Soma to Germline Information Transfer via MicroRNA in Sperm

A few months ago, I posted about an article which  speculated that the evolution of the modern human brain was a result of Lamarckian evolution. To recap — this means that a trait is acquired during one’s life experience, and that trait is transferred to the offspring. The classic example is that giraffes have long necks because a precursor animal stretched its neck to reach high foliage, the next generation was born with longer necks because of its parents’ reaching. The next generation reached yet higher, and the next generation had yet longer necks. In humans, the example is something like a blacksmith has big muscles from working at a forge all day, he passes on his big-muscles to his son because of the use of his arms.

For something like brain development to be influenced by life experiences, I speculated that hormonal changes (e.g., corticotropin release hormone, ACTH, cortisol, norepinephrine) as a result of psychological stress or trauma would have to induce epigenetic changes in sperm.

Imagine my surprise when I directed my web browser to Nature News where researchers at the Brain Research Institute at the University of Zurich discovered that specific microRNAs were indeed increased in the sperm of male mice exposed to psychological trauma (being forced to be away from their mother during rearing, who was undergoing stressful experiences, i.e.: cold-stress or forced swimming)…. and these microRNA increases persisted for yet one more generation, and also was increased in their hypothalamus and cortex. So this is one interesting piece of the puzzle.  The Pubmed Link.

They do not yet know the mechanism of the microRNA-induced changes. But there are several steps that need to be taken to be sure that the observed effect is real, and a few grains of salt.

  1. The study used high-throughput analysis, and screening-type methodologies. These should always be followed up with low-throughput analyses because the reliability of any one target in a high throughput screen of RNA quantity is low. We did this with our PLOS One study. We used a different methodology to quantitate a panel of several microRNAs from our high throughput screen which quantitated 380. We chose some that were up, some that were down and some that were not different. We plotted the signal in the single-target method vs. the high-throughput method to validate that they matched. This, in my opinion, is a must-do, if you plan to make a claim about any one transcript.
  2. The mechanism is not understood. How do the microRNA’s change in the sperm? One good place to start would be to look at the promoter region for the candidate microRNAs that were altered — are these transcription factor sites or hormone response elements (e.g., that would respond to cortisol)?  Are there methylation sites?
  3. The next additional step is to show that changing the concentrations of those microRNAs has some effect on prenatal CNS development.
There are several variable sequences located the the 3` untranslated region (3`UTR) .... which is where the microRNA action takes place. We don't know yet if there are functional microRNA response elements here, but several are "predicted" by the power of having sequenced the human genome. One function of this gene is to feedback-inhibit signaling of hormones, including those responding to stress, but also involved in development & metabolism.
There are several variable sequences located the the 3` untranslated region (3`UTR) …. which is where the microRNA action takes place. We don’t know yet if there are functional microRNA response elements here, but several are “predicted” by the power of having sequenced the human genome. One function of this gene is to feedback-inhibit signaling of hormones, including those responding to stress, but also involved in development & metabolism.

This topic is very near and dear to my own research plans and goals. I’m going to recreate here a figure that I used to illustrate the point of the FKBP5 gene. This protein’s function is to modulate the glucocorticoid receptor nuclear translocation, it essentially inhibits it; so it serves as a feedback mechanism for particular cells to “turn off” cortisol signaling very quickly after it starts. But if FKBP5 is too high … no cortisol signaling was allowed in the first place. There are gene polymorphism in FKBP5 associated with major depression … and one of my future research plans is to determine the big how and why.  One potential way is by altering microRNA response element sequences.   …. aaaand it comes full circle. I would be interested to know of any of the microRNAs discovered to be changed in the sperm of traumatized male mice might also bind to FKBP5.  Cool stuff, huh?

 

Undergraduate Biology Should Teach More Evolution

I have been researching the literature in science education, specifically neuroscience, genetics, and microbiology, and I’m surprised to find that not much import is given to the theory of evolution (or natural selection). Given that “Nothing in biology makes sense except in the light of evolution” (a 1973 essay), I really expected to find a unit on evolution or at least this theme within the curricula of these disciplines.

Neuroscience

Kerchner, Hardwick, and Thornton surveyed faculty of undergraduate neuroscience programs to determine which “Core Competencies” were most important for undergraduate neuroscience majors (for the record, when I was an undergrad, very few colleges offered this field of study as a major, it was regarded to be a specialty reserved for graduate study — for example, you could major in biology, molecular genetics, biochemistry,  evolution-ecology-organismal biology, and microbiology, but not neuroscience at Ohio State).  The three most important core competencies for a neuroscience program:  1. Ability to engage in critical & integrative thinking, 2. Basic neuroscience knowledge, and 3. Scientific Inquiry / Research Skills (in that order). Interestingly, quantitative ability was ranked the least essential by the greatest proportion of faculty.

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If Mendel Had Dogs

Meet Eli

Our dog, Eli, a Rhodesian Ridgeback - Mastiff mix.
Our dog, Eli, a Rhodesian Ridgeback – Mastiff mix.
Example of Rhodesian Ridgeback sitting and the ridge. (Note white chest like Eli's).
Example of Rhodesian Ridgeback sitting and the ridge. (Note white chest like Eli’s).

I have a dog, named Eli, he’s four years old and a Rhodesian Ridgeback – Mastiff mix. Here’s a picture of him. Usually when I tell people his breed origins, they are quite surprised. He only weighs about 65 lbs, stands about 23 inches at the withers, has the same coloration & fur as a Ridgeback, but he completely lacks the ridge. A remarkable feature of the Rhodesian Ridgeback is the line of fur growing in the opposite direction along the spine (photos from wikipedia). Like many dogs, the fur on Eli’s spine will stand when he’s excited, and is a bit darker in coloration than the rest of his back, but all the fur grows in a consistent direction. In contrast, the normal male Ridgeback stands 26-29 inches tall and weighs 85 lbs. Also in contrast to Eli, the full breed Mastiff weighs 160 – 200 lbs and stands 32-36 inches tall. Because of these apparent contrasts, most people are in disbelief that Eli could be a mix of the two breeds.

Rhodesian-Ridgeback, Eli, and a Mastiff
Rhodesian-Ridgeback, Eli, and a Mastiff

In fact, over the years, I myself had been questioning whether he really could be half Mastiff until I was browsing books at a store and I came across a book on Mastiffs and when I saw the photo of the face, I thought I could be looking at Eli’s parent or cousins. So here’s a side-by-side comparison of Mastiff, Eli, and a Ridgeback. I have little doubt now that Eli is half Mastiff. This whole episode got me to thinking about two common misconceptions about genetics and inheritance.

Mendelian Inheritance and Segregated Alleles

First, many people have the misconception that the offspring is always a “blend” of its parents. Usually when I tell people that Eli is half Ridgeback, they comment on him lacking a ridge entirely, expecting to see, if not a ridge, then at least a half ridge or a part ridge feature on his back. This is actually unlikely if what breeders (and Eli’s vet) assume about the genetics of the ridge. It’s assumed to be a dominant allele. Meaning that about a quarter of full-bred Ridgebacks are born without the ridge, and some sources indicate that (as cruel as it sounds), that they are culled at birth if that is the case. (This isn’t widespread, usually they are taken out of consideration for breeding and labeled a “mutt”). This practice, however, will never get rid of ridgeless Ridgebacks in the Ridgeback population. Further, if it is a dominant allele, that makes it all the more likely that Eli will not carry the ridge. If it is (as I suspect), due to one allele, or a set of genes with 100% cosegregation.

So let’s say that there’s allele, R, which if a dog carries on her chromosomes, she’ll have the ridge, and it’s counterpart, r, which is the allele for no ridge. So if we do the classic Mendelian calculations; knowing that all individuals carry two copies of each allele, assuming random mating; we can calculate expected allelic frequencies in the Ridgeback population. This is: RR (25%), Rr (50%), and rr (25%).  Or, in frequency terms 1 = 0.25RR + 0.5Rr + 0.25rr. Since Eli does not have a ridge, we know that his Ridgeback parent could not have been RR, and must have been either Rr or rr. We don’t know which one the parent was, but we do know that it was twice as likely to be Rr as it was to be rr. So that leave us with   1 = ⅔Rr + ⅓rr. Eli could only have inherited one allele from the Ridgeback parent, R or r. So when Eli’s parent’s spermatagonia or oocytes went through meiosis, the chromosomes separated in a way such that the sperm (or egg) that successfully went on to become Eli that I know and love will only carry either either R or r. And we can calculate the probability by expanding the above equation.  1 = ⅓R + ⅓r + ⅙r + ⅙r. This adds up to the probability of Eli getting the R being ⅓ and the probability of Eli getting the r being ⅓+⅙+⅙ = ⅔.

So Eli only had a ⅓ chance of getting the ridge and a ⅔ chance of not getting the ridge. An important feature of this is the all or nothingness of it. One allele yields the ridge, the other doesn’t. This is similar Mendel’s peas. When he bred tall peas of Tt with dwarf peas of tt, half the offspring were dwarf, none were in between. He had an easy way of determining a plant’s genotype (though he had no concept of genotype), which we do not with canines, he had the advantage of being able to back-cross. That is, he could mate a tall baby pea plant with its tall parent, and deduce whether the tall pea was Tt or TT given the proportions of its offspring. Given that we know the consequences of consanguineous mating for mammals, I don’t think any ridgeback owners will be doing to that with the species that is putatively our best friend.

Cannot Breed Away Ridgelessness

So as we can see, there is not really any easy way of knowing whether a particular individual Ridgeback with the ridge is Rr or RR. Therefore culling the puppies that lack the ridge will never, ever make 100% of Rhodesian Ridgebacks have the ridge. In fact, if all ridgeless Ridgebacks were removed from breeding, then only RR and Rr will breed; and we can calculate that the adult population will be ⅓ RR and ⅔ Rr; and newborn Ridgebacks will be ⅜RR, ½Rr, and ⅛rr. They’d be dedicated to excluding ⅛ of every litter. Despite the AKC’s definition that “The ridge must be regarded as the characteristic feature of the breed,” the fact remains that like ¼ of them do not have it (at minimum ⅛); and Ridgelessness is a disqualification for it being considered as a member of the breed. It seems irrational to disqualify a quarter of the population from being considered a member of its breed, even if it’s purebred. I think the other characterstics are much better defining features of Rhodesian Ridgebacks:

A mature Ridgeback is a handsome, upstanding and athletic dog, capable of great endurance with a good amount of speed. Of even, dignified temperament, the Ridgeback is devoted and affectionate to his master, reserved with strangers.

This quite accurately describes Eli.

Inheritance is not Additive

The second misconception about genetics that I alluded to is that of additivity. When I tell people that Eli is a Ridgeback-Mastiff mix; they think, Ridgeback is big, Mastiff is big, Eli must be REALLY big.  As we just saw with the ridge example, if bigness were a set of many genes, each with factors leading the bigness that followed Mendelian pattern of inheritance, this would not occur. Let’s say … bone length, Ll; bone thickness, Tt; muscle mass, Mm; and hide thickness Hh …. and the dominant form of each contributing to a total trait, bigness, we could run these probabilities through a simulation and prove that it is actually more likely for him to end up smaller than the typical individual of either of his parent breeds. If I were better at programing in R, I’d run through a simulation (perhaps another time). An another note, there are lots of variations on this paradigm. Some traits are close enough on a chromosome that they always segregate together; sometimes there is codominance, and sometimes there’s less than 100% penetrance. It’s nice, though, to have an understanding of these things when we look at the world around us and contemplate the origins of our best friends.