So, we’ve already discussed the fact that genomic imprinting is mediated through epigenetic differences between the maternally and paternally inherited gene copies. That is, at an imprinted locus, the maternally inherited allele will have one pattern of epigenetic modifications, while the paternally inherited allele has a different pattern. These differences are first established in the male and female germ lines, when the alleles that will eventually become maternally and paternally derived are in physically different locations. It is not hard to imagine, then, how these differences could be established. One pattern of gene expression in spermatogenesis results in the paternal-specific epigenetic modifications. A different pattern of gene expression in oogenesis results in maternal-specific epigenetic modifications.

But what are these epigenetic modifications, and how do they change the expression pattern of the gene?

There are a number of modifications involved in imprinting, but for the moment, we’re going to focus specifically on the simplest and best-understood mechanism: DNA methylation.

The two horizontal lines in this picture represent the two copies of a gene.  The big, solid box is the part of the gene that actually codes for the protein. The open box is the promoter region, which is the part of the DNA sequence responsible for regulating expression of the gene. The lollipop things indicate DNA methylation on cytosine residues (the “C” of the A, C, G, T alphabet that makes up DNA).

In this simplest type of scenario, the DNA sequence in the promoter region binds to a variety of proteins that recruit the molecular machinery that will transcribe the gene, leading eventually to production of the corresponding protein. The addition of methyl groups to the DNA changes its binding properties, so that it no longer binds to this machinery, and that copy of the gene is not transcribed.

If you’re not a molecular biologist, you can think of it like this. The transcription machinery is a bit like a Xerox machine, and the gene is like the master copy of some document. The promoter region is like a lock that has to be unlocked before you can copy this particular document. There are a number of proteins called “transcription factors” that function like a key to this lock. These transcription factors fit nicely on the promoter region, unlocking the gene and resulting in the production of many copies of the gene product.

Adding methylation to the promoter region is a bit like squirting epoxy into the lock. The presence of the methyl groups actually changes the physical shape and chemical properties of the DNA. So, when you try to put the key in, it no longer fits right, and the gene can not be copied.

In the top part, we see the red transcription factor binding to the black promoter region, which will activate transcription from the gene. In the bottom part, methyl (CH3) groups have been chemically added to the promoter region, preventing binding, and thereby preventing transcription.

So, these relatively subtle chemical changes are able to completely alter the functional properties of the gene.

Next time, we’ll talk about how these methylation patterns are maintained through development, and how the two gene copies are able to maintain distinct epigenetic states across multiple rounds of cell division and DNA replication. Make sure to tune in, because it’s really slick!

The two references represent the first proposals that DNA methylation might be the thing that permits the stable transmission of patterns of gene expression across cell divisions.

Holliday, R., & Pugh, J. (1975). DNA modification mechanisms and gene activity during development Science, 187 (4173), 226-232 DOI: 10.1126/science.1111098

Riggs, A. (1975). X inactivation, differentiation, and DNA methylation Cytogenetic and Genome Research, 14 (1), 9-25 DOI: 10.1159/000130315

So, in the previous installment, we introduced the “Loudest Voice Prevails” principle, which describes the evolutionarily stable pattern of gene expression at an imprinted locus where there is an intragenomic conflict over the total level of gene expression. Basically, the allele that favors lower expression becomes transcriptionally silenced. Expression from the other allele (the “louder” voice) evolves to the level that maximizes its inclusive fitness. In this sense, the active allele at an imprinted locus “wins.”

But what is going to happen if we have a pair of imprinted genes that exert opposite effects on the phenotype? If we have a paternally expressed growth enhancer, it will evolve to bring the growth phenotype up to the paternal optimum. If we have a maternally expressed growth suppressor, it will evolve to bring the growth phenotype down to the maternal optimum. But what if we have both?

Well, intuitively, if there is conflict between maternally and paternally derived genes over the optimal growth phenotype, then the phenotype can’t simultaneously satisfy the paternal and maternal optima. One or the other (or both) of these genes will always be under selection to increase its gene expression level (or, equivalently, the activity or longevity of the gene product, etc.). Thus, these two opposing genes will become involved in a kind of arms race.

In the simplest possible model that we can write down, this arms race goes on indefinitely, with natural selection driving each of the genes towards infinite expression. Clearly, in a real biological situation, this will not be the case, and something will step in to bring this escalation to a halt. The questions then become: What stops the escalation? And, what does the system look like at its new, escalated, evolutionarily stable state?

To think about this, let’s return to our analogy from last time, where Pat and Chris are sharing an office, but disagree about what temperature the office should be kept at. Recall that genes are totally passive aggressive, so Pat and Chris don’t compromise or communicate. They just use the tools at their disposal to move the office closer to their preferred temperature. Pat wants the office at 71 degrees. Chris wants it at 70.

We saw that if Pat and Chris both have space heaters, eventually Chris’s space heater is off, while Pat’s holds the temperature at 71. On the other hand, if they both have air conditioners, Pat will turn his/her A/C off, and Chris will get to have the room at 70.

If each of them has a space heater and an air conditioner, we have an arms race on our hands. Whenever the temperature is below 71, Pat will turn up the space heater. Whenever it is above 70, Chris will turn up the air conditioner. In passive-aggressive-allele fashion, this will go back and forth until the space heater and air conditioner are both blasting away. In the absence of any constraints or side effects, it will go on until both are blasting away infinitely.

There are several ways that the escalation could stop, however, each of which has a biological analog.

     (1) Mechanical limitation. There will be some limit beyond which gene expression / activity can not increase. Once one of the genes reaches its limit, the other will win. Like if Pat’s Tufnel-brand space heater goes to eleven, Pat wins. Of course, this will depend on the mechanisms through which the two genes exert their influence. For instance, if Chris’s air conditioner is actually a combination air conditioner / food processor / exfoliator, Chris might have to turn it way way up to get the air conditioning equivalent of a little bit of space heating. Similarly, a gene product might perform multiple tasks, and this pleiotropy could limit its competitive ability in the arms race.

     (2) Production costs. One difference between the single-locus solution and the two-locus solution is the level of energy consumption. If Chris’s space heater is off, Pat’s holds the temperature at 71. If Chris’s air conditioner is maxed out at ten, Pat’s space heater (which goes to eleven, remember) holds the temperature at 71. The difference is that the second solution comes with a huge-ass electricity bill. Can this sort of cost actually halt the escalation? Maybe. This requires either that there are diminishing returns to increased escalation, or that there are accelerating costs to production (like utility rates where your thousandth kilowatt-hour costs more than your first one).

     (3) Intervention. In a real office, we might expect that the manager would come in and yell at Pat and Chris, telling them to turn down their space heater and air conditioner. Maybe the manage would mandate an office temperature of 70.5 degrees. Does this ever happen with genes? Could a consortium of unimprinted genes step in and stop the escalation? There is no evidence to my knowledge of such things happening in the context of genomic imprinting, but this type of intervention is thought to be responsible for meiotic sex-chromosome inactivation, where the autosomes all gang up and put the sex chromosomes in a headlock in order to prevent meiotic drive.

     (4) Side effects. What if turning up Pat’s space heater also makes the music louder in the office? What if Chris’s air conditioner draws so much power that it causes occasional brown-outs? This is the other way in which the escalation between imprinted genes might be self limiting. If we consider a monolithic “growth phenotype” in isolation, then each allele has a simple, monolithic optimum. But genes are seldom like that. A paternally expressed allele may benefit from increased expression due to the effect of that increased expression on growth. But what if that increased expression has other consequences, as well? Maybe those other effects are detrimental to the allele’s inclusive fitness. If those deleterious side effects outweigh the growth-related benefits, then natural selection will not drive further escalation.

In future installments, we’ll look at some specific examples of escalating genes. But first, we’ll step back and look at some of the other features and consequences of imprinted genes.

Kondoh, M., & Higashi, M. (2000). Reproductive Isolation Mechanism Resulting from Resolution of Intragenomic Conflict The American Naturalist, 156 (5), 511-518 DOI: 10.1086/303409

Wilkins, J., & Haig, D. (2001). Genomic imprinting of two antagonistic loci Proceedings of the Royal Society B: Biological Sciences, 268 (1479), 1861-1867 DOI: 10.1098/rspb.2001.1651