My best slide: Sex-Linked Traits

In genetics class yesterday, we began discussing sex-linked traits - like color-blindness. I'm a deuteranope (red-green color-blind), a heritable genetic disorder. I explained to students (in case they were unsure) that I'm a male (with an X chromosome inherited from mom, and a Y chromosome from dad). However, neither of my sisters (XX), nor my mother (XX) or father (XY) are color-blind. Why is this?

Human color vision is due to three opsin genes that encode proteins expressed in our eyes that absorb light of different wavelengths (generally called red, blue, and green opsins). The blue opsin gene is located on an autosome; red and green opsins are found on the X chromosome. Upon absorbance of light, opsin proteins then transmit signals to our brains to be interpreted. DNA mutations that cause amino acid changes in specific regions of opsin proteins can alter the specific colors absorbed by the opsin proteins, and thus fine-tune the colors of light that we can perceive.

In order to understand why color-blindness exhibits a sex-linked pattern (males have a much higher frequency of this disorder than females), we need to know something more about genetics. Because humans are diploid (have two copies of almost every chromosome), there are two copies per cell of the vast majority of genes. The benefit is that if one gene copy sustains a mutation (-), we still have one "good" (wild-type, +) copy of the gene to help our cells function. This tends to be true of color vision as well: if a retinal (eye) cell has one good copy and one mutant copy (+/-) of an opsin gene, the good version produces protein that allows "normal" color vision.

Because we have a "backup copy" of most genes, many mutations experienced by our genes are recessive: when there is still one good copy of the gene (+/-), we don't notice an effect of the mutation. Only when both copies of the gene have the mutation (-/-) do we exhibit the mutant trait. Under the (hopefully valid) assumption that very little inbreeding is occurring, the chance of inheriting the same mutation from both your mother and your father is very rare, which is why blue color-blindness is extremely rare in humans. But red-green color-blindness is fairly common in some human populations (and I'll address why this is important to scientists in a future post). This is entirely because of where the blue, red, and green opsin genes are found.

In order to understand why mutations on X-linked genes tend to cause higher incidence of mutant traits in men than women, we need to explore the history of the human X and Y chromosomes. Ages ago, our X and Y chromosomes were an autosomal pair and as genetically identical as any other pair of chromosomes. Then, a gene (called SRY) evolved to dictate which individuals would be male and which female. The rules here are simple: if you inherit SRY, you become male; if you don't have SRY, you become female. When SRY first came into existence, it was located on one member of an autosome pair (on the Y); the other member of the pair was thus defined as an X (lacking SRY).

Now the X and Y are (slightly) more genetically different: one has a gene that the other doesn't. This set off an amazing series of events that eventually caused the human Y chromosome to "degenerate." The human Y chromosome is physically much smaller than the X, and contains only a tiny fraction of the genes it used to share in common with the X - way back when they were still an autosome pair. The speciality field of sex chromosome evolution seeks to understand how this degenerative process occurs; this was the basis for my doctoral dissertation (but in stickleback fish, not humans).

Remember I said that we "have two copies of almost every chromosome" and "have a 'backup copy' of most genes." Human males (XY) do not have two functional copies of every chromosome: we have an XY "pair," but the X and Y are essentially genetically unrelated at this point in time. Our Y chromosome does not contain, for example, a red opsin gene or a green opsin gene. There are two tiny regions of DNA sequence similarity between the X and Y: the two "pseudoautosomal" regions (PAR1 and PAR2) that facilitate X and Y pairing at meiosis.

My best slides from this lecture (judging by student reaction) illustrate a very useful analogy for sex chromosomes:

This is entirely the basis for sex-linked traits: when a X-linked gene, like red opsin, is mutated, a mother can pass that mutant X chromosome to both her sons and daughters. However, the daughters (by virtue of also receiving an X from dad) don't exhibit the recessive trait. On the other hand, I received the Y chromosome from my father, by definition, and so my X from my mother. That X carries an opsin mutation, and I don't have a "normal" red opsin gene on my Y to provide me with "normal" color vision.

So, where did my mother get her mutant X chromosome from? Her color-blind father (my maternal grandfather). Hence, a typical pattern for X-linked traits: passed from affected grandfathers through their daughters to half of their grandsons. Why half? Because my mother has a wild-type X chromosome as well. I had a 50:50 chance of inheriting her "good" X, but I lost the coin toss.

Mendel the Magician

It is the start of the term in Biology 102 (Genetics), and thoughts turn to Mendel and his peas. Yes, I saw it in the faces of the students, and I told them that I saw it: the look. I know it because I made that face sometime during my undergraduate days. I don't recall whether it was in molecular biology or genetics, but when the instructor mentioned "Lac operon" I almost lost it. Seriously? The third time in as many years you're going to spend a couple of class sessions on the Lac operon?
So, I watch the faces of students particularly carefully when I say certain phrases, like "Mendel's peas", to judge whether they've heard this all before. Of course, my version has more detail, but in a class of 80 students, when you have to make sure that everybody is up to speed (the chemistry majors, the lone English major, etc.), it is incumbent on the instructor to try to make it enjoyable for everybody.
I thought I'd try a dramatic twist on Mendel's first law: segregation (of alleles into gametes). Mendel's laws were all inferred by analysis of phenotypic ratios of different traits in the offspring of crosses. In one cross, Mendel analyzed how the pea color phenotype (green or yellow) was inherited. Crossing green and yellow parents, he found that the F1 generation offspring all had yellow peas. Amazingly, if he mated these F1 together, the green color reappeared (as if by magic) in the next (F2) generation.

This was the teaser: how did one of the parental phenotypes disappear, and how did it reappear later? The answer is dominance, and to understand how this works, we need Mendel's first law: segregation (of alleles into gametes). Mendel had inferred that each pea has two versions (alleles) of the pea color gene, and that 50% of a plant's gametes contain one version and the other 50% the other version. The yellow parent has two copies of the Y allele (YY) and the green parent has two y (yy). So, all of the gametes from the yellow parent contains a Y; all of the gametes from the green parent contain a y.
Each F1 offspring, comprising genetic material inherited from both parents, have one Y and one y (Yy). That the F1 plants are all yellow defines the Y allele as conferring a dominant phenotype: being YY or Yy makes you yellow; only when you have no "dominant" alleles (yy) is the green phenotype evident. Assuming that gametes fuse randomly (without regard to what alleles they carry) at fertilization, we can predict the ratio of F2 generation phenotypes (yellow:green) with some simple probability calculations.
Probability? This time I saw some eye rolls and some seat-slumping. But I had anticipated and was ready for this. I handed a sealed envelope to a student sitting in one of the front rows, and then instructed each student in the class to choose a letter between A and F and write that letter down in their notes. Then I asked them to do the same: choose a whole number between 1 and 3 and write that down. "Please raise your hand if you chose the letter 'A.'" In my class of ~80 students (I hadn't taken roll so didn't know exactly how many were in attendance that day, and certainly wasn't going to take the time to count), about 9 had picked 'A.'
If you already know where I'm going with this, you probably feel the same way I did. The idea is that in a class of 80 students, if you give them a choice of six options (A, B, C, D, E, or F), then one-sixth of the students (on average) should choose each letter. 13 students should have picked 'A,' but of course the result (9) is just one sample from a probability distribution. Someday soon, when we start statistics (say, chi-square analysis), I'll use this example! Meantime, though, the demonstration isn't over yet.
"Please raise your hand if you picked the letter F." About twenty hands go up. "Please keep your hand raised if you also picked the number 2." Most of the hands drop. Four students in the class have chosen F2. "Please look around at your classmates and see that there are four students who have chosen the letter F and the number 2." Then I say, "Please open the envelope I handed you earlier and read the message inside." She reads: "Four students in class have chosen 'F2.'" Bam! Not a dry eye in the place.
And then, this!

Of course, the calculation is straightforward, I tell the students. With about 80 students in the class, about 1/6 should pick F, and about 1/3 should pick 2. Since these choices are independent events, we multiply the probabilities together to find that about 1/18 students should pick F2. 80 students * 1/18 students ~= 4 students that should pick F2.
Mendel had done the same calculations, presumably, I say. In the F1 generation of peas, 50% of gametes have Y, and 50% have y. If we assume that the gametes fuse randomly and that the two gametes that form an F2 plant are independent draws from the pool of F1 gametes, then the number of YY plants should be (50%)*(50%) = 25% of F2 plants. The number of yy plants should be (50%)*(50%) = 25% of F2 plants. The other 50% of the F2 plants are the heterozygotes (Yy and yY). Since only the yy plants have green peas (25% of the F2 generation), the rest of the F2s (75%) are yellow. Hence, there is a 3:1 ratio, which Mendel observed, of yellow:green peas.
"This was the first time I've tried this demonstration," I told the class. "And likely the last. Because if I know anything about probability, this is the only time I'll ever do this demonstration when it actually works they way I intended!"