Genes coding for cells?

[icakeov]

My understanding is that genes code for proteins that then do a certain function.

Apart from mitosis in an organism, I heard that cells (in forms of stem cells) are also produced and released into the body. I guess these would be all the floating around the body cells? Or the nerve cells that are sent off to climb up the spine to find its place?

My question is, do genes "indirectly" code for cells by creating proteins that will then build a new cell, or stimulate a cell to divide itself? And if yes, is there classification for groups of genes that for example, code for the red blood cell, or for a muscle cell?

 

[Ygggdrasil]

Apart from mitosis in an organism, I heard that cells (in forms of stem cells) are also produced and released into the body. I guess these would be all the floating around the body cells? Or the nerve cells that are sent off to climb up the spine to find its place?

I'm not an expert in stem cells, but IIRC, stem cells often occupy specific niches in the body (e.g. bone marrow) that provide a specific environment to promote stem cell self renewal. Stem cells an also divide asymmetrically to produce one differentiated cell and one stem cell, and the differentiated cell migrate away from the niche to occupy other parts of the body. One of the best studied examples of this behavior is the intestinal[/PLAIN] [Broken] crypt.

My question is, do genes "indirectly" code for cells by creating proteins that will then build a new cell, or stimulate a cell to divide itself? And if yes, is there classification for groups of genes that for example, code for the red blood cell, or for a muscle cell?

Whereas high school genetic often focuses on traits and diseases we know to be controlled by a single gene, most traits are influenced by many genes and most genes influence many traits. Many of the same proteins that make up a red blood cell are also present in muscle cells, and vice versa. Cell types are largely thought to be defined by the entire complement of genes that are turned on in that specific cell type. However, there is a hypothesis that there exist "master regulator" genes that specify certain cell types. These master regulators are thought to be genes that can turn many other genes on and off, getting the cell to express the right combination of proteins to make a red blood cell or muscle cell.

The most striking evidence favoring this hypothesis is the famous Yamanaka experiment, which formed the basis for the 2012 Nobel Prize in Physiology or Medicine. In this experiment, Shinya Yamanaka and a postdoctoral researcher, Kazutoshi Takahashi, discovered a set of four proteins, that when introduced into a differentiated cell, could transform that differentiated cell back to a state that pleuripotent stem cells (pleuripotent stem cells are the stem cells in the embryo that are capable of differentiating into all of the body's tissues). This research suggests that the four "Yamanaka factors" are the set of master regulators that specify pleuripotent stem cells. Subsequent experiments have identified other potential sets of master regulator genes for other cell types.

 

[icakeov]

This is fantastic! Thanks @Ygggdrasil!
Do you know if there is an official name for these groups of genes that are expressed for a cell (through master regulators or not)? Sort of "gene groups" or something more "elegant"?

 

[Ygggdrasil]

Do you know if there is an official name for these groups of genes that are expressed for a cell (through master regulators or not)? Sort of "gene groups" or something more "elegant"?

Probably the term to use would be "transcriptome."

 

[icakeov]

Nice, that's elegant enough! Thanks! :)

 

[Fervent Freyja]

This is fantastic! Thanks @Ygggdrasil!

I agree, Ygggdrasil is hardcore and his responses are always accurate. I almost always learn something from his posts.

 

[votingmachine]

The genes that control cell destiny are generally called the haematopoiesis genes. Wikipedia is not a verifiably reliable source but:

https://en.wikipedia.org/wiki/Haematopoiesis

 

[icakeov]

Thanks for your response @votingmachine
Would haematopoiesis genes then be an example of "master regulator" genes for blood cells mainly? Or is it a bit of a catch phrase for any cells that get differentiated in this way?
Furthermore, do each of these new cells would have their own "transcriptome", a set of all expressed genes, creating messenger RNA molecules?

 

[votingmachine]

Thanks for your response @votingmachine
Would haematopoiesis genes then be an example of "master regulator" genes for blood cells mainly? Or is it a bit of a catch phrase for any cells that get differentiated in this way?
Furthermore, do each of these new cells would have their own "transcriptome", a set of all expressed genes, creating messenger RNA molecules?

Haematopoiesis is generally used in specifically the blood cell differentiation.

I've always been fascinated by the Homeobox genes and how they control cell differentiation. But there are many important cell differentiation genes. Some mutations of the Homeobox genes have led to some crazy dismorphology. They are well worth a quick glance.

http://www.evolution.berkeley.edu/evosite/history/hox.shtml [Broken]

Generally, a transcriptome should be different for different cell types. But a transcriptome is also different for the same cell types in different environments. I used to do Micrarrays on transcriptomes and we would look at plant tissues that were put into different environments (eg, drought, cold, heat, soil types, etc). Cell type differences might be very subtle, and environmental response can be very large. So much of the transcriptome is going to be the common housekeeping genes anyway.

 

[BillTre]

I guess these would be all the floating around the body cells? Or the nerve cells that are sent off to climb up the spine to find its place?

Most cells don't do a lot of moving during embryogenesis. Exceptions are the neural crest cells and the blood cells (which of course circulate). There may be others. Many embryonic movements involve masses of cells moving as either a linked unit or individual cells.
Nerve cells don't climb up the spine. The vertebrate central nervous system (CNS) forms from a defined area of dorsal (top) ectoderm (outside layer embryonic, like skin) that after being instructed to form skin by signals from underlying tissues, rolls up into a tube which sinks into the dorsal body along the head to tail axis of the developing embryo. This forms the neural tube which is the precursor of the nervous system. The neural crest forms from cells at the border of the induced neural tube and the ectoderm it used to be continuous with. The cells go all over the place and make lots of interesting tissues including much of the peripheral (non-CNS) nervous system. Eventually some of the cells in the neural tube become neurons in the structure of the tube (made of other cells). Some migrate around a bit, but not like the neural crest and not up the spinal cord. Their axons in the other hand act like little migrating cells when they grow out, but maintain a connection with the cell body via the axon that strings out behind them as they move out to their final location. These growing axons can go great distances. Motorneurons (which innervate muscles) residing in your spinal cord project axons down to muscles in you feet among other areas. Corresponding distances in other animals, like a giraffe, can be even longer.

Master Regulatory Genes:
There are two classical lines of evidence for master regulatory genes. They were originally conceived of as a single gene, at the top of a regulatory hierarchy, turning on, producing a protein that then binds control sequences for other genes. These in turn may turn on other genes, etc., thereby turning on a whole set of genes for a particular cell type.
One line of evidence for master regulatory genes are mutations found in animals that result in changed fates of developing cells in certain areas of the embryo.
For example, homeotic mutations like bithorax can change whole body segments from one fate (such as second thoracic segment to first thoracic segment). These pictures show the wild type condition (normal) and mutants similar to bithorax. the normal have two large wings (one pair on the first segment) and two small "balancers" (on the second segment). Fruitflies evolved the second pair into the balancers, while dragonflies, which did not evolve this, have 2 pair of large wings. Its really shocking to see these mutants if you are used to seeing the normal flies.
There many mutations like this, so master regulatory genes are an easy explanation, but it is not necessarily the only explanation. Undirected (meaning produced randomly) mutations like these basically cause a malfunction in the machinery underlying the developmental process. Its been compared to throwing a monkey wrench into a veery complex machine resulting in a problem. It does not rule out a requirement of a coordinated action of many genes for proper development. Developmental regulation is often complex. Taking one gene out may cause some effect, but the same or a different effect may result from taking out a different gene.

Another line of evidence in support of master regulatory genes in forcing gene expression in some cells which results in those cells taking a particular cell fate.

Now, the expression of many or maybe all genes expressed in a cell (or cell type; a cell's transcriptome as described above) can be followed and recombinant organisms can be made. Transcriptomes of different cell types vary. These new tools provide many ways to test/manipulate the cells and hypotheses, but I am no longer current on them.

 

[icakeov]

Wow! Thanks @BillTre! Amazing!
What a great thread, my question got really answered :)