Genes Have Play, Stop and Pause Buttons

You probably remember from biology class that genes hold information that is used to construct protein and RNA molecules which do various tasks in the cell. A gene is copied in a process known as transcription. In the case of a protein-coding gene the transcript is edited and converted into a protein in a process known as translation. What you may not have learned is the elaborate regulatory processes that occurs before, during and after this sequence of transcription, editing and translation. Genetic regulation is fascinating and you can read more here, here, here, here, here, here, here, here, here, here, here, here, here, here, here and here.

Background: Post translation regulation

Regulatory processes are constantly at work in the cell, practically at all levels. Consider the enzymes in the glycolysis pathway which metabolize food intake. There are about a dozen such enzymes and they team up to break down the six-carbon sugar known as glucose into two three-carbon molecules. Like a factory production line, each enzyme catalyzes a specific reaction, using the product of the upstream enzyme, and passing the result to the downstream enzyme. If just one of the enzymes is not present or otherwise not functioning then the entire process doesn’t work.

In addition to breaking down glucose, glycolysis also produces energy-carrying molecules called ATP. These are in constant demand in the cell as they are used wherever energy is needed. So like most pathways, glycolysis is interconnected with other pathways within the cell. The molecular products of glycolysis are used elsewhere and so the rate at which the glycolysis pathway proceeds is important. Too fast and its products won’t be useful, too slow and other pathways have to slow down.

Glycolysis is regulated in a number of ways. The first enzyme in the glycolysis pathway is regulated by its own product. This enzyme alters glucose to form an intermediate product, but if the rest of the pathway is not keeping up then the intermediate product will build up, and this will cause the enzyme to shut down temporarily. The enzyme is designed to be controlled by the presence of its product.

Two other enzymes in the pathway have even more sophisticated regulation. They are sensitive to a number of different molecules which either increase or decrease the enzyme activity. For example, these enzymes are partly controlled by the energy level of the cell. This makes sense since glycolysis helps supply energy to the cell. A good indicator of the cell’s energy level is the relative concentrations of ATP and spent ATP. High levels of ATP indicate a strong energy supply. Hence the enzyme activity is inhibited (and therefore the glycolysis pathway is slowed) when ATP is abundant. But high levels of spent ATP counteract this effect.

How do these molecules control enzyme activity? The molecules are tiny compared to the big enzymes they control. Just as a small key is used to start up and turn off a big truck, so too these small molecules have big effects on their target enzyme. And just as the truck has an ignition lock that can be turned only by the right key, so too the enzyme has several docking sites that are just right for a particular small molecule, such as ATP, spent ATP, or the intermediate products.

Not only does ATP fit just right into its docking site, but it perturbs the enzyme structure in just the right way so as to diminish the enzyme activity. There is another docking site that only a spent ATP will fit into. And if this occurs then the enzyme structure is again perturbed just right so as to encourage activity and reverse the ATP docking effect.

Background: Pre translation regulation

The regulation of protein enzymes discussed above is the last in a sequence of processes that regulate genes and their products. Just before this there are processes that regulate the very production of proteins.

For instance, some of our DNA which was thought to be of little use actually has a key regulatory role. This DNA is transcribed into strands of about 20 nucleotides, known as microRNA. These short snippets bind and interfere with RNA transcripts—copies of DNA genes—when the production of the gene needs to be slowed. And microRNAs do not only come from a cell’s DNA. MicroRNAs can also be imported from nearby cells, thus allowing cells to communicate and influence each other. This helps to explain how cells can differentiate in a growing embryo according to their position within the embryo.

And MicroRNAs, like instructions of use, can come from the food we eat. In other words, food not only contains carbohydrates, proteins, fat, minerals, vitamins and so forth, it also contains information—in the form of these regulatory snippets of microRNA—which regulate our gene production.

And while microRNAs regulate the production of proteins from the RNA transcripts, the microRNAs themselves also need to be regulated. So there is a network of proteins that tightly control microRNA production as well as their removal. “Just the sheer existence of these exotic regulators,” explained one scientist, “suggests that our understanding about the most basic things—such as how a cell turns on and off —is incredibly naïve.”

Background: Pre transcription regulation

The next step upstream is the regulation of the transcription process, which copies the DNA gene into an RNA transcript. This is done with the help of transcription factors—proteins that bind to DNA and influence which genes are expressed (transcribed). These transcription factors bind to special, short, sequences of DNA that are before or after the gene they regulate. In so doing the transcription factors influence the huge molecular machine known as RNA polymerase which opens the DNA double helix and makes the RNA transcript copy of the gene.

Exactly how the transcription factors influence the RNA polymerase machine is a complicated topic. Equally complicated is the question of how the transcription factors know when and where to bind to the DNA. One way is with the help of DNA methylation in which a small molecule (a methyl group) is added to the DNA macromolecule at particular locations. Like a barcode or marker, the methyl group indicates, for instance, which genes in the DNA are to be turned on. This DNA methylation is accomplished via the action of a protein machine that adds the methyl group at precisely the right location in the DNA strand.

The methylation occurs at certain target sites along the DNA sequence where specific short DNA sequences appear. These sequences are found by protein machines as they move along the DNA. The protein machine binds to the DNA, twists the helix so the DNA base rotates into a precisely shaped pocket in the protein, and the protein then facilitates the transfer of the methyl group from a short donor molecule to the DNA base.

In bacterial studies it has been found that the short donor molecule does more, however, than just supply a methyl group. It also helps to control the protein. First, the short donor molecule binds to the pocket of the protein so the methyl group is ready for transfer. But the donor molecule also binds to another site on the protein. This binding serves to alter the structure of the protein, enhancing its function. So the protein is designed to do its job when it is charged with a donor molecule.

But not all of the DNA target sequences are methylated. This complex DNA methylation function doesn’t occur if the target sequence is protected by another protein that binds to the sequence. This protein binds to some of these DNA target sequences but not all. The result is a particular DNA methylation pattern which influences which genes are expressed.

Furthermore, the methyl group marker can, itself, be modified. That is, the mark can be marked, thus adding another layer of information. For instance, the methyl group can be hydroxylated. And of course a different molecular machine is required for that task, and the information of when and where to go to work is needed.

All of this makes for a complex DNA methylation pattern which is superimposed on the DNA macromolecule. In addition to the DNA macromolecule, methyl groups are also used to tag the histone proteins about which the DNA is wrapped. The histones have a hub, around which the DNA wraps, and a tail that sticks out on which chemical markers are attached. As with DNA methylation, these histone markers are signals for the protein machinery. And like DNA, these tags are removed as well. Such modifications and removal of these chemical tags means that these codes are dynamic, and there are protein inspectors that double-check these complex encodings.

In addition to methylation, histones can also vary by tiny differences in their amino acid sequence. This histone sequence variation serves as yet another type of tag used for gene regulation.

Furthermore, histone variants are not merely static sign posts that influence gene expression. These variants are moved, by other proteins, between different locations in the genome, resulting in migration patterns that occur in the embryonic development phases. DNA methylation can also be transmitted across generations.

And finally this transcription factor binding and methylation patterns are heavily context dependent. In spite of expectations to the contrary, the transcription factor binding sites are not well conserved across different species. In fact, divergence between transcription factor binding sites even shows up in very similar species, such as different species of yeast.

Furthermore the methylation patterns vary substantially across different regions of the DNA and between the two alleles of a given gene and this allele-specific methylation can be tissue-specific. In one type of cell a histone modification may turn off a gene whereas in another type of cell the same histone modification may turn on the gene. As one writer put it, the regulatory architecture has been rewired on a substantial scale. Another explained, these findings “hint at an unimagined complexity of the genome.”

New finding: A pause button

Regulation of genes and their products is complex and occurs at all levels. At the level of transcription where the DNA gene is copied, genes can be turned off and on. It is as though they have a start and stop button. But new research now shows they also have a pause button. That is, transcription factors can not only start and stop the RNA polymerase copy machine, they can also pause the machine after it has begun. And other transcription factors turn off the pause, so the transcription process may continue. This pausing function, which may allow for a more rapid response when needs arise, seems to be a general feature of transcription.

With each new research study we learn more about evolution’s capabilities. There is, of course, no question that evolution created all of these regulatory processes and mechanisms because evolution is well known to be a fact. What is not known is the extent of evolution’s capabilities. No one would have thought evolution could have produced such elaborate designs. But as science advances so too does our knowledge of this incredible process.