce sperm, and the paramesonephric (Mullerian) ducts do not degenerate. |
| Estrogen | Estrogen injected into fetuses will not cause any change in the fetus’ development. Males still develop as males and females as females. |
| AMH | Regression of the Mullerian ducts in the male is under the control of anti-Mullerian duct hormone (AMH, a TGF-β) secreted by testis’ Sertoli cells. |
Conclusion: The development of the male phenotype in mammals depends on the development of the testis, which then controls secondary sexual development by producing testosterone and AMH. As a side-note, testosterone is secreted by the Leydig cells of the testis and estrogen is produced by the ovary.
The gene SRY has been cloned from the human Y chromosome and is required to confer maleness in mammals. This gene has a close homolog in mice, is expressed in gonad at the time of testis differentiation, is not expressed in ovaries, and is a DNA or RNA-binding protein. Transgenic SRY mice always had a male phenotype even when they had an XX genotype. However, male XXSRY were incapable of spermatogenesis since sperm cell differentiation requires additional Y chromosome proteins. This shows that the presence of the SRY gene is sufficient to drive almost all aspects of male sexual differentiation.
Sox9 is an autosomal gene necessary for maleness in all vertebrates. Sox9-/- causes a female phenotype regardless of genotype. The current hypothesis is that in mammals and marsupials, SRY controls the expression of Sox9. The role of Sox9 as a determinant of testes formation appears to be conserved among all vertebrates. This is true even in vertebrates other than mammals, which do not have the Sry gene. It is not known why expression of Sox9 came under the control of Sry in mammals. In vertebrates such as fish and reptiles, where sex is determined by hormones or the temperature at which the embryo develops, it is thought that Sox9 activity is influenced by sex hormones.
Researchers have not deciphered how sex is determined in animals that use a ZW system (including birds). This is largely due to the impossibility genetic screens or other genetic manipulations in birds. However, RNAi has revealed that the DNA-binding protein DMRT1 is sex-determining. DMRT1 is required for the gonad to differentiate as a testis in birds. Interestingly, DMRT1 is highly conserved. It is expressed in mammals and in Drosophila its homolog (Doublesex) determines sex in flies. As a side-note, monotreme mammals (egg layers such as platypus and echidna) use a ZW system, indicating that the XY system evolved rather recently.
Neural crest cells form at the anterior end of the neural plate, at the border of the epidermis and neural plate. This is where BMP levels are intermediate. Sensory placodes arise from this region and are induced by the same signals. Neural crest cells migrate through the anterior half of the somite but avoid the posterior half due to repulsive ephrin signals from somite’s posterior half.
Neural crest cells form dorsal root ganglia (sensory neurons) and melanocytes (pigment cells). Dorsal root ganglia form the adrenal medula and also sympathetic ganglia in the gut. Other neural crest derivatives are head mesenchyme and Schwann cells. Head mesenchyme includes bones, connective tissue and dental papilae (tooth pulp). Schwann cells myelinate peripheral neurons.
When Neural Crest Cells begin to migrate, they lose their adhesion to the neural tube and adjacent epidermis. This involves losing expression of both N-cadherin and E-cadherin.
Neural Crest Cells are guided by similar mechanisms as axons, consisting of short-range (cell-surface) and long-range (diffusible) signals of attraction and repulsion.
Short-range attractive cues include cadherins; short-range repulsive cues include ephrins. Ephrins are recognized by neural crest ephrin receptors. The posterior half of each somite expresses ephrin, relegating neural crest cells to migrate through the anterior half of each somit.
Long-range attractive cues include netrins. Long-range repulsive cues include semaphorins.
The extracellular matrix is the substrate over which a neural crest cell migrates. The cells bind primarily to laminin and secondarily to fibronectin and collagen. Cues guide neural crest cells across the extracellular matrix.
Ephrins are short-range repulsive cues to prevent cell mixing between adjacent somites. The posterior half of the somite produces a repulsive signal called ephrin. Loss of Ephrin-B1 induces NCC migration defects.
Retinal neurons send a bundle of axons (the optic nerve) to precise locations in the tectum (a region of the brain). The precisely ordered connections are known as a retino-tectal map. This map is broadly established by a gradient of ephrin and ephrin receptors, and refined by additional interactions.
Retinal neurons express the ephrin EphA3 in a graded fashion, with the highest levels on the side furthest from the nose. A corresponding gradient of ephrins A2 and A5 is seen in the tectum, where the lowest [ephrins] is at the anterior side and the highest [ephrins] is at the posterior side.
Retinal neurons from the nasal side of the retina express low levels of EphA3, and are thus insensitive to the repulsive effects of ephrins A2 and A5. They thus project only to the anterior side of the tectum. In contract retinal neurons furthest from the nose will project to the posterior side of the tectum to avoid repulsion.
If the optic nerve is severed and the eye rotated 180°, the retinotectal map will still form properly. This indicates that the retina and tectum release certain signals which define the retinotectal map, regardless of orientation.
The extracellular matrix is a substrate over which axonal growth cones can migrate. Laminin is the primary active component in the extracellular matrix, followed by fibronectin and collagen.
Netrins are long-range chemoattractants. They are secreted by floorplate cells, thus attracting neurons to the midline. Commisural neurons first extend ventrally, then project to netrin+/+ floorplate cells.
Floorplate or floorplate extract can be placed on agar. Axons within 250µm of this will reorientate their growth toward it. In netrin-/- knockouts, commisural axons fail to grow to the floorplate (midline).
Slit and semaphorin are repulsive cues. Netrin and slit signaling systems play opposing roles during positioning of longitudinal tracts along the midline in the ventral nerve cord of Drosophila embryos. Slit is present outside of the midline, and is taken up in a Roundabout (Robo) independent manner along the commissural tracts into the longitudinal connectives. Guidance is partially or fully ablated in null mutants of Slit or Robo.
Netrin draws commissural neuron growth cones toward the floorp-plate/midline. Then Slit (secreted by ventral midline) and Semaphorin (secreted by neural tube) divert the commisural neuron growth cones toward the brain. Thereby nerves extend themselves from the body to the brain. First they reach the midline due to the attractant Netrin, then they travel up to the brain along a narrow path defined by the repellents Slit and Semaphorin.
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