Eukaryotic Genes

EUKARYOTIC GENES

Remember that eukaryotic genes are linear rather than circular. These are imbedded into nucleosomes, which pack the DNA together. The genome size does not relate to the actual size of the organism; small organisms can have much larger genomes than humans, for example. In humans, thee are about 20,000 different transcribing genes in the genome. Eukaryotic cells also have mitochondrial genomes and plants have chloroplast genomes. These two other genomes are much smaller so that, in humans, the number of base pairs in mitochondrial DNA is just about 16,500 base pairs.

Gene regulation in eukaryotes is more complex than it is in bacteria. The main expression occurs at the level of transcription—particularly at the start of transcription. There are proteins in eukaryotic genes that will modulate the activity of RNA polymerase. These proteins and the regulation of transcription is, of course, different in each type of cell in a multicellular organism. This is a necessity because different cell types need to make different proteins and enzymes. There are different regulatory proteins in the different types of cells. Methylation of DNA also adds to cellular complexity.

With bacteria and eukaryotes, there are cis-acting genes or sequences, which are genes that are located together or adjacent to one another. Genes are transcribed by RNA polymerase II; each gene has two promotor elements. The first is called the TATA box and the second is called the INR sequence. These bind general transcription factors.

There are also sequences called enhancers, which can be located far upstream from the actual genes that get transcribed. These enhancer sequences allow for the more efficient transcription of the genes. Enhancers can also be located downstream from transcribed gene sites. Without an enhancer, the gene will only be transcribed at a low level. Enhancers bind to proteins that change the activity of RNA polymerase.

Because of looping of the DNA molecule, the enhancer does not have to be near the promotor site. This allows transcription factors bound to a specific enhancer to act in similar ways to the promotor sites. This basically means that enhancers are really no different from promotor sites and other regulatory sequences on cis-acting genes.

Interestingly, these enhancers have since been discovered in bacterial cells as well as eukaryotic cells.

Certain hormones and growth factors act directly to control gene expression. These act as proteins that turn on some genes and turn off other genes. This is also why mammalian cells act differently depending on the cell type involved. Enhancers themselves can be big so that they bind many different regulator proteins. What this means is that, if there is a mutation of part of the enhancer sequence, the enhancer will work partly but does not fail to work completely. It may be that there is redundancy in these enhancer sequences. In addition, enhancers can promote gene expression in some cells while simultaneously blocking gene expression in other cell types.

There are many different protein-based transcription factors that bind to DNA in order to allow for the regulation of gene expression in eukaryotic genes. Transcription factors can be different for different cells in a multicellular organism. It is hard to study these transcription factors because they represent a tiny fraction of the total cell protein in a given cell. Researchers use what’s called “DNA-affinity chromatography”, which can isolate these specific transcription factors.

Some transcription factors are known as transcriptional activators, which bind to regulatory sequences on DNA and activate the transcription process. They can bind to either promotor sequences or enhancer sequences on the DNA molecule. There are two parts to a transcription activator. One part binds to the DNA sequence specifically, while another part binds to the transcription machinery in order to start the transcription process.

As mentioned, hormones can act as transcription factors. The hormones that specifically do this are the steroid hormones. Steroid hormones are lipophilic so they can get into the cell and into the nucleus, binding to DNA and turning on or turning off transcription.

In eukaryotes, gene expression can be turned off with eukaryotic repressor proteins. These will bind to specific DNA sequences and block the transcription process. These can block the interaction of the RNA polymerase with the DNA sequence at the promotor site. Repressors will compete with activators for specific regulator sites. They

can bind to the regulator sites so that activators cannot bind. Other repressor proteins will interact with general transcription factors so that transcription cannot happen. Repressors can cause a lack of transcription in cells for which the transcription of DNA in the cell would be inappropriate.

Remember, though, that DNA in the cell is never naked but is bound with histones in order to form chromatin. Nucleosomes are wrapped up and together are looped into larger loops so the DNA can be highly condensed. This DNA cannot easily be transcribed. Repressors and activators can function by changing the looping and configuration of this chromatin. The chromatin gets decondensed in order for it to be transcribed. You should know, though, that it takes more than decondensed DNA to be able to transcribe. Nucleosomes are still present in decondensed DNA, making it difficult to transcribe this.

Nucleosome formation can be inhibitory to transcription. It is relieved by the acetylation of histones and by binding to two nonhistone proteins that alter the nucleosome structure so that transcription can take place. Acetylation will weaken the attachment of histone proteins to DNA and will affect the shape of the nucleosome. This facilitates the binding of transcription factors to DNA. On the other hand, deacetylation will activate transcriptional repressor proteins.

There are also nucleosome remodeling factors that will change the accessibility of nucleosomal DNA to the transcription process. The mechanism by which these do this is not known but it can be done without removing histone proteins or dismantling the nucleosome.

DNA methylation is another way to control the transcription process. Cytosine in the DNA of vertebrates can be modified through methylation. This will reduce the ability to transcribe these areas of DNA. It occurs primarily where cytosines and guanines are together on the same DNA chain. There is a protein that binds to these areas so that transcription is repressed. The same protein will also form a complex with histone deacetylase, which further suppresses transcription by acting on the nucleosome. This methylation particularly affects gene expression in mammalian embryos and