Unit 14: Embryonic Development and its Regulation - Biology

Unit 14: Embryonic Development and its Regulation - Biology

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Embryogenesis is the process by which the embryo forms and develops. In mammals, the term refers chiefly to early stages of prenatal development, whereas the terms fetus and fetal developmentdescribe later stages. Embryogenesis starts with the fertilization of the egg cell (ovum) by a sperm cell, (spermatozoon).

  • 14.1: Embryonic Development
    The genome of the zygote contains all the genes needed to make the hundreds of different types of cells that will make up the complete animal. There are two major categories of these genes: "housekeeping" genes and tissue-specific genes. However, every cell descended from the zygote has been produced by mitosis and thus contains the complete genome of the organism (with a very few exceptions).
  • 14.2: Frog Embryology
    The frog egg is a huge cell; its volume is over 1.6 million times larger than a normal frog cell. During embryonic development, the egg will be converted into a tadpole containing millions of cells but containing the same amount of organic matter.
  • 14.3: Cleavage
    Cleavage refers to the early cell divisions that occur as a fertilized egg begins to develop into an embryo.
  • 14.4: The Organizer
    In the embryonic development of a zygote, gradients of mRNAs and proteins, deposited in the egg by the mother as she formed it, give rise to cells of diverse fates despite their identical genomes. But is the embryo fully patterned in the fertilized egg? It is difficult to imagine that the relatively simple gradients in the egg could account for all the complex migration and differentiation of cells during embryonic development. And, in fact, the answer is no.
  • 14.5: Segmentation - Organizing the Embryo
    Insects, like all arthropods, are segmented. The body of Drosophila melanogaster is built from 14 segments, but what signals guide segment formation? The process begins with the gradients of messenger RNA (mRNA) that the mother deposited in her egg before it was fertilized. Shortly after fertilization, these are translated into their proteins with a gradient of bicoid diminishing from anterior to posterior and a gradient of nanos diminishing from posterior to anterior.
  • 14.6: Homeobox Genes
    Insect (Drosophila) and frog (Xenopus) development passes through three rather different (although often overlapping) phases.
  • 14.7: Stem Cells
    Stem cells are cells that divide by mitosis to form either two stem cells, thus increasing the size of the stem cell "pool", or one daughter that goes on to differentiate, and one daughter that retains its stem-cell properties. How the choice is made is still unknown. However, several genes have been found whose activity prevents a daughter cell from differentiating.
  • 14.8: Embryonic Stem Cells
    a research team led by James Thomson of the University of Wisconsin reported (in the 6 November 1998 issue of Science) that they were able to grow human embryonic stem (ES) cells in culture. At the time of implantation, the mammalian embryo is a blastocyst. It consists of the trophoblast — a hollow sphere of cells that will go on to implant in the uterus and develop into the placenta and umbilical cord. inner cell mass (ICM) that will develop into the baby as well as the extraembryonic amnion
  • 14.9: Germline vs. Soma
    Could a mutation in one of your liver cells ever be passed on to your children? No! Why not? The fusion of one sperm cell and one egg cell represents the only genetic link between the bodies of parents and the body of their child and the cells destined to produce sperm and eggs are set aside very early in embryonic life.
  • 14.10: Regeneration
    Regeneration is the ability to replace lost or damaged body parts. This ability varies greatly among living things.

Thumbnail: Human embryo, 8-9 weeks, 38 mm. (CC BY-SA 3.0; Anatomist90).

The cis-regulatory dynamics of embryonic development at single-cell resolution

Understanding how gene regulatory networks control the progressive restriction of cell fates is a long-standing challenge. Recent advances in measuring gene expression in single cells are providing new insights into lineage commitment. However, the regulatory events underlying these changes remain unclear. Here we investigate the dynamics of chromatin regulatory landscapes during embryogenesis at single-cell resolution. Using single-cell combinatorial indexing assay for transposase accessible chromatin with sequencing (sci-ATAC-seq), we profiled chromatin accessibility in over 20,000 single nuclei from fixed Drosophila melanogaster embryos spanning three landmark embryonic stages: 2-4 h after egg laying (predominantly stage 5 blastoderm nuclei), when each embryo comprises around 6,000 multipotent cells 6-8 h after egg laying (predominantly stage 10-11), to capture a midpoint in embryonic development when major lineages in the mesoderm and ectoderm are specified and 10-12 h after egg laying (predominantly stage 13), when each of the embryo's more than 20,000 cells are undergoing terminal differentiation. Our results show that there is spatial heterogeneity in the accessibility of the regulatory genome before gastrulation, a feature that aligns with future cell fate, and that nuclei can be temporally ordered along developmental trajectories. During mid-embryogenesis, tissue granularity emerges such that individual cell types can be inferred by their chromatin accessibility while maintaining a signature of their germ layer of origin. Analysis of the data reveals overlapping usage of regulatory elements between cells of the endoderm and non-myogenic mesoderm, suggesting a common developmental program that is reminiscent of the mesendoderm lineage in other species. We identify 30,075 distal regulatory elements that exhibit tissue-specific accessibility. We validated the germ-layer specificity of a subset of these predicted enhancers in transgenic embryos, achieving an accuracy of 90%. Overall, our results demonstrate the power of shotgun single-cell profiling of embryos to resolve dynamic changes in the chromatin landscape during development, and to uncover the cis-regulatory programs of metazoan germ layers and cell types.


Extended Data Figure 1. Summary of read…

Extended Data Figure 1. Summary of read distributions across the three sampled time points

Extended Data Figure 2. Enhancer enrichments for…

Extended Data Figure 2. Enhancer enrichments for LSI clades at 6-8hrs and 10-12hrs

Extended Data Figure 3. Relationship between transcription…

Extended Data Figure 3. Relationship between transcription factor binding motifs and LSI clade-specific accessibility

Extended Data Figure 4. Similarities and differences…

Extended Data Figure 4. Similarities and differences in accessibility across all three time points

Extended Data Figure 5. Sex of individual…

Extended Data Figure 5. Sex of individual cells identified by ratio of X:autosomal reads

Extended Data Figure 6. Temporal ordering of…

Extended Data Figure 6. Temporal ordering of cells at 2-4hrs using Monocle

Extended Data Figure 7. Library complexity and…

Extended Data Figure 7. Library complexity and fraction of X chromosome reads highlights clusters of…

Extended Data Figure 8. LSI defined clades…

Extended Data Figure 8. LSI defined clades and t-SNE clusters show strong correspondence

Extended Data Figure 9. Cell cluster assignment…

Extended Data Figure 9. Cell cluster assignment is similar using either enhancer or gene tissue…

Extended Data Figure 10. sci-ATAC-seq can predict…

Extended Data Figure 10. sci-ATAC-seq can predict tissue-specific enhancer usage during development

All candidate clade-specific…

Figure 1. Single cell profiling of chromatin…

Figure 1. Single cell profiling of chromatin accessibility across Drosophila embryogenesis

Figure 2. Temporal dynamics and spatial heterogeneity…

Figure 2. Temporal dynamics and spatial heterogeneity in chromatin accessibility in the early embryo

Figure 3. Single cells are readily assigned…

Figure 3. Single cells are readily assigned to tissues and cell types based on chromatin…

Figure 4. Prediction of tissue-specific enhancer activity…

Figure 4. Prediction of tissue-specific enhancer activity using sci-ATAC-seq

Part 2: Gene Regulation: Why So Complex?

00:00:01.03 My name is Bob Tjian,
00:00:02.19 I'm a professor at the University of California at Berkeley,
00:00:06.19 where I've taught many years in Molecular Biology and Biochemistry,
00:00:11.02 and more recently, I've also taken on the job of being the President of the Howard Hughes Medical Institute.
00:00:16.26 And it's my pleasure today to continue with my second lecture in this series,
00:00:22.29 to describe to you some exciting ideas about how gene regulation works,
00:00:30.25 particularly in more complex organisms.
00:00:34.21 Now, in my last set of lectures, I left you with this view of the type of complexity that has to be evolving
00:00:48.26 to allow the type of gene expression patterns that we see in the many, many organisms that we know exist on this planet.
00:01:00.29 And so, there's some really intriguing questions that I'm going to address in this second lecture.
00:01:09.15 And one thing I left you with was an image of the interplay of many molecules that have to come together,
00:01:18.26 and to land on a particular site of the DNA molecule that's part of the chromosome of an organism
00:01:24.25 or within a cell of an organism, and how this process might work.
00:01:31.04 But, I think the question that's plagued us for decades,
00:01:35.20 now that we had a better idea of what this molecular machinery looks like that's involved in decoding DNA information into gene expression,
00:01:49.07 we wondered why is it so complex?
00:01:53.20 And to sort of begin to address this issue, let me just take you back to a simple concept.
00:02:01.10 And you remember that different organisms have different sizes of their genomes,
00:02:08.00 that is, the amount of DNA that is required to encode the particular organism.
00:02:14.23 And here are some examples of both bacteria, simple, single-celled prokaryotic organisms,
00:02:22.18 as well as single-cell eukaryotic organisms like the baker's yeast, and then there's the little, round soil worm C. elegans,
00:02:30.25 and then you can go up to up mammals and vertebrates.
00:02:33.29 And you'll see first of all that the amount of DNA can vary a lot from a few million base pairs
00:02:40.17 all the way up to 3 billion base pairs or more.
00:02:45.00 To go along with this sort of expanding level of DNA and chromosome length, you also have different levels of genes.
00:02:54.13 Now, you'll notice that the range of genes is a lot less than the range of DNA length,
00:03:00.20 so this partly informs us about maybe why we need the complexity that we ultimately discovered is involved
00:03:10.26 in forming this molecular machinery that's responsible for reading the genetic information.
00:03:17.22 So this is just a little table to reemphasize that these more complex genomes, which also means more complex organisms,
00:03:28.15 which really means a lot of different cell types, many different behaviors, complex interactions with their environment and so forth,
00:03:38.24 how is all this information really decoded from our genomes?
00:03:43.03 And on one side here, you see the prokaryotic core gene regulatory machinery,
00:03:50.07 or the core transcription machinery, and in almost all bacteria,
00:03:54.20 it's only a few polypeptides. 5, 6, 7 polypeptides.
00:04:00.00 Then, on this side, you'll see that the so-called eukaryotic organisms,
00:04:05.00 and particularly when you talk about multicellular metazoan organisms, now you see huge diversity and number of proteins or,
00:04:15.17 as we call, transcription factors, that are necessary to assemble into very large, multi-subunit ensembles
00:04:25.18 that are required to transcribe the 10,000 to 30,000 genes that define these more complex organisms.
00:04:33.21 So, right away you can see that there's this proliferation of the subunits and the machinery and the complexity.
00:04:43.00 So, in this lecture, I'm going to give you a little sense of maybe why this is the case,
00:04:49.11 and what's special about the more complex, multicellular organism,
00:04:55.11 and why this machinery may have to have been more elaborated through evolution, compared to simpler organisms.
00:05:05.07 Now, one of the first things that you realize when you look into the cell,
00:05:10.03 or particularly the nucleus of a higher organism, let's say our own cells, versus a bacteria,
00:05:17.10 is that the DNA, the very molecule that makes up the genetic information, is kind of packaged away in a very different way.
00:05:25.11 So, in all eukaryotes, the double-stranded DNA doesn't sit there in the form that we would call
00:05:33.29 the "naked" DNA, which is shown up at the top here. But rather,
00:05:38.17 this DNA is wrapped up with a set of proteins, very basic proteins, called "nucleosomes,"
00:05:46.00 and these are in turn further packaged all the way to highly condensed form
00:05:52.09 that ultimately forms the chromosomes that you'll be able to see under a microscope.
00:05:57.26 And the blue figures over here and green figures just give you a view of the
00:06:02.29 high-resolution structure of a nucleosome with DNA wrapped around it.
00:06:09.00 So, what is the consequence of having all of our DNA,
00:06:14.04 all our chromosomes, condensed and wrapped up in this way?
00:06:18.09 You can think of it as packaged away.
00:06:20.15 Well, one thing is that you can shove all this down into a small nucleus,
00:06:25.15 so if we strung out our DNA in every cell in our body, out from end to end
00:06:31.20 and stretched it out like a string, it's almost a meter long.
00:06:35.12 And yet, you have to cram all that into a tiny, little volume.
00:06:39.10 And part of the way that that happens is that you can compact the DNA by these structures.
00:06:46.24 Now, the consequence of that is, of course, you somehow have to negotiate
00:06:52.18 through this highly compacted form of DNA to get access to the DNA information and the genes.
00:07:00.12 So, to put it another way, you have to have a machinery,
00:07:04.24 a transcriptional apparatus whose job is to read DNA and, you remember from the first lecture,
00:07:10.27 convert that DNA information into RNA, an intermediate molecule
00:07:14.23 which ultimately then gets translated into a protein product.
00:07:18.19 Well, clearly one of the reasons we have this highly elaborated transcriptional machinery
00:07:25.02 is in part to deal with having to navigate through a chromatin template, as opposed to a naked DNA template.
00:07:33.24 And so there are various proteins and protein complexes that are called
00:07:38.29 "chromatin remodeling complexes," "chromatin modifying complexes,"
00:07:44.12 and these have to coordinate with the transcriptional machinery down here in the yellow and the orange,
00:07:50.01 in order to navigate and basically express a series of interactions
00:07:55.08 that are transactions between the protein machinery and the DNA.
00:08:00.29 So this is a very challenging problem.
00:08:04.10 So that's part of the problem, or part of the reason why we think there's such complexity.
00:08:09.11 So, how did we come to this picture?
00:08:12.05 How did we finally get to figuring out that there were over 85 proteins that all have to assemble on a chromatin template,
00:08:21.16 to give you gene expression and transcription, in the right place, in the right time?
00:08:26.25 And I want to just give you one sort of quick look into a technology that one can use to address the issue of,
00:08:37.03 how do we break down this complex machinery into understandable units?
00:08:42.29 And as I said in the first lecture, there are many tools that molecular biologists
00:08:47.18 and biochemists can use to try to tease out these complex molecular transactions.
00:08:53.18 One of them, of course, is to use genetics, which is to use genetic mutation
00:08:58.29 to either remove or alter one particular gene product and then ask what is the consequence.
00:09:05.06 The other way to do it is to actually take a cell with all of its complexity
00:09:10.02 and break it down literally into its component parts, and then try to put it back together
00:09:14.09 again in a functional form. And that's what I'm going to show you today.
00:09:18.00 And it's a technology I kind of call the "biochemical complementation assay."
00:09:23.03 And it's very simple: You ask, what are the minimal components,
00:09:27.24 for example, in the case of a human gene. what are the minimal protein components of the transcriptional apparatus
00:09:33.29 that you can extract from the nucleus of a cell that you need to put into a test tube
00:09:38.19 that will allow you to essentially reconstruct or, as we say,
00:09:42.19 reconstitute the activity that will allow you to read the gene in an accurate fashion?
00:09:48.19 And you can keep adding or taking away different proteins,
00:09:53.13 the yellow ones, the green ones, the orange ones, and so forth,
00:09:56.24 and ask, does it make any difference?
00:09:59.11 And by playing this adding and subtracting, or "biochemical complementation," assay,
00:10:04.29 you can very quickly discover what are the minimal components you need to activate a gene in a regulated fashion,
00:10:11.12 and what are other things that might be necessary to support this activity.
00:10:16.15 So, the first question that was asked was from the biochemical analysis of about
00:10:24.02 four dozen different proteins: What are really necessary and sufficient?
00:10:30.07 In other words, what's the minimal component set that you need to give you regulated transcription?
00:10:36.29 So we're now asking a more complicated question.
00:10:39.09 Not only what is necessary to just simply give you transcription, in other words the conversion of DNA into RNA,
00:10:45.29 but to do it in a regulated fashion.
00:10:47.27 Because after all, that's what's really interesting.
00:10:50.23 is why one cell does it in one way and a different cell has a different program.
00:10:55.25 And this experiment here says that our sequence-specific classical transcription factor that
00:11:02.00 binds DNA at its regulatory promoter region, together with what we will call the "core" or
00:11:09.07 "basal" machinery of transcription, is necessary but not sufficient.
00:11:14.07 So, plus or minus the activator Sp1 doesn't make any difference,
00:11:19.16 even though we know that in a living cell, Sp1 is highly activating this gene that we're looking at.
00:11:26.16 So, that means there's something missing in this reconstitution experiment.
00:11:31.16 So, how do we go find what's missing?
00:11:35.03 And this biochemical complementation really relies on our ability to take the cells that contain the necessary components
00:11:43.25 and the sufficient components, and then start to extract it
00:11:47.28 and to find which molecules are missing that we're not adding to our reaction yet.
00:11:54.05 And to do that, we basically have to take the cells, in this case, human cells,
00:11:58.28 break the cells apart, extract the nucleus, remove all the proteins from the nucleus,
00:12:04.03 and begin to separate the thousands of different proteins
00:12:08.05 that are in the nucleus into different pools, if you like.
00:12:12.08 And we separate them based on their physical and chemical properties,
00:12:17.19 and some of you probably have had some experience in running column chromatographs.
00:12:23.16 This is basically a way of separating proteins based on their positive charge, negative charge, molecular size,
00:12:32.16 hydrophobicity (in other words, how greasy they are. how well they interact with water), and so forth.
00:12:38.20 So if you do that iteratively, as is shown here in a series of different anion exchange
00:12:45.23 and cation exchange, as well as gel filtration, chromatographs,
00:12:50.12 you can eventually separate the thousands of different components of a nuclear extract into its individual parts.
00:12:59.00 And then you can test each one to see if they're the missing piece.
00:13:03.15 And when you do that, lo and behold, you find that there are a couple of missing pieces
00:13:07.22 that are necessary for you to add back, in other words, reconstitute, the reaction
00:13:13.12 so that now you have regulated transcription.
00:13:15.27 So unlike the previous data that I showed you,
00:13:19.14 now you can see that the machinery is more complex and, most importantly,
00:13:24.23 you can see also that the machinery is now responsive to the activator.
00:13:29.19 So, the signal with the activator, plus Sp1, is much darker than in the signal without Sp1.
00:13:36.13 That means that there is activated transcription that is Sp1-, a classical transcription factor, dependent.
00:13:43.11 So that allowed us to identify two very important, key components that we didn't know about before we did this experiment:
00:13:51.29 One is a multi-subunit complex called the "Transcription factor II D,"
00:13:57.25 and the other one is called the Mediator complex.
00:14:01.01 And these turn out to actually define an entirely new class of transcription factors, which are the so-called co-factors.
00:14:09.27 So I'm going to tell you a little bit more about one of these co-factors,
00:14:13.15 because they both really perform similar functions,
00:14:16.13 but we happen to know quite a bit more about one of them than the other.
00:14:20.17 So this so-called TFIID complex has roughly 15 subunits, in other words,
00:14:25.28 15 separate proteins that have to mesh together to form a complex.
00:14:31.22 And it's a very large macromolecule, so it's a million daltons.
00:14:36.23 that's a very, very large, floppy molecule, with many pieces to it.
00:14:41.12 One of its functions you already know about,
00:14:43.16 because it contains as one of its subunits the so-called "TATA-binding protein."
00:14:48.12 That's that saddle-shaped molecule that binds to double-stranded DNA,
00:14:55.02 at the AT-rich sequence called a TATA box,
00:14:58.06 which is associated with many genes in animal cells.
00:15:02.09 But what we've come to learn in the last decade or so is that this little complex
00:15:07.22 is doing much more than just simply binding to the TATA box
00:15:11.18 it's doing a whole bunch of other things that we didn't have any idea about.
00:15:15.12 And now that we knew the existence of this activity and that it was critical not only for TATA binding,
00:15:22.08 but also for mediating or potentiating transcription activation, we then could break down
00:15:28.04 more of its functions of individual subunits, because you remember there's 15 different polypeptides here.
00:15:34.09 And this is just a little summary showing you that this complex of proteins
00:15:38.11 is doing a lot of different functions.
00:15:41.18 It's recognizing the nucleosomes, which have a basic protein called a "histone,"
00:15:49.26 and so it recognizes histones only when it's got
00:15:53.09 a certain chemical modification called an acetylation event.
00:15:59.12 This big orange complex also itself has enzymatic activity, including kinase activity,
00:16:06.06 which can put phosphate groups on other proteins and enzymes.
00:16:10.04 It has acetylase activity, and of course, it has to interact directly
00:16:15.05 with activators in order to potentiate their function in turning on transcriptional activation.
00:16:22.07 And I'm probably safe in speculating that
00:16:26.20 there are yet unknown functions of this large complex that we still have to discover,
00:16:32.23 because we've really only understood maybe half of the subunits, and even there,
00:16:37.25 only partially understood the functions of that half of the subunits that are part of this complex.
00:16:44.05 So, there's clearly much more work to be done, but I think what's clear from these experiments
00:16:48.25 is that these proteins are doing a lot more than just binding DNA.
00:16:53.08 They're what I would think of as integrators of information.
00:16:58.01 So, this integrator of information means that this structure and the function is very complex, and so,
00:17:04.27 one of the things that we've had to do.
00:17:08.00 it's been a very challenging problem that remains challenging,
00:17:11.21 because we haven't solved all the technical problems.
00:17:13.18 is that because it's a large, megadalton, floppy molecule, solving the three-dimensional
00:17:19.25 structure of such large assemblies has proven to be rather technically challenging.
00:17:26.08 And we have to use many different techniques to try to address this in:
00:17:31.28 X-ray crystallography, NMR.
00:17:34.07 but one of the techniques that's emerging, that's very, very powerful
00:17:38.09 for solving the structures of these large assemblies is something called "cryo-electron microscopy."
00:17:46.24 It's basically a way of freezing these large assemblies in place,
00:17:52.18 and then solving their structure by microscopy.
00:17:55.29 And this is just about a 25 angstrom, so relatively low-resolution structural determination,
00:18:03.17 of the human TFIID complex and, most importantly,
00:18:08.24 its relationship to two other transcription factors that are part of the assembly
00:18:14.03 that has to align itself up on the promoter to start transcription,
00:18:18.08 and that's the other two transcription factors TFIIA and B, which are shown in green and purple here.
00:18:24.13 So you can slowly start building up the entire complex in pretty accurate three-dimensional space
00:18:33.00 to figure out what its shape will inform us about its function,
00:18:37.15 and that's something that's an ongoing project in many laboratories in molecular biology.
00:18:43.01 So, this cartoon. and again I want to emphasize that
00:18:46.27 all the figures there and the colored blobs are more a part of our imagination at this point,
00:18:53.16 although, as I just showed you, we actually have real structures of some components of this pre-initiation complex.
00:19:02.25 This slide just emphasizes the point that there's a lot of information integration going on,
00:19:09.22 and that there is protein-protein and protein-nucleic acid interactions
00:19:15.06 that are critical for the regulatory functions of these large, macromolecular assemblies.
00:19:21.02 And this also reminds you that there are at least three separate classes of transcription factors
00:19:27.17 that are playing a key role in the regulation of genes:
00:19:30.28 the classical activator and repressor that are sequence-specific DNA-binding proteins,
00:19:35.26 like the Sp1 protein I talked to you about earlier, just shown here in pink
00:19:41.11 there are the components of the core machinery, which are shown in yellow
00:19:45.27 and then you have these things we call co-factors or co-activators,
00:19:49.12 that are integrating information between the activators and the core machinery.
00:19:56.06 So this kind of gives you a slightly better view of why there's this kind of complexity,
00:20:04.06 but it still doesn't really address all of the issues with respect to:
00:20:09.22 Why do you need 85 proteins to do this?
00:20:12.09 So, let me dig a little deeper into this.
00:20:15.00 So, first, let me just pose some of the questions that are really still largely unresolved in the field,
00:20:21.14 even though this is a pretty mature area of study
00:20:24.10 we've been trying to address these issues for a couple of decades,
00:20:28.14 and it goes to show how difficult it is to really tease apart this complex molecular machinery.
00:20:34.23 And I should say that the complexity of this machinery is not unique
00:20:38.19 to the transcriptional apparatus. Many other biological processes are also dependent on
00:20:43.23 macromolecular machines that are very similar in complexity to this one.
00:20:49.04 So I think things that we learn about the transcriptional machinery could be applied in principle to many other machineries.
00:20:56.20 So, couple of interesting questions:
00:21:00.20 What are the transcriptional mechanisms that regulate complex cell types?
00:21:06.29 Because, after all, multicellular organisms evolved to having many, many different
00:21:13.12 cell types, so our bodies are made up of many different cell types,
00:21:18.23 which means that each cell's performing a different function.
00:21:22.02 Our hair follicle cells are producing hair, our red blood cells are
00:21:27.02 producing hemoglobin and doing something else, our skin cells are protecting us.
00:21:31.17 Each cell type is doing a different thing, so how does this happen,
00:21:36.01 how do we generate this diversity of cell types through the gene regulatory networks?
00:21:42.17 And then, knowing what we now know about the first level of complexity of the machinery
00:21:49.04 that's responsible for decoding this information, what more can we learn about the process of regulation now?
00:21:57.03 Particularly, what is the division of labor between the core machinery
00:22:03.24 (which binds to the promoter), the activators, and the co-activators?
00:22:08.22 So, what is their relationship, and what's their respective roles in defining cell type-specific gene expression?
00:22:16.19 That's really the last topic that I want to cover in this lecture.
00:22:21.06 So, let's review a few basic facts about individual cell types.
00:22:26.13 So, let's take two well-recognized cell types: fat cells and muscle cells.
00:22:33.12 Very different cells that perform very different functions,
00:22:36.27 but every cell in a particular organism has the same genetic information.
00:22:43.04 It has the same DNA, it has the same set of chromosomes.
00:22:46.08 That means that these two cells have to be using different parts of the information
00:22:52.09 from the genome to give it their distinct identities.
00:22:56.20 So, each cell must only express some subset of the genes,
00:23:03.21 and that particular subset would define the function of a fat cell versus a muscle cell.
00:23:10.11 And, so then the question becomes:
00:23:12.26 Okay, that makes sense, but how do you get there?
00:23:15.02 How do you get cell type-dependent differential gene expression patterns?
00:23:20.16 How do you turn on the right genes to make fat
00:23:22.27 versus keeping the muscle cell gene functions turned off, and vice versa?
00:23:29.06 So that is a fundamental question of trying to understand the process of cellular differentiation,
00:23:36.19 cell-specific function, and really, developmental biology.
00:23:41.09 Another set of interesting points to make is that, of the 20,000 to 30,000 genes
00:23:46.18 that a typical metazoan organism encodes, a pretty big chunk of it is devoted
00:23:54.03 to the very machinery that I'm talking about, in other words, the transcription factors.
00:23:59.04 So roughly somewhere between 5 and 10% of the entire coding capacity
00:24:04.02 of genes in a genome is devoted to encoding transcription factors.
00:24:10.11 So this is clearly a very important class of molecules.
00:24:13.02 So that means there are several thousand transcription factors.
00:24:16.28 But now if you start thinking about the many, many thousands of cell types and the behavior of different cells,
00:24:23.16 are a few thousand transcription factors, in and of themselves, enough to generate the diversity of function?
00:24:31.14 And this is where we have to start thinking about,
00:24:33.21 how do you create really large numbers of distinct transcriptional networks?
00:24:40.28 And they really are networks, as you'll see in a minute.
00:24:43.15 And one thing that became clear as we defined what genes look like and what a promoter as a transcriptional unit looks like,
00:24:51.22 we come to understand that the only way to create the kind of huge levels of diversity of distinct transcriptional
00:24:58.20 components and patterns, is to do it by combinatorial regulation.
00:25:03.12 And what do I mean by that?
00:25:04.27 So, one way to think about it is that you might only have ten cards,
00:25:09.25 but if you shuffle those ten cards and pick four at a time,
00:25:13.06 you can have many, many combinations.
00:25:15.11 So here's a perfect example of three different cell types, could be in the same organism,
00:25:20.11 and each of those symbols represents binding sites,
00:25:25.22 and then the little boxes and triangles above them represent the binding proteins.
00:25:32.18 And you can see that those three cell types might express these sets of genes in similar ways,
00:25:38.25 but they use different combinations of proteins to do it.
00:25:42.08 And this is really the notion of combinatorial mechanisms for gene regulation,
00:25:46.27 and we now know that that is indeed the way, at least in part,
00:25:51.05 that gives us the ability to create many different specific transcription patterns.
00:26:00.04 I have to now also tell you about another, I would say, defining,
00:26:04.23 unusual property of transcription in animal cells,
00:26:09.06 and this is a hard one sometimes to get your head around.
00:26:12.19 And that is that these different little units of DNA that specify the activity of a gene
00:26:18.20 don't have to be sitting, linearly and spatially, directly next to the gene that it's activating or repressing.
00:26:26.21 They can sit tens of thousands of base pairs away from the site.
00:26:32.04 So these we call long-distance enhancers or silencers, so they can both upregulate a gene.
00:26:39.01 in other words, make more of the gene or less or the gene.
00:26:41.27 And the thing that was so surprising was that the intervening DNA can be very, very long
00:26:48.04 it can be thousands and maybe even millions of base pairs.
00:26:53.00 So how does this work?
00:26:53.28 How can something sit so far away actually influence transcription at a very remote site?
00:27:00.26 And this is one of the big conundrums that we still face in the field.
00:27:05.15 We have some models and we have some ideas that we can test,
00:27:08.09 and I'll end my lecture with a few speculations about that.
00:27:11.24 But clearly, we don't fully understand this so-called long-distance regulation,
00:27:16.27 which clearly is regulated by activators and repressors just like
00:27:21.09 the same players that we've been talking about, like the Sp1 molecule and other activators.
00:27:26.12 But yet, how they can reach across long distances of the chromosome to grab on to the core machinery to actually impart information
00:27:36.06 and to create the kind of specific regulatory events is still somewhat obscure.
00:27:43.28 So, another thing that I should say is that,
00:27:47.07 because of the combinatorial mechanisms of generating diversity was so dependent
00:27:54.18 on the distinct sets of sequence-specific DNA-binding proteins,
00:28:00.12 over the last two decades we've come to kind of a traditional model that the core machinery stays relatively invariant.
00:28:10.04 In fact, we kind of think of it as universal, because if you break open a nucleus of a very
00:28:15.11 simple organism like yeast, or you break open the nucleus of a human cell,
00:28:21.22 that machinery looks remarkably similar to each other.
00:28:24.26 And yet, their gene networks are very, very different, so we thought,
00:28:29.05 well, maybe it's all having to do with the sequence-specific DNA-binding proteins,
00:28:34.07 that will generate the diversity through combinatorial regulation.
00:28:38.25 And that's probably true in fact, there's a lot of evidence to support that.
00:28:42.27 But it was only part of the story.
00:28:45.04 So, a kind of related question would be:
00:28:47.25 Are we really right in thinking that the core machinery is universal and invariant?
00:28:54.03 And that turns out to be an oversimplification.
00:28:57.06 So it turns out evolution didn't work that way.
00:29:02.26 And when we looked very carefully in the last few years, particularly at individual,
00:29:07.02 different, distinct cell types, let's say muscle versus fat, or neuron, or liver cell,
00:29:13.01 we certainly see differences in the activators, as we would expect, and indeed they are working in combinatorial fashion,
00:29:20.02 but they're not only working combinatorially with each other,
00:29:23.06 but they are combining in different combinations with the core machinery, which is itself variable.
00:29:29.23 And that was kind of a revelation that's really become more clear just in the last few years.
00:29:35.29 So, in addition to the sequence-specific binding proteins and their diversity,
00:29:41.10 there turns out to be a much greater degree of diversity in the core machinery,
00:29:46.09 the parts that we thought were invariant, than we ever imagined.
00:29:50.11 Now, once you realize that that's the case,
00:29:54.07 that opens up a whole other level of generating diversity that we didn't anticipate,
00:29:59.13 and that of course really allows multicellular organisms to diversify in unbelievable ways.
00:30:06.18 So, let's drill down finally a little bit at how did we find this out, and where are we going?
00:30:13.08 So now, unlike a few decades ago when we first began to study the process of transcription
00:30:20.02 and discovered all of this initial complexity, in those days we mainly worked on just a few different cell types.
00:30:28.13 But today, we have the ability technically to work with just about any cell type,
00:30:33.18 from the most complex, such as embryonic stem cells,
00:30:37.13 to perhaps the simple cell, like the skeletal muscle, and everything in between.
00:30:41.18 liver cells, neuronal cells, and so forth.
00:30:45.03 And this has really opened up our view of just how diverse, interesting,
00:30:51.17 and variable the transcriptional apparatus is, that is probably really necessary
00:30:56.18 from an evolutionary standpoint to drive the diversity of gene expression and cell types that we see.
00:31:04.10 The first hint that this core machinery that we thought was so invariant may not be so invariant,
00:31:10.14 came from studying the development of the skeletal muscle.
00:31:14.21 So when you go from a precursor cell called a myoblast, which looks like most every other mammalian cell,
00:31:21.13 with its standard, prototypic core machinery, and then when you look at it when that cell type differentiates, in other words,
00:31:29.16 specializes into a myotube (which will ultimately form skeletal muscle, which is the muscle around your large bones
00:31:37.03 that makes you be able to move),
00:31:39.16 it turns out that it not only shifts which transcriptional activators it uses,
00:31:45.05 but it also jettisons the prototypic core machinery and substitutes it with some modified versions of that core machinery,
00:31:53.21 which is shown down here in the purple and the bright blue.
00:31:57.29 So this was really a change in the paradigm of the way we're thinking about regulation,
00:32:03.08 and of course, this was just the first example.
00:32:07.08 One wanted to know if similar things were happening in other different cell types, and very quickly,
00:32:13.04 if you look at hepatocytes or liver cells, if you look at adipocytes or fat cells,
00:32:18.21 if you look at neuronal cells, and you compare what's going on in muscle,
00:32:23.07 in every case, one can find changes in the core machinery, either because a particular component
00:32:28.28 like one of the TBP-associated factors is highly upregulated (that means its concentration went way up,
00:32:35.15 when all the other ones went down), or some other permutation.
00:32:39.09 In other words, clearly, components of the so-called core machinery were variable from cell type to cell type,
00:32:46.20 and that really changed the way we thought about how regulation of multicellular organisms works.
00:32:54.28 At the same time that we were looking at these,
00:32:57.17 what we would call mature, terminally differentiated cell types,
00:33:01.20 we were also looking at perhaps one of the most interesting cell types that we could study,
00:33:06.18 particularly if we're interested in understanding the process of mammalian development,
00:33:11.23 and those are of course the embryonic stem cells.
00:33:14.14 These are those amazing cells that, when tickled with just the right chemicals or physiological signals,
00:33:21.08 can turn themselves into every cell type of an organism, maybe 10,000 different cell types.
00:33:31.06 So, this so-called pluripotency made these human and mouse embryonic stem cells very special for all kinds of reasons,
00:33:41.05 partly because they are amazing models to study this process of development and differentiation,
00:33:46.18 but partly because of biomedical possibilities for cell regeneration and therapeutics.
00:33:57.02 So we've studied this, and these are very, very new studies,
00:34:01.27 and I'll just very quickly touch on it. We really were curious,
00:34:05.23 how can these cells be so pluripotent?
00:34:09.08 That is, their capacity to turn into every other cell type seems so amazing, what is the mechanism,
00:34:15.07 what's the machinery that's going to allow these cells to be able to differentiate into every cell type in the body?
00:34:22.16 And so, we began to probe this.
00:34:24.27 In some cases, we did it by the genetic technology, which is we made
00:34:29.08 mutations in certain candidate regulatory factors and transcription factors,
00:34:34.10 and then asked, does that have a consequence on the development of different cell types?
00:34:41.10 In other cases, we used a standard biochemical complementation technology to figure out what's going on.
00:34:47.21 So, I'll finish with two quick stories.
00:34:51.06 So, using the genetic tools of knocking genes out and asking
00:34:55.02 what effect it has on differentiation and pluripotency, we discovered that
00:35:01.15 a component of the core machinery (or at least we used to think of it as being purely of the core machinery),
00:35:07.07 that is, one of the TBP-associated factors, particularly TAF3,
00:35:11.26 turns out to be extremely important for the regulation and
00:35:15.23 expression of genes that will ultimately define the so-called endoderm.
00:35:23.17 And that's true for both the so-called primitive endoderm and the definitive endoderm,
00:35:28.04 which ultimately will give rise to the placenta, the yolk sac, lungs, liver,
00:35:32.12 pancreas, intestines, and so forth.
00:35:34.17 At the same time, knocking out this TAF3 had the opposite effect on the other two major germ layers,
00:35:42.09 which are the mesoderm and the ectoderm.
00:35:44.13 So here was a really beautiful case of differential function of a transcription factor
00:35:50.28 that was not a standard sequence-specific binding protein.
00:35:55.09 This core machinery factor, which by the way, probably on its own doesn't even bind to DNA directly,
00:36:01.20 when you knock it out, you lose the ability to form endoderm,
00:36:05.22 but you elevate the probabilities of forming mesoderm and ectoderm.
00:36:09.18 In other words, the balance between these different cell types gets messed up,
00:36:13.20 and of course this will cause major difficulties for a developing embryo.
00:36:21.16 Even more interesting and intriguing, and this really goes to show the level of information that we still lack,
00:36:28.15 although TAF3 was originally defined both genetically
00:36:32.04 and biochemically as part of the TFIID core promoter recognition complex,
00:36:37.02 and it is absolutely true that that is the case,
00:36:40.04 it had another life that it led that we didn't know about.
00:36:43.17 So TAF3, it turns out, it doesn't have to strictly function as part of this large multi-subunit core promoter complex,
00:36:52.17 but it can also do other jobs, and in this case, it pairs up, or partners up,
00:36:57.06 with a different transcription factor called CTCF (doesn't really matter what the name is)
00:37:03.02 and now it does its job in a completely different way.
00:37:06.16 And in fact, the most recent experiments suggest that TAF3 and CTCF get together
00:37:12.03 to partly allow that amazing property of long-distance regulation.
00:37:17.25 So, regulators bound at thousands of base pairs away from the site of activity
00:37:24.21 can be brought together in three-dimensional space by what's known as "DNA looping,"
00:37:31.04 and it turns out that TAF3 is involved in this DNA looping, together with a whole bunch of other proteins,
00:37:38.00 whose relationship to TAF3 is still not entirely clear.
00:37:45.02 And we find it particularly intriguing and exciting that this type of long-distance function is being
00:37:50.06 carried by a TAF and in the context of embryonic stem cell differentiation potential to form endoderm.
00:37:57.19 So this is a very, very new type of way of thinking about the core transcription factors.
00:38:06.11 Likewise, when we looked at the embryonic stem cell transcriptional circuitry and asked,
00:38:13.20 what other transcriptional co-regulators, or regulators and co-factors,
00:38:17.18 are necessary to allow this so-called pluripotency program?
00:38:23.01 This amazing ability of these cells to be able to differentiate into every other cell type,
00:38:27.03 how does that happen? What is allowing that to happen
00:38:30.23 in this particular cell type, and not in other cell types?
00:38:33.23 And again, using the biochemical complementation technology,
00:38:38.00 we recently were able to identify a new co-factor complex, again a multi-subunit complex,
00:38:45.15 called the SCC, or "stem cell co-factor."
00:38:49.25 And remarkably, this SCC-B turns out to be a well-known protein that again had a different lifestyle in other cell types.
00:38:59.18 It's a protein complex that had previously been described as XPC,
00:39:03.29 which stands for "Xeroderma pigmentosum, complex C,"
00:39:08.22 which means that it's involved in DNA repair.
00:39:11.07 So up until now, we thought XPC was only functioning as a DNA repair complex,
00:39:16.14 and now we know that it's doing something quite different,
00:39:19.12 but only in the context of ES cells, which is to form a co-factor complex that will potentiate
00:39:25.27 the activity of two critical transcriptional activators, Oct4 and Sox2,
00:39:31.21 which define the pluripotent, self-renewing state of ES cells.
00:39:36.20 So these are just two examples of sort of what we're learning about,
00:39:41.21 the continuing saga of how transcriptional machinery evolved and works in animal cells.
00:39:50.26 And I'll finish with this last model slide,
00:39:54.00 which just simply reiterates what I just said:
00:39:57.00 We have to keep in mind that, in generating large sets of combinatorial, specific gene networks,
00:40:07.07 we have to use the diversity not only of sequence-specific DNA-binding proteins,
00:40:11.29 but we more and more see examples that components of the previously thought to be invariant core machinery
00:40:19.14 are an integral part of diversifying the combinatorial regulation of gene expression.
00:40:26.18 And this of course opens up many new possibilities,
00:40:30.08 and I suspect that there are many question marks yet about what exactly each of these components
00:40:36.27 is doing to drive complex regulation that gives rise to complexity like human beings,
00:40:44.12 the human brain, all the physiology that goes on.
00:40:48.03 And of course, as we understand these mechanisms in greater detail,
00:40:51.23 I think we have a much better chance of tackling the problems of human disease and diseases of other organisms.
00:40:59.10 Because ultimately, we have to understand the molecular basis of disease,
00:41:03.21 and I think a big part of that is understanding the mechanisms of gene regulation.

  • Part 1: Gene Regulation: An Introduction

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Table of Contents:

Nature and Scope of Biology

  • Systematics
  • Viruses
  • Kingdom Monera
  • Kingdom Protista
  • Fungi, Lichen and Mycorrhiza
  • Plant Classification
  • Algae
  • Bryophyta
  • Pteridophyta
  • Gymnosperms
  • Angiosperms
  • Evolutionary Trends & Classification of Animals
  • Protozoa
  • Non-Chordates
  • Chordates
  • Tools and Techniques in Cytology
  • A cell as a Unit of Life
  • Biomembrane
  • Structural Organization of Cell
  • Biomolecules
  • Enzymes
  • Cellular Metabolism
  • Cell Reproduction
  • Origin of Life
  • Relationship Among Organisms and Evidence of Evolution
  • Theories of Evolution
  • Human Evolution
  • Plant Taxonomy
  • Morphology of Flowering Plants
  • Anatomy of Flowering Plants
  • Animal Tissue
  • Integumentary System
  • Morphology and Anatomy of Animals (Frog, Cockroach, Rabbit, Earthworm)
  • Water Relations of Plants
  • Mineral Nutrition in Plants
  • Photosynthesis
  • Respiration in Plants
  • Nutrition & Digestive System
  • Breathing & Exchange of Gases
  • Locomotion and Movement
  • Body Fluids and Circulation
  • Excretory System
  • Nervous System
  • Sense Organs
  • Endocrine System
  • Reproduction in Flowering Plants
  • Plant Growth and Movement
  • Phytohormones
  • Human Reproduction
  • Embryonic Development
  • Growth, Repair, Regeneration, Ageing & Death
  • Heredity and Variation
  • Genes & Chromosomes
  • Genetic Material & Protein Synthesis
  • Gene Expression & Regulation
  • Human Genetics and its Disorders
  • Organisms and Environment
  • Population, Biotic Community & Succession
  • Ecosystem
  • Natural Resources and Their Conservation
  • Biodiversity
  • Pollution & Global Environmental Changes
  • Wildlife and Conservation
  • Biotechnology and Genetic Engineering
  • Domestication of Plants and Crop Improvement
  • Plant Tissue Culture
  • Economic Botany
  • Plant Pathology
  • Pesticides and Biofertilizers
  • Mental health, Addiction, and Community health
  • Immune System & Defence Mechanisms
  • Common Human Diseases
  • Biomedical Technologies
  • Domestication and Improvement of Animals
  • Animal Behaviour
  • Bioenergy
  • Growth of Human Population


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Section Summary

The early stages of embryonic development begin with fertilization. The process of fertilization is tightly controlled to ensure that only one sperm fuses with one egg. After fertilization, the zygote undergoes cleavage to form the blastula. The blastula, which in some species is a hollow ball of cells, undergoes a process called gastrulation, during which the three germ layers form. The ectoderm gives rise to the nervous system and the epidermal skin cells, the mesoderm gives rise to the muscle cells and connective tissue in the body, and the endoderm gives rise to the digestive system and other internal organs. Organogenesis is the formation of organs from the germ layers. Each germ layer gives rise to specific tissue types.

ABOUT THE BOOK Scott Gilbert Developmental Biology 11th Edition PDF free download

A classic gets a new coauthor and a new approach: Developmental Biology, Eleventh Edition, keeps the excellent writing, accuracy, and enthusiasm of the Gilbert Developmental Biology book, streamlines it, adds innovative electronic supplements, and creates a new textbook for those teaching Developmental Biology to a new generation.

Several new modes of teaching are employed in the new Gilbert and Barresi textbook. The videos explaining development—as well as those from Mary Tyler’s Vade Mecum—are referenced throughout the book, and several other valuable new elements have been added.

Additional updates include:

* An increased emphasis on stem cells, which are covered extensively and early in the book.
* Sex determination and gametogenesis, instead of being near the end of the volume, are up front, prior to fertilization.
* Greatly expanded coverage of neural development, comprising a unit unto itself.
* Coverage of new experiments on morphogenesis and differentiation, as well as new techniques such as CRISPR.

Significantly enhanced for the eleventh edition, and referenced throughout the textbook, the Developmental Biology Companion Website provides students with a range of engaging resources, in the following categories:

* NEW Dev Tutorials: Professionally produced video tutorials, presented by the textbook’s authors, reinforces key concepts.

* NEW Watch Development: Putting concepts into action, these informative videos show real-life developmental biology processes.

* Web Topics: These extensive topics provide more information for advanced students, historical, philosophical, and ethical perspectives on issues in developmental biology, and links to additional online resources.

* NEW Scientists Speak: In these question-and-answer interviews, developmental biology topics are explored by leading experts in the field.

* Plus the full bibliography of literature cited in the textbook (most linked to their PubMed citations).

DevBio Laboratory: Vade Mecum3

Included with each new copy of the textbook, Vade Mecum3 is an interactive website that helps students understand the organisms discussed in the course, and prepare them for the lab. The site includes videos of developmental processes and laboratory techniques, and has chapters on the following organisms: slime mold (Dictyostelium discoideum), planarian, sea urchin, fruit fly (Drosophila), chick, and amphibian.

Instructor’s Resource Library (available to qualified adopters)

The Developmental Biology, Eleventh Edition, Instructor’s Resource Library includes the following resources:

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* Developmental Biology: A Guide for Experimental Study, Third Edition, by Mary S. Tyler: The complete lab manual, in PDF format.

Unit 14: Embryonic Development and its Regulation - Biology

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This text is based on Openstax Biology for AP Courses, Senior Contributing Authors Julianne Zedalis, The Bishop's School in La Jolla, CA, John Eggebrecht, Cornell University Contributing Authors Yael Avissar, Rhode Island College, Jung Choi, Georgia Institute of Technology, Jean DeSaix, University of North Carolina at Chapel Hill, Vladimir Jurukovski, Suffolk County Community College, Connie Rye, East Mississippi Community College, Robert Wise, University of Wisconsin, Oshkosh

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From Metabolism to Gene Expression and Homeostasis

The disturbance in embryo metabolism, proliferative capacity, signaling competence, and maternal developmental cues associated with a suboptimal environment, either in vitro or in vivo, will activate a condition of stress, which in turn will promote further responses within embryos to maintain homeostatic balance [ 15, 16]. Environmental influence on embryo gene expression is a sensitive measure of stress increased expression of hsp70.1 and the growth-arrest gene CHOP-10 occurs in response to diverse stresses in rodent and bovine embryos [ 110, 111]. Expression of growth-regulating genes is also susceptible to the environment. Mouse embryos developing in culture express lower levels of the growth factors Igf-1 and -2 than do embryos in vivo [ 112, 113], while culture in KSOM medium with amino acids results in gene expression of Igf-1 and -2 and their receptors at a higher level that in embryos cultured in Whitten medium and more similar to in vivo embryos [ 114].

A range of metabolic and differentiation-related genes has been shown to alter their expression profile in response to culture conditions in bovine embryos [ 115, 116]. For example, genes critical in trophectoderm differentiation and intercellular junction formation are expressed at different levels dependent on in vivo or in vitro derivation and, for the latter, the type of medium used [ 117]. In the case of the human, in vitro-cultured embryos show significant variation in expression of genes involved in apoptotic [ 118, 119] and differentiation [ 120, 121] pathways and show wide variation in apoptotic rate and blastocyst cell numbers [ 122], indicative of variable developmental potential.

Extraembryonic Structures and Chick Embryo | Embryology

The embryo of chick possesses four extra­embryonic or foetal membranes: namely, the yolk sac, the allantois, the amnion and the serosa or chorion. In amphibian embryo, the yolk sac and the allantois are present in rudimentary condition.

The amnion and the serosa are developed in the reptilian embryo for the first time in evolutionary history of the vertebrates. In birds these two structures are retained while in mam­mals these are also present in a modified form. All the extraembryonic mem­branes are discarded at hatching while the yolk sac is incorporated into the small intestine.

As development goes on, the closely set ectoderm and somatopleure (somatic mesoderm) as well as the endoderm and splanchnopleure (splanchnic mesoderm) extend into the extraembryonic area. The developing embryo becomes located at the central area of the blastodisc.

The embryo becomes separated by undercutting grooves formed by limiting body folds. These folds initiate with the formation of crescentic head fold which extends backward as the body folds. The body folds subsequently merge with the tail fold. By this, way the embryo undercuts and separates itself from the underlying yolk mass.

Formation of Yolk Sac and its Fate :

The yolk, though supplies nourishment to the embryo, is not considered as part of the embryo. But in cases where the quantity of yolk is very large, special yolk sac develops to store the yolk. As the em­bryo raises itself, the yolk is enclosed by the yolk sac. The yolk sac develops from the margin of the blastoderm which advances around the yolk mass until it surrounds the mass completely.

In chick embryo, the gut is represented by a round cavity beneath the primitive streak at about sixteen hours of incubation. At about 24 hours, a small enteric pocket develops into the developing head as the foregut. The foregut is surrounded by mesoderm.

At about 48-hour stage, with the formation of tail bud, a sac-like hind- gut develops. The undifferentiated portion of the gut between the fore- and hindgut is called the midgut which remains as a small portion of the small intestine as the embryo grows older.

The midgut leads into the reduced yolk sac by yolk stalk (Fig. 5.43 A1). The yolk sac becomes smaller due to consumption of the yolk and before hatching the yolk sac exists as a projection from the small intes­tine. The yolk sac is covered by splanchnopleure. The yolk sac is finally incorpora­ted with the small intestine.

The yolk is used as food by the embryo. The endoderm of the yolk sac secretes en­zymes which break the yolk into diffusible substances. These substances are carried by the vitelline veins and finally to the heart. From the heart these are conveyed to the different parts of the embryo and extra­embryonic structures.

Formation of Amnion and Serosa :

The amnion and the serosa (or chorion) are the two extraembryonic membranes which develop together. The amnion is actually a membrane covering the em­bryo and thus housing it like a bag. It separates the embryo from the immediate contact with the environment. Between the embryo and the amnion, there is a space called the amniotic cavity containing amniotic fluid, a saline solution.

The amnion as well as the amniotic fluid pro­tect the developing embryo from desicca­tion and also equalise the pressure against

the embryo by physical forces. The fluid acts as a buffer and gives protection from any kind of shock. Adhesion of the embryo to the amniotic wall is prevented by the rhythmic movement of the amnion.

As the embryo grows, the weight of the body is enhanced and as a result the embryo-sinks into the soft yolk. Due to this, the blastodisc remains elevated over the em­bryo. At 30 hours of incubation, a well- formed head of the embryo of chick pushes forward and sinks into the underlying yolk.

This causes the elevation of a blastodermic fold called the amniotic head fold. This fold bends backward over the head and covers it as a hood.

The lateral ends of the head fold prolong backward along the two sides of the embryo as lateral amniotic folds. The lateral folds come over the embryo and fuse with each other along the antero­posterior direction. As a consequence of fusion, the embryo becomes more or less covered by folds.

After 48 hours of incubation another fold appears from the posterior end of the embryo (tail bud) which is called the amniotic tail fold. This fold proceeds forward over the embryo and finally meets and fuses with amniotic head fold during the 4th day of incubation (Fig. 5.43 A2). The region of union of the amniotic folds is marked by a scar called the seroamniotic connection.

The amniotic fold is composed of two layers—an inner and an outer. So the fusion of such folds will result in the for­mation of an inner and an outer layer. The inner layer is named as the amnion and the outer one is called the serosa (the name chorion is reserved from the same layer in mammals by many embryologists). The amnion is composed of somatic mesoderm on the outer side and ectoderm on the inner side.

The serosa has the somatic mesoderm on the inner side and the ecto­derm on the outerside (Fig. 5.43 A2). In between the serosa and the amnion lies the extraembryonic coelom which is continuous with the intraembryonic coelom of the embryo proper. The serosa grows around the yolk sac and encloses it completely at the end of second week.

Formation of Allantois:

The allantois develops in conjunction with the serosa and differs in nature from the other extraembryonic membranes. It is not discarded in mammals but its intra­embryonic portion is retained as the uri­nary bladder.

The allantois starts its development as a ventral diverticulum in the 72-hour old chick embryo from the hindgut. This out­growth consists of an inner endoderm with a layer of splanchnic mesoderm on the outer side. The diverticulum grows rapidly to invade the extraembryonic coelom (Fig. 5.43 B1, B2) and into the space between the yolk sac, the amnion and the serosa.

Although the distal part of the allantois expands considerably, it remains connect­ed with the hindgut by a narrow allantoic stalk. As the embryo separates itself from the extraembryonic parts, the allantoic stalk is enclosed together with the yolk stalk to form the umbilical cord. The allan­tois is connected with the extraembryonic circulation by paired allantoic arteries and veins.

The allantois is partly excretory in func­tion and also acts as a reservoir by storing uric acid. It also serves as a respiratory surface by supplying oxygen to the em­bryo. It also helps to absorb a large quantity of albumen. With the develop­ment of allantoic circulation a considerable portion of calcium is absorbed from the egg shell.

This absorbed calcium is utilised by the embryo for the formation of bones. The egg shell by losing calcium becomes thin and delicate and thus facilitates hatch­ing.

28.2 Embryonic Development

Throughout this chapter, we will express embryonic and fetal ages in terms of weeks from fertilization, commonly called conception. The period of time required for full development of a fetus in utero is referred to as gestation (gestare = “to carry” or “to bear”). It can be subdivided into distinct gestational periods. The first 2 weeks of prenatal development are referred to as the pre-embryonic stage. A developing human is referred to as an embryo during weeks 3–8, and a fetus from the ninth week of gestation until birth. In this section, we’ll cover the pre-embryonic and embryonic stages of development, which are characterized by cell division, migration, and differentiation. By the end of the embryonic period, all of the organ systems are structured in rudimentary form, although the organs themselves are either nonfunctional or only semi-functional.

Pre-implantation Embryonic Development

Following fertilization, the zygote and its associated membranes, together referred to as the conceptus , continue to be projected toward the uterus by peristalsis and beating cilia of the epithelial cells of the Fallopian tube. During its journey to the uterus, the zygote undergoes five or six rapid mitotic cell divisions. Although each cleavage results in more cells, it does not increase the total volume of the conceptus (Figure 28.4). Each daughter cell produced by cleavage is called a blastomere (blastos = “germ,” in the sense of a seed or sprout).

Approximately 3 days after fertilization, a 16-cell conceptus reaches the uterus. The cells that had been loosely grouped are now compacted and look more like a solid mass. The name given to this structure is the morula (morula = “little mulberry”). Once inside the uterus, the conceptus floats freely for several more days. It continues to divide, creating a ball of approximately 100 cells, and consuming nutritive endometrial secretions called uterine milk while the uterine lining thickens. The ball of now tightly bound cells starts to secrete fluid and organize themselves around a fluid-filled cavity, the blastocoel . At this developmental stage, the conceptus is referred to as a blastocyst . Within this structure, a group of cells forms into an inner cell mass , which is fated to become the embryo. The cells that form the outer shell are called trophoblasts (trophe = “to feed” or “to nourish”). These cells will develop into the chorionic sac and the fetal portion of the placenta (the organ of nutrient, waste, and gas exchange between mother and the developing offspring).

The inner mass of embryonic cells is totipotent during this stage, meaning that each cell has the potential to differentiate into any cell type in the human body. Totipotency lasts for only a few days before the cells’ fates are set as being the precursors to a specific lineage of cells.

As the blastocyst forms, the trophoblast excretes enzymes that begin to degrade the zona pellucida. In a process called “hatching,” the conceptus breaks free of the zona pellucida in preparation for implantation.

Interactive Link

View this time-lapse movie of a conceptus starting at day 3. What is the first structure you see? At what point in the movie does the blastocoel first appear? What event occurs at the end of the movie?


At the end of the first week, the blastocyst comes in contact with the uterine wall and adheres to it, embedding itself in the uterine lining via the trophoblast cells. Thus begins the process of implantation , which signals the end of the pre-embryonic stage of development (Figure 28.5). Implantation can be accompanied by minor bleeding. The blastocyst typically implants in the fundus of the uterus or on the posterior wall. However, if the endometrium is not fully developed and ready to receive the blastocyst, the blastocyst will detach and find a better spot. A significant percentage (50–75 percent) of blastocysts fail to implant when this occurs, the blastocyst is shed with the endometrium during menses. The high rate of implantation failure is one reason why pregnancy typically requires several ovulation cycles to achieve.

When implantation succeeds and the blastocyst adheres to the endometrium, the superficial cells of the trophoblast fuse with each other, forming the syncytiotrophoblast , a multinucleated body that digests endometrial cells to firmly secure the blastocyst to the uterine wall. In response, the uterine mucosa rebuilds itself and envelops the blastocyst (Figure 28.6). The trophoblast secretes human chorionic gonadotropin (hCG) , a hormone that directs the corpus luteum to survive, enlarge, and continue producing progesterone and estrogen to suppress menses. These functions of hCG are necessary for creating an environment suitable for the developing embryo. As a result of this increased production, hCG accumulates in the maternal bloodstream and is excreted in the urine. Implantation is complete by the middle of the second week. Just a few days after implantation, the trophoblast has secreted enough hCG for an at-home urine pregnancy test to give a positive result.

Most of the time an embryo implants within the body of the uterus in a location that can support growth and development. However, in one to two percent of cases, the embryo implants either outside the uterus (an ectopic pregnancy ) or in a region of uterus that can create complications for the pregnancy. If the embryo implants in the inferior portion of the uterus, the placenta can potentially grow over the opening of the cervix, a condition call placenta previa .

Disorders of the.

Development of the Embryo

In the vast majority of ectopic pregnancies, the embryo does not complete its journey to the uterus and implants in the uterine tube, referred to as a tubal pregnancy. However, there are also ovarian ectopic pregnancies (in which the egg never left the ovary) and abdominal ectopic pregnancies (in which an egg was “lost” to the abdominal cavity during the transfer from ovary to uterine tube, or in which an embryo from a tubal pregnancy re-implanted in the abdomen). Once in the abdominal cavity, an embryo can implant into any well-vascularized structure—the rectouterine cavity (Douglas’ pouch), the mesentery of the intestines, and the greater omentum are some common sites.

Tubal pregnancies can be caused by scar tissue within the tube following a sexually transmitted bacterial infection. The scar tissue impedes the progress of the embryo into the uterus—in some cases “snagging” the embryo and, in other cases, blocking the tube completely. Approximately one half of tubal pregnancies resolve spontaneously. Implantation in a uterine tube causes bleeding, which appears to stimulate smooth muscle contractions and expulsion of the embryo. In the remaining cases, medical or surgical intervention is necessary. If an ectopic pregnancy is detected early, the embryo’s development can be arrested by the administration of the cytotoxic drug methotrexate, which inhibits the metabolism of folic acid. If diagnosis is late and the uterine tube is already ruptured, surgical repair is essential.

Even if the embryo has successfully found its way to the uterus, it does not always implant in an optimal location (the fundus or the posterior wall of the uterus). Placenta previa can result if an embryo implants close to the internal os of the uterus (the internal opening of the cervix). As the fetus grows, the placenta can partially or completely cover the opening of the cervix (Figure 28.7). Although it occurs in only 0.5 percent of pregnancies, placenta previa is the leading cause of antepartum hemorrhage (profuse vaginal bleeding after week 24 of pregnancy but prior to childbirth).

Embryonic Membranes

During the second week of development, with the embryo implanted in the uterus, cells within the blastocyst start to organize into layers. Some grow to form the extra-embryonic membranes needed to support and protect the growing embryo: the amnion, the yolk sac, the allantois, and the chorion.

At the beginning of the second week, the cells of the inner cell mass form into a two-layered disc of embryonic cells, and a space—the amniotic cavity —opens up between it and the trophoblast (Figure 28.8). Cells from the upper layer of the disc (the epiblast ) extend around the amniotic cavity, creating a membranous sac that forms into the amnion by the end of the second week. The amnion fills with amniotic fluid and eventually grows to surround the embryo. Early in development, amniotic fluid consists almost entirely of a filtrate of maternal plasma, but as the kidneys of the fetus begin to function at approximately the eighth week, they add urine to the volume of amniotic fluid. Floating within the amniotic fluid, the embryo—and later, the fetus—is protected from trauma and rapid temperature changes. It can move freely within the fluid and can prepare for swallowing and breathing out of the uterus.

On the ventral side of the embryonic disc, opposite the amnion, cells in the lower layer of the embryonic disk (the hypoblast ) extend into the blastocyst cavity and form a yolk sac . The yolk sac supplies some nutrients absorbed from the trophoblast and also provides primitive blood circulation to the developing embryo for the second and third week of development. When the placenta takes over nourishing the embryo at approximately week 4, the yolk sac has been greatly reduced in size and its main function is to serve as the source of blood cells and germ cells (cells that will give rise to gametes). During week 3, a finger-like outpocketing of the yolk sac develops into the allantois , a primitive excretory duct of the embryo that will become part of the urinary bladder. Together, the stalks of the yolk sac and allantois establish the outer structure of the umbilical cord.

The last of the extra-embryonic membranes is the chorion , which is the one membrane that surrounds all others. The development of the chorion will be discussed in more detail shortly, as it relates to the growth and development of the placenta.


As the third week of development begins, the two-layered disc of cells becomes a three-layered disc through the process of gastrulation , during which the cells transition from totipotency to multipotency. The embryo, which takes the shape of an oval-shaped disc, forms an indentation called the primitive streak along the dorsal surface of the epiblast. A node at the caudal or “tail” end of the primitive streak emits growth factors that direct cells to multiply and migrate. Cells migrate toward and through the primitive streak and then move laterally to create two new layers of cells. The first layer is the endoderm , a sheet of cells that displaces the hypoblast and lies adjacent to the yolk sac. The second layer of cells fills in as the middle layer, or mesoderm . The cells of the epiblast that remain (not having migrated through the primitive streak) become the ectoderm (Figure 28.9).

Each of these germ layers will develop into specific structures in the embryo. Whereas the ectoderm and endoderm form tightly connected epithelial sheets, the mesodermal cells are less organized and exist as a loosely connected cell community. The ectoderm gives rise to cell lineages that differentiate to become the central and peripheral nervous systems, sensory organs, epidermis, hair, and nails. Mesodermal cells ultimately become the skeleton, muscles, connective tissue, heart, blood vessels, and kidneys. The endoderm goes on to form the epithelial lining of the gastrointestinal tract, liver, and pancreas, as well as the lungs (Figure 28.10).

Development of the Placenta

During the first several weeks of development, the cells of the endometrium—referred to as decidual cells—nourish the nascent embryo. During prenatal weeks 4–12, the developing placenta gradually takes over the role of feeding the embryo, and the decidual cells are no longer needed. The mature placenta is composed of tissues derived from the embryo, as well as maternal tissues of the endometrium. The placenta connects to the conceptus via the umbilical cord , which carries deoxygenated blood and wastes from the fetus through two umbilical arteries nutrients and oxygen are carried from the mother to the fetus through the single umbilical vein. The umbilical cord is surrounded by the amnion, and the spaces within the cord around the blood vessels are filled with Wharton’s jelly, a mucous connective tissue.

The maternal portion of the placenta develops from the deepest layer of the endometrium, the decidua basalis. To form the embryonic portion of the placenta, the syncytiotrophoblast and the underlying cells of the trophoblast (cytotrophoblast cells) begin to proliferate along with a layer of extraembryonic mesoderm cells. These form the chorionic membrane , which envelops the entire conceptus as the chorion. The chorionic membrane forms finger-like structures called chorionic villi that burrow into the endometrium like tree roots, making up the fetal portion of the placenta. The cytotrophoblast cells perforate the chorionic villi, burrow farther into the endometrium, and remodel maternal blood vessels to augment maternal blood flow surrounding the villi. Meanwhile, fetal mesenchymal cells derived from the mesoderm fill the villi and differentiate into blood vessels, including the three umbilical blood vessels that connect the embryo to the developing placenta (Figure 28.11).

The placenta develops throughout the embryonic period and during the first several weeks of the fetal period placentation is complete by weeks 14–16. As a fully developed organ, the placenta provides nutrition and excretion, respiration, and endocrine function (Table 28.1 and Figure 28.12). It receives blood from the fetus through the umbilical arteries. Capillaries in the chorionic villi filter fetal wastes out of the blood and return clean, oxygenated blood to the fetus through the umbilical vein. Nutrients and oxygen are transferred from maternal blood surrounding the villi through the capillaries and into the fetal bloodstream. Some substances move across the placenta by simple diffusion. Oxygen, carbon dioxide, and any other lipid-soluble substances take this route. Other substances move across by facilitated diffusion. This includes water-soluble glucose. The fetus has a high demand for amino acids and iron, and those substances are moved across the placenta by active transport.

Maternal and fetal blood does not commingle because blood cells cannot move across the placenta. This separation prevents the mother’s cytotoxic T cells from reaching and subsequently destroying the fetus, which bears “non-self” antigens. Further, it ensures the fetal red blood cells do not enter the mother’s circulation and trigger antibody development (if they carry “non-self” antigens)—at least until the final stages of pregnancy or birth. This is the reason that, even in the absence of preventive treatment, an Rh − mother doesn’t develop antibodies that could cause hemolytic disease in her first Rh + fetus.

Although blood cells are not exchanged, the chorionic villi provide ample surface area for the two-way exchange of substances between maternal and fetal blood. The rate of exchange increases throughout gestation as the villi become thinner and increasingly branched. The placenta is permeable to lipid-soluble fetotoxic substances: alcohol, nicotine, barbiturates, antibiotics, certain pathogens, and many other substances that can be dangerous or fatal to the developing embryo or fetus. For these reasons, pregnant women should avoid fetotoxic substances. Alcohol consumption by pregnant women, for example, can result in a range of abnormalities referred to as fetal alcohol spectrum disorders (FASD). These include organ and facial malformations, as well as cognitive and behavioral disorders.

  • Mediates diffusion of maternal glucose, amino acids, fatty acids, vitamins, and minerals
  • Stores nutrients during early pregnancy to accommodate increased fetal demand later in pregnancy
  • Excretes and filters fetal nitrogenous wastes into maternal blood
  • Mediates maternal-to-fetal oxygen transport and fetal-to-maternal carbon dioxide transport
  • Secretes several hormones, including hCG, estrogens, and progesterone, to maintain the pregnancy and stimulate maternal and fetal development
  • Mediates the transmission of maternal hormones into fetal blood and vice versa


Following gastrulation, rudiments of the central nervous system develop from the ectoderm in the process of neurulation (Figure 28.13). Specialized neuroectodermal tissues along the length of the embryo thicken into the neural plate . During the fourth week, tissues on either side of the plate fold upward into a neural fold . The two folds converge to form the neural tube . The tube lies atop a rod-shaped, mesoderm-derived notochord , which eventually becomes the nucleus pulposus of intervertebral discs. Block-like structures called somites form on either side of the tube, eventually differentiating into the axial skeleton, skeletal muscle, and dermis. During the fourth and fifth weeks, the anterior neural tube dilates and subdivides to form vesicles that will become the brain structures.

Folate, one of the B vitamins, is important to the healthy development of the neural tube. A deficiency of maternal folate in the first weeks of pregnancy can result in neural tube defects, including spina bifida—a birth defect in which spinal tissue protrudes through the newborn’s vertebral column, which has failed to completely close. A more severe neural tube defect is anencephaly, a partial or complete absence of brain tissue.

The embryo, which begins as a flat sheet of cells, begins to acquire a cylindrical shape through the process of embryonic folding (Figure 28.14). The embryo folds laterally and again at either end, forming a C-shape with distinct head and tail ends. The embryo envelops a portion of the yolk sac, which protrudes with the umbilical cord from what will become the abdomen. The folding essentially creates a tube, called the primitive gut, that is lined by the endoderm. The amniotic sac, which was sitting on top of the flat embryo, envelops the embryo as it folds.

Within the first 8 weeks of gestation, a developing embryo establishes the rudimentary structures of all of its organs and tissues from the ectoderm, mesoderm, and endoderm. This process is called organogenesis .

Like the central nervous system, the heart also begins its development in the embryo as a tube-like structure, connected via capillaries to the chorionic villi. Cells of the primitive tube-shaped heart are capable of electrical conduction and contraction. The heart begins beating in the beginning of the fourth week, although it does not actually pump embryonic blood until a week later, when the oversized liver has begun producing red blood cells. (This is a temporary responsibility of the embryonic liver that the bone marrow will assume during fetal development.) During weeks 4–5, the eye pits form, limb buds become apparent, and the rudiments of the pulmonary system are formed.

During the sixth week, uncontrolled fetal limb movements begin to occur. The gastrointestinal system develops too rapidly for the embryonic abdomen to accommodate it, and the intestines temporarily loop into the umbilical cord. Paddle-shaped hands and feet develop fingers and toes by the process of apoptosis (programmed cell death), which causes the tissues between the fingers to disintegrate. By week 7, the facial structure is more complex and includes nostrils, outer ears, and lenses (Figure 28.15). By the eighth week, the head is nearly as large as the rest of the embryo’s body, and all major brain structures are in place. The external genitalia are apparent, but at this point, male and female embryos are indistinguishable. Bone begins to replace cartilage in the embryonic skeleton through the process of ossification. By the end of the embryonic period, the embryo is approximately 3 cm (1.2 in) from crown to rump and weighs approximately 8 g (0.25 oz).

Interactive Link

Use this interactive tool to view the process of embryogenesis from fertilization through pregnancy to birth. Can you identify when neurulation occurs in the embryo?

Watch the video: Unit 3 AOS 1 Biology: Gene Structure and Regulation (July 2022).


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