Embryomics is the identification, characterization and study of the diverse cell types which arise during embryogenesis, especially as this relates to the location and developmental history of cells in the embryo. Cell type may be determined according to several criteria: location in the developing embryo, gene expression as indicated by protein and nucleic acid markers and surface antigens, and also position on the embryogenic tree.
Embryome
There are many cell markers useful in distinguishing, classifying, separating and purifying the numerous cell types present at any given time in a developing organism. These cell markers consist of select RNAs and proteins present inside, and surface antigens present on the surface of, the cells making up the embryo. For any given cell type, these RNA and protein markers reflect the genes characteristically active in that cell type. The catalog of all these cell types and their characteristic markers is known as the organism's embryome. The word is a portmanteau of embryo and genome. “Embryome” may also refer to the totality of the physical cell markers themselves.
Embryogenesis
As an embryo develops from a fertilized egg, the single egg cell splits into many cells, which grow in number and migrate to the appropriate locations inside the embryo at appropriate times during development. As the embryo's cells grow in number and migrate, they also differentiate into an increasing number of different cell types, ultimately turning into the stable, specialized cell types characteristic of the adult organism. Each of the cells in an embryo contains the same genome, characteristic of the species, but the level of activity of each of the many thousands of genes that make up the complete genome varies with, and determines, a particular cell's type (e.g. neuron, bone cell, skin cell, muscle cell, etc.).
During embryo development (embryogenesis), many cell types are present which are not present in the adult organism. These temporary cells are called progenitor cells, and are intermediate cell types which disappear during embryogenesis by turning into other progenitor cells, or into mature adult somatic cell types, or which disappear due to programmed cell death (apoptosis).
The entire process of embryogenesis can be described with the aid of two maps: an embryo map, a temporal sequence of 3-dimensional images of the developing embryo, showing the location of cells of the many cell types present in the embryo at a given time, and an embryogenic tree, a diagram showing how the cell types are derived from each other during embryogenesis.
The embryo map is a sequence of 3-D images, or slices of 3-D images, of the developing embryo which, if viewed rapidly in temporal order, forms a time-lapse view of the growing embryo.
The embryogenic tree is a diagram which shows the temporal development of each of the cell lines in the embryo. When drawn on a piece of paper, this diagram takes the form of a tree, analogous to the evolutionary tree of life which illustrates the development of life on Earth. However, instead of each branch on this tree representing a species, as in the tree of life, each branch represents a particular cell type present in the embryo at a particular time. And of course, an embryogenic tree covers the gestation period of weeks or months, instead of billions of years, as in the case of the evolutionary tree of life.
Human embryogenesis is the referent here, but embryogenesis in other vertebrate species closely follows the same pattern. The egg cell (ovum), after fertilization with a sperm cell, becomes the zygote, represented by the trunk at the very bottom of the tree. This single zygote cell divides in two, three times, forming first a cluster of two-cells, then four-cells, and finally eight-cells. One more cell division brings the number of cells to 16, at which time it is called a morula, instead of a zygote. This ball of 16 cells then reorganizes into a hollow sphere called a blastocyst. As the number of cells grows from 16 to between 40 and 150, the blastocyst differentiates into two layers, an outer sphere of cells called the trophoblast and an inner cell mass called the embryoblast.
The spherical outer cell layer (trophoblast), after implantation in the wall of the uterus, further differentiates and grows to form the placenta.