Answering the questions about how cells, tissues, and organisms form, precedes the question of how they can eventually diversify, evolve, change and morph from one species to another through a macroevolutionary primary speciation transition zone, where novel organismal features arise, like wings, eyes, ears, legs, arms, and so forth. The fact is, that science is still FAR from being able to answer that question in an exhaustive manner. One of the crucial questions is cell fate determination and differentiation, tissue formation, and what, what cell phenotype type each cell will become. Many questions have been provided, but many open questions remain.
Within an embryo, several processes play out at the cellular and tissue level to create an organism. These processes include cell proliferation, differentiation, and cellular movement 7
Cell determination starts early and progressively narrows the options as the cell steps through a programmed series of intermediate states—guided at each step by its genome, its history, and its interactions with neighbors. The process reaches its limit when a cell undergoes terminal differentiation to form one of the highly specialized cell types of the adult body. Although there are cell types in the adult that retain some degree of pluripotency, their range of options is generally narrow.
1. Cell-Cell communication and transcriptional control through up to eleven different signaling pathways
2. Genes required specifically for animal development
3. Genes that encode proteins used for cell-cell adhesion and cell signaling; hundreds of human genes encode signal proteins, cell-surface receptors, cell adhesion proteins, or ion channels that are either not present in yeast or present in much smaller numbers.
4. Genes encoding proteins that regulate transcription and chromatin structure: more than 1000 human genes encode transcription regulators, but only about 250 yeast genes do so. The development of animals is dominated by cell-cell interactions and by differential gene expression.
5. Noncoding RNAs that encode microRNAs (miRNAs); there are at least 500 of these in humans. Along with the regulatory proteins, they play a significant part in controlling gene expression during animal development, but the full extent of their importance is still unclear.
6. Transcription factors — proteins that regulate which genes are transcribed in a cell — appear to be essential to determining the pathway particular stem cells take as they differentiate.
7. Cell Memory Underlies Cell Decision-Making Underlying the richness and astonishingly complex outcomes of development is cell memory. Both the genes a cell expresses and the way it behaves depend on the cell’s past, as well as on its present circumstances.
8. The chromatin state — the packaging of DNA with both histone and non-histone proteins — has marked effects on gene expression and is believed to contribute to the establishment and the maintenance of cell identities. Many histone modifiers and chromatin remodelers have been implicated in stem cell pluripotency, cellular differentiation and development.
9. The DNA methylation code is like a barcode or marker, the methyl group indicates, for instance, which genes in the DNA are to be turned on.
10. The Sugar Code forms information-rich structures that influence the arrangement of different cell types during embryological development.
11. Factors secreted into its cytoplasm during cleavage. (proteins, small regulatory RNAs and mRNA) Early cleavage patterns appear to bias blastomeres to a particular fate
12. Positive feedback can create asymmetry from homogeneity. In cases where the external or stimuli that would cause asymmetry are very weak or disorganized, through positive feedback the system can spontaneously pattern itself.
13. Concentration-gradients of morphogens: Cell-extrinsic process that relies on cues and interactions between cells or from concentration-gradients of morphogens.
14. Positional value: cell specification occurs based on where within the embryo the cell is positioned Position within the morula ( early-stage embryo consisting of 16 cells) being the most significant contributor to eventual cell fate decisions.
15. The primitive endoderm (PE) is an extra-embryonic cell type whose descendants provide patterning cues and nutrient supplies to the developing embryo.
Modes of specificationThere are three general ways a cell can become specified for a particular fate; they are autonomous specification, conditional specification and syncytial specification.
Autonomous specificationThis type of specification results from cell-intrinsic properties; it gives rise to mosaic development. The cell-intrinsic properties arise from a cleavage of a cell with asymmetrically expressed maternal cytoplasmic determinants (proteins, small regulatory RNAs and mRNA). Thus, the fate of the cell depends on factors secreted into its cytoplasm during cleavage.
Positive feedback can create asymmetry from homogeneity. In cases where the external or stimuli that would cause asymmetry are very weak or disorganized, through positive feedback the system can spontaneously pattern itself. Once the feedback has begun, any small initial signaling is magnified and thus produces an effective patterning mechanism. This is normally what occurs in the case of lateral inhibition in which neighboring cells induce specification via inhibitory or inducing signals (see Notch signaling). This kind of positive feedback at the single cell level and tissue level is responsible for symmetry breaking, which is an all-or-none process whereas once the symmetry is broken, the cells involved become very different. Symmetry breaking leads to a bistable or multistable system where the cell or cells involved are determined for different cell fates. The determined cells continue on their particular fate even after the initial stimulatory/inhibitory signal is gone, giving the cells a memory of the signal.
Conditional specificationIn contrast to the autonomous specification, this type of specification is a cell-extrinsic process that relies on cues and interactions between cells or from concentration-gradients of morphogens. Inductive interactions between neighboring cells is the most common mode of tissue patterning. In this mechanism, one or two cells from a group of cells with the same developmental potential are exposed to a signal (morphogen) from outside the group. Only the cells exposed to the signal are induced to follow a different developmental pathway, leaving the rest of the equivalence group unchanged. Another mechanism that determines the cell fate is regional determination (see Regional specification). As implied by the name, this specification occurs based on where within the embryo the cell is positioned, it is also known as positional value. This was first observed when mesoderm was taken from the prospective thigh region of a chick embryo, was grafted onto the wing region and did not transform to wing tissue, but instead into toe tissue.
Syncytial specificationThis type of a specification is a hybrid of the autonomous and conditional that occurs in insects. This method involves the action of morphogen gradients within the syncytium. As there are no cell boundaries in the syncytium, these morphogens can influence nuclei in a concentration-dependent manner.
At first glance, one would no more expect the worm, the flea, the eagle, and the giant squid all to be generated by the same developmental mechanisms than one would suppose that the same methods were used to make a shoe and an airplane. Remarkably, however, research in the past 30 years has revealed that much of the basic machinery of development is essentially the same in all animals—not just in all vertebrates, but in all the major phyla of invertebrates too. Recognizably similar, related molecules define the specialized animal cell types, mark the differences between body regions, and help create the animal body pattern. Homologous proteins are often functionally interchangeable between very different species. Thus, a human protein produced artificially in a fly, for example, can perform the same function as the fly’s own version of that protein.
The shared anatomical features of animals develop through conserved mechanisms. After fertilization, the zygote usually divides rapidly, or cleaves, to form many smaller cells; during this cleavage, the embryo, which cannot yet feed, does not grow. This phase of development is initially driven and controlled entirely by the material deposited in the egg by the mother. The embryonic genome remains inactive until a point is reached when maternal mRNAs and proteins rather abruptly begin to be degraded. The embryo’s genome is activated, and the cells cohere to form a blastula—typically a solid or a hollow fluid-filled ball of cells. Complex cell rearrangements called gastrulation (from the Greek “gaster,” meaning “belly”) then transform the blastula into a multilayered structure containing a rudimentary internal gut
The early stages of development, as exemplified by a frog.
(A) A fertilized egg divides to produce a blastula—a sheet of epithelial cells often surrounding a cavity. During gastrulation, some of the cells tuck into the interior to form the mesoderm (green) and endoderm (yellow). Ectodermal cells (blue) remain on the outside.
(B) A cross-section through the trunk of an amphibian embryo shows the basic animal body plan, with a sheet of ectoderm on the outside, a tube of endoderm on the inside, and mesoderm sandwiched between them. The endoderm forms the epithelial lining of the gut, from the mouth to the anus. It gives rise not only to the pharynx, esophagus, stomach, and intestines, but also to many associated structures. The salivary glands, liver, pancreas, trachea, and lungs, for example, all develop from the wall of the digestive tract and grow to become systems of branching tubes that open into the gut or pharynx. The endoderm forms only the epithelial components of these structures— the lining of the gut and the secretory cells of the pancreas, for example. The supporting muscular and fibrous elements arise from the mesoderm. The mesoderm gives rise to the connective tissues—at first, to the loose mesh of cells in the embryo known as mesenchyme, and ultimately to cartilage, bone, and fibrous tissue, including the dermis (the inner layer of the skin). The mesoderm also forms the muscles, the entire vascular system—including the heart, blood vessels, and blood cells—and the tubules, ducts, and supporting tissues of the kidneys and gonads. The notochord forms from the mesoderm and serves as the core of the future backbone and the source of signals that coordinate the development of surrounding tissues. The ectoderm will form the epidermis(the outer, epithelial layer of the skin) and epidermal appendages such as hair, sweat glands, and mammary glands. It will also give rise to the whole of the nervous system, central and peripheral, including not only neurons and glia but also the sensory cells of the nose, the ear, the eye, and other sense organs.
Some cells of the blastula remain external, constituting the ectoderm, which will give rise to the epidermis and the nervous system; other cells invaginate, forming the endoderm, which will give rise to the gut tube and its appendages, such as lung, pancreas, and liver. Another group of cells moves into the space between ectoderm and endoderm and forms the mesoderm, which will give rise to muscles, connective tissues, blood, kidney, and various other components. Further cell movements and accompanying cell differentiations create and refine the embryo’s architecture. The ectoderm, mesoderm, and endoderm formed during gastrulation constitute the three germ layers of the early embryo. Many later developmental transformations will produce the elaborately structured organs. But the basic body plan and axes set up in miniature during gastrulation are preserved into adult life, when the organism may be billions of times larger.
Concomitant with the refinement of the body plan, the individual cells become more and more restricted in their developmental potential. During the blastula stages, cells are often totipotent or pluripotent—they have the potential to give rise to all or almost all of the cell types of the adult body. The pluripotency is lost as gastrulation proceeds: a cell located in the endodermal germ layer, for example, can give rise to the cell types that will line the gut or form gut-derived organs such as the liver or pancreas, but it no longer has the potential to form mesoderm-derived structures such as skeleton, heart, or kidney. Such a cell is said to be determined for an endodermal fate. Thus, cell determination starts early and progressively narrows the options as the cell steps through a programmed series of intermediate states—guided at each step by its genome, its history, and its interactions with neighbors. The process reaches its limit when a cell undergoes terminal differentiation to form one of the highly specialized cell types of the adult body. Although there are cell types in the adult that retain some degree of pluripotency, their range of options is generally narrow.
The lineage from blastomere to differentiated cell type.
As development proceeds, cells become more and more specialized. Blastomeres have the potential to give rise to most or all cell types. Under the influence of signalling molecules and gene regulatory factors, cells acquire more restricted fates until they differentiate into highly specialized cell types, such as the pancreatic β-islet cells that secrete the hormone insulin.
Genes involved in Cell-Cell communication and transcriptional control are especially important for animal development
What are the genes that animals share with one another but not with other kingdoms of life? These would be expected to include genes required specifically for animal development but not needed for unicellular existence. Comparison of animal genomes with the genome of budding yeast—a unicellular eukaryote— suggests that three classes of genes are especially important for multicellular organization.
The first class includes genes that encode proteins used for cell-cell adhesion and cell signaling; hundreds of human genes encode signal proteins, cell-surface receptors, cell adhesion proteins, or ion channels that are either not present in yeast or present in much smaller numbers.
The second class includes genes encoding proteins that regulate transcription and chromatin structure: more than 1000 human genes encode transcription regulators, but only about 250 yeast genes do so. The development of animals is dominated by cell–cell interactions and by differential gene expression.
The third class of noncoding RNAs has a more uncertain status: it includes genes that encode microRNAs (miRNAs); there are at least 500 of these in humans. Along with the regulatory proteins, they play a significant part in controlling gene expression during animal development, but the full extent of their importance is still unclear.
The loss of individual miRNA genes in C. elegans, where their functions have been well studied, rarely leads to obvious phenotypes, suggesting that the roles of miRNAs during animal development are often subtle, serving to fine-tune the developmental machinery rather than to form its core structures.
Each gene in a multicellular organism is associated with many thousands of nucleotides of noncoding DNA that contains regulatory elements. These regulatory elements determine when, where, and how strongly the gene is to be expressed, according to the transcription regulators and chromatin structures that are present in the particular cell.
Genetically identical human cells are classified by their distinct behaviors into cell types, implying that nongenetic factors—including chromatin organization—contribute to their distinctive gene expression patterns. 1 Being stably heritable through cell division, both chromatin organization and the unique pattern of gene expression are therefore epigenetic. In higher organisms, all cells share the same genome, but every cell expresses only a limited and specific set of genes that defines the cell type. During cell division, not only the genome but also the cell type is inherited by the daughter cells. This intriguing phenomenon is achieved by a variety of processes that have been collectively termed epigenetics. governed by extremely rich and exquisitely multiscale physical mechanisms. 2 These include chemical modifications of DNA and histone proteins, and the physics that govern the three-dimensional organization of the genome in cell nuclei. Cells use many different physical principles, electrostatic and mechanical properties related to chemical modifications of DNA and histones. A limited set of physical rules ( instructional information ) plays a key role in cell differentiation.
During development, the determination of the cell type (cell fate) depends on DNA methylation which is a key control parameter of this process: genes that are specific for the desired tissue are kept unmethylated, whereas the others are methylated. Moreover, patterns of DNA methylation are faithfully propagated throughout successive cell divisions. The gene body DNA methylation codes are universal similar to the universality of the genetic code and
should consequently be considered as part of the inheritance system. 3 Living organisms incorporate complex interaction between genes and epigenetic factors and the environment which shapes the organismal form that develops and adapts over time.
For a complete understanding of biological processes such as development and adaptation, it is necessary to understand as many integrative elements of biological systems as possible. Epigenetic information can be stored in a multitude of bearers such as histone modifications, non-coding RNA, the topology of the nucleus, and methylation of DNA.
Transcription factors — proteins that regulate which genes are transcribed in a cell — appear to be essential to determining the pathway particular stem cells take as they differentiate. 4
Cell Memory Underlies Cell Decision-Making
Underlying the richness and astonishingly complex outcomes of development is cell memory. Both the genes a cell expresses and the way it behaves depend on the cell’s past, as well as on its present circumstances. The cells of our
body—the muscle cells, the neurons, the skin cells, the gut cells, and so on—maintain their specialized characters largely because they retain a record of the extracellular signals their ancestors received during development, rather than because they continually receive such instructions from their surroundings. Despite their radically different phenotypes, they retain the same complete genome that was present in the zygote; their differences arise instead from differential gene expression.
Several Model Organisms Have Been Crucial for Understanding Development
The differences between species are usually more striking to our human eye than the similarities. But at the level of the underlying molecular mechanisms and the macromolecules that mediate them, the reverse is true: the similarities among all animals are profound and extensive. All animals have retained unmistakably similar sets of genes and proteins that are responsible for generating their body plans and for forming their specialized cells and organs. This astonishing degree of evolutionary conservation ( non-evolution) was discovered not by broad surveys of animal diversity, but through intensive study of a small number of representative species. For animal developmental biology, the most important have been the fly Drosophila melanogaster, the frog Xenopus laevis, the roundworm Caenorhabditis elegans, the mouse Mus musculus, and the zebrafish Danio rerio.
Chromatin modifiers and remodelers: regulators of cellular differentiation
Nearly all cells of an organism share the same genome but show different phenotypes and carry out diverse functions. Individual cell types, which are characterized by distinct gene expression patterns, are generated during development and are then stably maintained. The chromatin state — the packaging of DNA with both histone and non-histone proteins — has marked effects on gene expression and is believed to contribute to the establishment and the maintenance of cell identities. Indeed, developmental transitions are accompanied by dynamic changes in chromatin states. The assembly and the compaction of chromatin are regulated by multiple mechanisms, including DNA modifications (for example, cytosine methylation and cytosine hydroxymethylation), post-translational modifications (PTMs) of histones (for example, phosphorylation, acetylation, methylation, and ubiquitylation), the incorporation of histone variants (for example, H2A.Z and H3.3), ATP-dependent chromatin remodeling and non-coding RNA (ncRNA)-mediated pathways. PTMs of histones may either directly affect chromatin compaction and assembly or serve as binding sites for effector proteins, including other chromatin-modifying or chromatin-remodeling complexes, and ultimately influence transcription initiation and/or elongation.
Many histone modifiers and chromatin remodelers have been implicated in stem cell pluripotency, cellular differentiation and development. 5
The make and maintenance of specialized Cell types
The organization of DNA in an intricate, dynamic nucleoprotein assembly termed chromatin is accomplished by a remarkable feat of biological engineering. Although all cells must be able to switch genes on and off in response to changes in their environments, the cells of multicellular organisms have this capacity to an extreme degree. Transcription factors are positioned at multiple sites along long stretches of DNA and that these proteins bring into play coactivators and co-repressors. The Drosophila Even-skipped (Eve) gene expression plays an important part in the development of the Drosophila embryo. If this gene is inactivated by mutation, many parts of the embryo fail to form, and the embryo dies early in development. This cytoplasm contains a mixture of transcription factors that are distributed unevenly along the length of the embryo, thus providing positional information that distinguishes one part of the embryo from another. Although the nuclei are initially identical, they rapidly begin to express different genes because they are exposed to different transcription regulators.
Molecular genetic mechanisms that create and maintain specialized cell types
Although all cells must be able to switch genes on and off in response to changes in their environments, the cells of multicellular organisms have this capacity to an extreme degree. In particular, once a cell in a multicellular organism becomes committed to differentiate into a specific cell type, the cell maintains this choice through many subsequent cell generations, which means that it remembers the changes in gene expression involved in the choice. This phenomenon of cell memory is a prerequisite for the creation of organized tissues and for the maintenance of stably differentiated cell types.
Complex genetic switches that regulate Drosophila development are built up from smaller molecules
Drosophila Even-skipped (Eve) gene expression plays an important part in the development of the Drosophila embryo. If this gene is inactivated by mutation, many parts of the embryo fail to form, and the embryo dies
early in development. At the stage of development when Eve begins to be expressed, the embryo is a single giant cell containing multiple nuclei in a common cytoplasm. This cytoplasm contains a mixture of transcription
factors that are distributed unevenly along the length of the embryo, thus providing positional information that distinguishes one part of the embryo from another.
The nonuniform distribution of transcription regulators in an early Drosophila embryo.
At this stage, the embryo is a syncytium; that is, multiple nuclei are contained in a common cytoplasm. Although not shown in these drawings, all of these proteins are concentrated in the nuclei.
Although the nuclei are initially identical, they rapidly begin to express different genes because they are exposed to different transcription factors. For example, the nuclei near the anterior end of the developing embryo are exposed to a set of transcription factors that is distinct from the set that influences nuclei at the middle or at the posterior end of the embryo. The regulatory DNA sequences that control the Eve gene “read” the concentrations of transcription factors at each position along the length of the embryo, and they cause the Eve gene to be expressed in seven precisely positioned stripes, each initially five to six nuclei wide. How is this remarkable feat of information processing carried out? Although there is still much to learn, several general principles have emerged from studies of Eve and other genes that are similarly regulated.
The blue stripes (top and bottom panels) are eve expression, the red in the center (bottom panel) is Kruppel expression, and each green dot represents a single nucleus. 1 The seven stripes of the protein encoded by the Evenskipped (Eve) gene in a developing Drosophila embryo. At this stage in development, the egg contains approximately 4000 nuclei. The Eve and Giant proteins are both located in the nuclei, and the Eve stripes are about four nuclei wide.
The regulatory region of the Eve gene is very large (approximately 20,000 nucleotide pairs). It is formed from a series of relatively simple regulatory modules, each of which contains multiple cis-regulatory sequences and is responsible for specifying a particular stripe of Eve expression along the embryo. 6