1. Introduction: Development is How You Became You

Many of the processes we’ve been discussing in these tutorials about eukaryotic gene regulation play a key role during embryonic development. During this early phase in life, the body changes in size and form from a fertilized egg into a complex multicellular organism. As you’ll see in the cards below, the biological story of how you became you is quite astonishing.

We cover the topic of development in detail in our college curriculum. As an AP Biology student, here’s what you need to know.

2. (Almost) All Cells in an Organism are Genomically Equivalent

We’ve mentioned this key principle before, but it bears repeating. In any multicellular organism, with just a few exceptions, all the cells have the same DNA. In other words, the cells in your body are genomically equivalent.  The cells that make up the lens of your eye have the same DNA as the cells that produce your toenails. The differences between cells are related to differences in gene expression, not to differences in the cells’ genetic material.

Biologists’ ability to clone animals through somatic cell nuclear transfer is proof of this principle. Cloning is a kind of asexual reproduction in which a somatic cell provides the genetic material from which an entire new organism is formed. A clone is an exact genetic copy of the organism from which it was cloned. You can think of a clone as a younger identical twin with the same exact genes.

Sir John Gurdon, the recipient of the 2012 Nobel Prize for Physiology or Medicine, carried out the experiment shown at left in the late 1950s. He extracted an intestinal cell (2) from a tadpole (1) and then extracted the nucleus from that intestinal cell (3). He separately took a frog egg cell (4) and removed its nucleus (5) creating an enucleated egg (6). Enucleated means that this egg cell had had its nucleus (and therefore its genetic material) removed. Gurdon then placed the intestinal cell’s nucleus into the enucleated frog egg cell (shown at 7). This egg cell was able to develop into a new tadpole: a genetic clone of tadpole number 1.

In 1996, Sir Ian Wilmut successfully cloned a mammal. To dramatize the outcome, he worked with two distinct breeds of sheep: a white-faced Finn Dorset (at “a”) and a Scottish Blackface (“e”). The process involved:

1. Taking a cell from a female Finn Dorset’s mammary glands (“b”).
2. Taking an unfertilized egg cell from a Scottish Blackface (“f”) and removing that cell’s nucleus (“g”).
3. Fusing the mammary gland cell with the enucleated egg cell (at “c”), resulting in a diploid zygote (at “d”).
4. The zygote grew into an embryo (h), which was then implanted into a surrogate mother (another Scottish blackface).
5. When the lamb was born (“j”) it had a Finn Dorset phenotype, and subsequent genetic analysis showed that it was a clone of “a.”

Here’s a musical explanation of the process. For the lyrics, click here. 

3. Cells Differentiate Because they Express Different Genes

What’s the takeaway from reproductive cloning? It’s that all cells have the genetic information to create an entire organism. Why then, are cells of different tissue types so different?

Differences in cell structure and function are the result of differential gene expression. In the diagram at left, the neuron and epithelial cell are genomically equivalent. But in the undifferentiated cells (at 2) that gave rise to these mature cells, tissue-specific genes were activated. The genes that were activated at 3 were genes that produced neuron proteins; conversely, the genes activated at 4 were genes that produced epithelial cell proteins.

4. Checking Understanding: Genomic Equivalence, Cloning, and Differentiation

5. Differentiation can be caused by differences in the distribution of transcription factors in an egg

Differentiation starts early in the life of the organism— often in the very first cleavage divisions that follow fertilization. What causes the daughter cells to differentiate has to do with differences in the concentration of molecules in the cytoplasm that they receive from their parent.

In the diagram on the left, you can see this represented by the distribution of the molecules represented by the red star and the brown sphere (at “e”), with more of the red star molecules on the top side of the egg, and more of the brown sphere molecules on the bottom side. This uneven distribution is maintained after fertilization (“d”). As a result, when the zygote (“f”) divides (“g”), the result is two daughter cells with different concentrations of these molecules in their cytoplasm. If these molecules are proteins or RNAs that interact with the DNA in the daughter cells, they’re called cytoplasmic determinants, and the result will be the activation of different genes, creating the stage for the differentiation in the cell lines that stem from cells “h” and “i.”

In the fruit fly Drosophila, an important model organism for developmental biology, one such cytoplasmic determinant is a type of mRNA named bicoid, which affects an embryo’s development of a head.

Here’s how bicoid works. Drosophila eggs (“d”), develop within a follicle (the entire structure shown on the right). At one end of the follicle are nurse cells  (“a”). The nurse cells produce bicoid mRNA (“b”), which diffuses into the egg, and winds up being much more concentrated on one end of the egg cell than the other. Note that all of the cells except for “d” are diploid, maternal cells.

During development, the bicoid mRNA is translated into bicoid protein. The image below shows a gradient of bicoid protein in an early Drosophila embryo. The dark spots in the drawing show how the bicoid protein is concentrated in the head end of the developing embryo. The graph below the image quantifies this gradient in wild-type flies (see the blue line labeled “wild type”), and also in flies with mutant mothers that don’t express the bicoid gene (red line).

The presence of bicoid mRNA and bicoid protein causes a head to develop (shown at “a” below: note the mouth and antennae). Bicoid mutant mothers that don’t produce sufficient bicoid have headless offspring (shown at “b”). These quickly die.

What might be happening? The important move, as an AP Bio student, is to connect the presence or absence of bicoid protein to the regulatory mechanisms behind gene expression that you’ve learned about in previous tutorials. We know that the presence of bicoid is connected with cells on the head side of the embryo activating tissue-specific genes that lead to the differentiation of these tissues into a head. The specific mechanism might be at the level of DNA packaging. This could include

• Acetylation of tissue-specific genes in the head region, allowing them to be expressed, or
• Methylation of these same genes in the tail region, causing them not to be expressed.

Or the regulation could be at the level of transcription. In this case, bicoid protein could be acting as a transcription factor that turns on tissue-specific genes in the head region. With those transcription factors absent, a head can’t properly develop.

6. Differentiation can be caused by induction

Cytoplasmic determinants like bicoid start the process of tissue differentiation that occurs during embryonic development. Another process connected with differentiation is induction.

Induction involves one cell (or a group of cells) influencing the development of other cells. The inducing cells do this through the release of molecules that act as transcription factors. Such molecules, because they impact the form of the developing embryo, are often referred to as morphogens.

In the diagram on the left, the inducing cells are the ones shaded blue-green at the bottom of the developing embryo. These cells (one of which is shown at “A”), release morphogens (“1”) that bind with membrane receptors (“2”) on another cell (“B”). When the morphogenetic signal binds with the receptor, it sets off a signal transduction cascade that ultimately reaches the nucleus, activating (or deactivating) genes.

In the 1920s, experimenters in Germany created a spectacular demonstration of induction. It was known that in newts, a bit of tissue called the dorsal lip of the blastopore was required for normal body development. (Note: the blastopore is an opening into the open space inside an early embryo. The dorsal lip is the tissue on the bottom of that hole. You don’t need to remember either of these terms).

Graduate student Hilde Mangold, working with her advisor Otto Spemann, surgically removed the dorsal lip of the blastopore from an early embryo of a donor newt  (shown in pink on the left embryo in the diagram below). They transplanted this tissue onto a second newt (the host, on the right) which now had two dorsal lips instead of one.

What happened is shown below.

With two dorsal lips, the embryo developed into a conjoined newt (4).

7. Checking Understanding: Cytoplasmic Influences and Induction

8. Developmental genes are expressed in a hierarchical sequence, from general to specific

The images below show five vertebrate embryos at equivalent phases of development. The top row consists of photographs of the embryos, some of which were modified in order to highlight their similarities. For example, a large yolk sac was removed from the salamander embryo. The bottom row shows drawings from Ernst Haeckel, a famous 19th-century biologist.

Haeckel created these drawings because he felt that they served as evidence for evolution, a topic that we’ll address in Unit 7 of our AP Biology course. For now, let’s use them to consider an important idea related to eukaryotic gene expression: the idea that developmental genes are expressed in a hierarchical sequence, from general to specific. 

Start by focusing on the column showing a human embryo. The embryo shown here is only a few weeks old. At that moment in development, the embryo has a variety of traits that it will later lose: these include a tail and what are called pharyngeal slits (also known as gill slits: click on the images on the right and below for a better view).

Pharyngeal slits are openings that extend from the neck area below the head into the back of the mouth cavity. In a fish, these slits are maintained in the adult form. They let water flow over the gills, creating a current that enhances the absorption of oxygen.

In all tailless vertebrates, like humans and birds, the tail gets broken down through apoptosis: programmed cell death. The material making up the tail gets recycled and is used to build other parts of the body. The same thing happens to the gill slits in all of the four-limbed vertebrates. That’s because all of these animals (amphibians, reptiles, birds, and mammals) absorb oxygen from the air using their lungs, rather than using gills to absorb oxygen from the water.

Why do the embryos of humans, rabbits, and chickens develop with tails and gill slits, only to break them down and absorb them later? It’s because having a tail (for example) is a part of a general developmental plan inherited from a vertebrate ancestor. In early embryonic forms, the genes for this plan are still expressed. The only reason our embryonic form possesses a tail is because a tail is part of a developmental program that we inherited from our ancestors.

Why haven’t the genes for these structures been deleted? We’ll focus on the tail. One possibility is that the developmental plan to build a 4-limbed vertebrate might require that at some moment in development, a tail be present. Without having an embryonic tail, the complex signaling that goes on between cells which results in the various parts of the body growing in the right place could be disrupted. So all vertebrates start life by building a tail, whether they keep it or not. The same is true of the gill slits.

Expression of genes in a hierarchical pattern, with genes for general features laid down before genes for specific features, can also be seen in the emergence of segmentation in arthropods like Drosophila.

As a Drosophila embryo develops, among the first genes expressed are those that lay down the head-to-tail axis (1). The next set of genes to be activated divide the embryo into a few major regions (2). The next divide these regions into specific segments (3 and 4), each of which has an anterior end and a posterior end.

Only once these segments have been established are additional genes expressed, leading to the emergence of specific appendages on each segment.

We’ll end by looking once again at  Haekel’s drawings about embryological development in vertebrates. What’s the takeaway? The key idea is that during development, gene activation and induction unfold in a hierarchical sequence. The most general features (in this case, the basic vertebrate body plan shown in row 1) are laid down first. In rows II and three, genes that are specific to each species are expressed, with the embryos becoming more and more differentiated as development proceeds.

How does this happen? Through all of the mechanisms we’ve seen in this and previous tutorials for controlling gene expressions. To review, these include:

• epigenetic modifications of DNA through chromatin packaging,
• control of transcription through transcription factors,
• post-transcriptional modifications of RNA,
• regulatory RNAs such as micro RNA.
• cytoplasmic determinants in the egg
• induction.

9. Eukaryotic Gene Expression and Development Flashcards

10. What’s Next?

Proceed to Topics 6.5 – 6.6, Part 6: Eukaryotic gene regulation and evolutionary change in the threespine stickleback (the next tutorial in AP Bio Unit 6).