The "Y" files
Not everyone believes in chance—the fortuitous
twist of fate that takes a person down an unforeseen
path. David Page
believes in chance. For him, fate came along on the
tip of a light brown wooden toothpick.
Page was a first-year medical student and research
assistant in Cambridge, Massachusetts, in 1979 when
he signed up for a study to map all the genes in the
human body. (Seven years later, this effort would become
known as the Human Genome Project.) His first task was
to analyze thousands of recombinant DNA clones, searching
for those most suitable for study. Each clone was selected
randomly, and rather unceremoniously, from a sea of
thousands. The instrument used for this scientific experiment:
a toothpick.
It was summertime and Page was spending hours in the
lab, waving a toothpick above trays of DNA clones, choosing
one, examining it, and choosing another. One afternoon
in particular stands out in his memory. What ended up
on the bottom of his toothpick that day was a clone
of DNA shared by the X and Y chromosomes—the sex
chromosomes whose combination determines whether a human
is male or female. He examined the clone, pondering
its potential for his project, just as he had done with
dozens of others. It’s only in hindsight, 24 years
later, that the magnitude of that random selection became
clear.
“When people ask how I picked the Y chromosome
for my research, I often say, ‘I didn’t.
It picked me,’” Page says. “If I hadn’t
picked that clone out of hundreds of thousands I’d
probably be a cardiologist.”
"The idea of the Y as a shiftless, no-good
degenerate chromosome is entirely too appealing
and attractive to resist for reasons that have little
to do with science and lots to do with sexual politics."
David Page |
Not a cardiologist, but a scientist at Whitehead Institute
and an investigator with Howard Hughes Medical Institute,
Page is considered to be among the world’s leading
experts
on the Y chromosome, the defining biological determinant
that makes males male. In 1992, his lab announced the
first successful cloning of a human chromosome—the
Y chromosome—and in June of this year, he led
a team that published the complete sequence of the Y
on the cover of Nature, work that offers not only a
road map for scientists who study male infertility,
but also casts doubt on a decades-old theory that destined
the Y to extinction.
And it all began with a fateful stab of a tiny wooden
stick.
The Y’s demise
Scientists marvel at the nuances of the human genome,
the mysterious alphabetical configurations of DNA and
the construction of cells and genes and chromosomes
that work together to help us live, reproduce, and evolve.
At the heart of human evolution is the body’s
ability to repair genetic flaws through a process called
sexual recombination.
All humans receive a set of chromosomes from Mom and
a matching set from Dad. Over the course of many generations,
chromosomal pairs can swap damaged genes for good ones
and fill in gene sequences that may be missing on one
chromosome but present on its mate. This swap—called
recombination—doesn’t fix all damaged or
missing gene sections. It’s up to natural selection
to eliminate those that make it through without repair.
If all chromosomes had a matching partner, the story
would end here. But the complexities of human biology
make things messy. Of the 24 chromosomes in the human
genome, 22 come in identical pairs in both males and
females. Women have another matching set—two X
chromosomes that together cast a developing fetus in
a female role. But men have a mismatched arrangement
of sex chromosomes—one X and one Y. Lacking a
mate, the Y can’t swap its defective genes for
good ones.
The Y has paid dearly for this bachelor status over
time. When sex chromosomes first evolved some 300 million
years ago, the X and Y each had about 1,000 genes, which
they swapped with each other. Somewhere along the way,
the Y lost its ability to share genes with the X. As
defects in the genetic structure appeared, the Y was
stuck with them and most of the chromosome’s genes
weakened or died out altogether.
Indeed, in the biological battle between the sexes,
the Y chromosome has suffered defeat after defeat. The
male-determinant has seen its gene supply shrink to
what scientists thought was only a handful of genes;
some speculated that there was just one lone gene on
the Y—the one responsible for maleness. It was
a downward trend predicted to continue until the Y disappeared
altogether.
X marks the spot…or does it?
David Page is a lone Y in a house full of Xs. He and
his wife Elizabeth have three daughters, an irony not
lost on a man whose research subject often provides
fodder for only half-feigned derogatory sarcasm from
the double-X gender. The Y chromosome long has been
the whipping post for all stereotypical male traits—all
negative stereotypical male traits—including everything
from an inability to ask for directions to the bewildering
memory skill that allows for instant recall of exact
dates of historical sporting events but not dates of
anniversaries and birthdays.
Subscribing to the “If you can’t beat ‘em,
join ‘em” philosophy, Page’s research
presentations often include a slide featuring certain
“genes” identified along the Y chromosome:
the genes for channel flipping (FLP), spitting (P2E),
the ability to identify aircraft from a distance of
10,000 feet (DC10), and selective hearing (HUH?).
Obviously, the 47-year-old Pennsylvania native has
a healthy sense of humor. He also has a fondness for
treading on uncharted territory. As a high school senior
in a small rural town near Three Mile Island, Page applied
to Swarthmore College, a private, liberal-arts
college, while many of his other classmates chose to
remain closer to home. He was accepted and enrolled
as a freshman intent on a career in environmental law.
While Page enjoyed a rich exposure to chemistry, physics,
and biology in high school (he calls the experience
a “Sputnik education,” sparked by the nation’s
1950s desires to outpace the Russians in space and science),
he also enjoyed the debate team, and law seemed a natural
step.
“When I was growing up, science was very much
an abstraction because I’d never met a scientist.
I had no idea what a scientist looked like or, for that
matter, if anyone actually was a scientist,” Page
recalls. It took a while for the science to take hold,
but by his junior year at Swarthmore, he “came
back to the Sputnik stuff.”
Page spent two summers as a research assistant in biology
labs, first at Brookhaven National Laboratory on Long
Island, New York, and then at the National Institutes
of Health in Bethesda, Maryland. At NIH, he studied
nucleosomes, basic subunits of the chromosome. He was
hooked.
He applied to the Health Sciences and Technology Program,
a joint initiative between Harvard University and Massachusetts
Institute of Technology that integrates education and
research in science, engineering, and medicine. To fulfill
a research thesis requirement, he joined the lab of
David Botstein at MIT, a pioneer of the Human Genome
Project who now leads Princeton University’s genomics
institute. It was there that Page had the chance meeting
with a gene clone shared by the X and Y. The Y wasn’t
all that interesting to genetic scientists at the time.
Seemed like a perfect fit for a man who enjoyed forging
paths rather than following them, so when Page received
his MD and joined Whitehead as a Fellow in 1984, he
continued the work he began at MIT—a project to
map the Y’s gene sequence.
Making a map
In 1992, four years after being named an Associate
Member at the Institute, Page’s lab cloned the
Y chromosome—the first time anyone had cloned
a human chromosome. Over the next 10 years, the scientist’s
work revealed new information about the evolution of
the Y and the function of its genes. In the late 1990s,
the biologist and his collaborators published findings
that suggested that infertile men who father children
through a common type of in vitro fertilization can
pass along to their male offspring the very genetic
flaws that caused their own infertility.
But the biggest advance—the completion of the
Y mapping project—was announced at a Washington,
D.C., press conference in June 2003. The effort, led
by Page and collaborators from Washington University
School of Medicine in St. Louis, yielded 78 genes on
the chromosome—far more than the handful rumored
to remain on what had come to be called the “rotting
Y.”
And there’s more: While it’s true that
over millions of years the male sex chromosome has lost
hundreds of genes and seen many others crippled, the
biggest concern has been gene health in the regions
of the Y that control sperm production. But this new
genetic map reveals a series of massive palindromes—stretches
of gene copies that are 99.9 percent identical to one
another. A palindrome is something that reads the same
forward and backward (i.e., MADAM I’M ADAM), and
the researchers found eight of them in the region of
the Y responsible for sperm production. The scientists
suspect that this genetic “hall of mirrors”
provides a mechanism for self-repair, a way for the
Y to prevent the erosion of these critically important
genes.
Technology has not yet provided a window to watch the
chromosome in action, which leaves the researchers to
infer the function of these duplicate gene sequences.
Say a gene copy along one of these palindromes suffers
a mutation. By bending into a hairpin formation, the
injured gene pairs with its copy, and the good gene
may overwrite the bad one. Essentially, the Y combines
with itself.
“This study shows that the Y chromosome has become
very efficient at preserving its important genes,”
says Richard K. Wilson, director of the Genome Sequencing
Center at Washington University School of Medicine in
St. Louis, where the Y was sequenced. “It’s
found different ways to do the things chromosomes must
do to evolve, survive, and thrive.”
But this secret weapon was not revealed easily. While
other chromosomes are known to have duplicate genetic
sequences, none contains quite as many. Wilson’s
team recently completed sequencing chromosome 7, a task
he considered among the biggest challenges his lab has
tackled. Duplicate sequences constitute about 8 percent
of that chromosome; they make up half of the Y.
“There are some things that just don’t
like to be sequenced,” Wilson says. “They
can be a bit resistant to being deciphered by the usual
biochemistry methods we use. So, we had to use some
alternative biochemistry for the Y.”
Researchers mapped the gene sequence of a Y chromosome
from an anonymous male, as well as parts of a Y chromosome
from a chimpanzee. This technically challenging process
involved delicately unwrapping the two arms on each
of the eight palindromes and analyzing the near-identical
gene sequences inside.
“Most chromosomes are like a typical thousand-piece
jigsaw puzzle—a pretty picture split into pieces
with easily identifiable markings,” says Wilson.
“The Y chromosome, on the other hand, was like
a picture of a small sailboat on the ocean with lots
of blue sky, no clouds, and hundreds of pieces that
looked exactly alike. Determining exactly where each
piece went in the grand scheme required a lot of work.”
Key to these findings is that researchers identified
this gene repair technique not only in a human Y chromosome,
but also in a chimp Y.
“When we look at the human Y, compared with the
chimp Y,” Page says, “what we can infer
is that during the last 5 million years, since we and
chimps parted company, this overwriting of one gene
copy by another has been going on frequently in our
Y chromosome and in the chimp Y chromosome.”
Questions answered, questions raised
Studies of the Y chromosome in humans and other species
haven’t always caught the collective eye of biologists.
In fact, the Y chromosome has not been studied in comparable
detail in any other species.
But the small number of people interested in the Y
has steadily increased in the last few years. Today,
the field is populated with researchers interested in
a variety of projects in which the Y chromosome is implicated,
including the mystery surrounding the origins of modern
populations (called the search for Y-Chromosomal Adam)
and male infertility.
Millions of couples in the United States alone have
trouble conceiving a child. In about 30 percent of those
cases, the problem is related only to male infertility.
Steve Rozen and Helen Skaletsky, scientists in the Page
lab and coauthors of the Nature studies, are interested
in applying the information they’ve learned about
the Y’s genetic makeup to their male infertility
studies. Of all the genes the team identified on the
chromosome, all but 18 are active in the testes, Rozen
says.
“Some of these genes are essential for normal
sperm production. For others, the fact that the gene
is active in the testes merely suggests a role in sperm
production,” Rozen notes. “We are interested
in looking for damage to these genes in men who do not
produce normal numbers of sperm. Finding a newly damaged
gene in a man with poor sperm production tells us that
the damage caused the sperm production problems.”
Understanding the structure of the Y chromosome may
be a significant step forward in the effort to treat
male infertility. But, Rozen cautions, science moves
at its own pace, which is hardly ever fast.
For some scientists, though, the payoff of this work
is more immediate.
“I thought about, talked about, wrote about the
Y as a rotting chromosome that really only had one important
gene—the one that determines sex,” says
Scott Hawley, a biologist with the Stowers Institute
for Medical Research in Kansas City, Missouri, who studies
chromosomal pairing. But these new findings make “perfectly
good sense,” Hawley adds. “It’s one
of those ‘Ah-ha!’ experiences that, after
you hear it, you think, ‘It had to be that way.
Why didn’t we think of this before?’ It’s
just revolutionary work.”
The research could perhaps have the most significant
effect on studies of heterochromatin, highly condensed
chromatin (portion of a cell nucleus that contains all
the nucleus’s DNA) strains once thought to be
useless genetic wastelands but now known to be essential
for normal chromosomal behavior.
“David’s really given us an analytical
approach to studying heterochromatic regions on a larger
scale,” says Hawley, who authored a review of
the Page lab findings for the journal Cell. “It’s
a new paradigm for thinking about the structure of the
heterochromatic regions, and there are a lot of people
who think about this kind of stuff.”
Getting a little respect
“I often say that the Y chromosome is the Rodney
Dangerfield of the chromosome world,” Page jokes.
“It gets no respect.”
No respect and little credence: When the completion
of the mouse genome was announced in 2002, it was not
really complete. The mouse Y has not yet been sequenced.
A 2002 article in Nature by two Australian scientists
rang a death knell for the Y chromosome, claiming that
“The original Y chromosome contained around 1,500
genes, but during the ensuing 300 million years, all
but about 50 were inactivated or lost… . At the
present rate of decay, the Y chromosome will self-destruct
in around 10 million years.”
There’s no denying the Y has problems. While
this new research shows that there are more genes on
the chromosome than once thought, as Page points out,
the Y still has lost a lot of genes. But to expend its
energy on protecting the genes that are most important,
the ones that keep it from extinction—now that,
Page says, is clever.
“The Y has found a way to keep these genes coherent
despite a rather unstable structure,” says Robert
Waterston, now a scientist at the University of Washington
who was a lead researcher at the Genome Sequencing Center
at Washington University during these studies. “That
instability of structure could be disastrous for a particular
individual, but it won’t be disastrous for the
Y, because the deleted Ys would not be passed on.”
Still, not everyone is convinced that this justifies
a newfound respect
for the Y chromosome. The oft-targeted male chromosome
took a thrashing in a column published in early July
in the Boston Globe by David Bainbridge, a fellow of
St. Catharine’s College in Cambridge, United Kingdom,
and author of The X in Sex: How the X Chromosome Controls
our Lives.
“Page’s research appears to demonstrate
that the Y chromosome contains clear evidence of trying
to patch up its wounds by swapping bits with itself.
Of course, this is still an inefficient way of losing
damaged genes. It may hold things together in the short
run, but it’s no healthy way for a self-respecting
chromosome to carry on,” Bainbridge wrote.
Attacks such as this confound Page at times. He acknowledges
that the Y likely will always be the butt of many jokes.
Still, when the abuse is heaped on by other scientists,
it gives him pause.
“The common perception of boys and girls, of men
and women, greatly impacts biologists’ perceptions
of the X and the Y,” Page says. “The science
and the sexual politics become blurred. The idea of
the Y as a shiftless, no-good degenerate chromosome
is entirely too appealing and attractive to resist for
reasons that have little do with science and lots to
do with sexual politics.”
The road ahead
Over the last two decades, the Y chromosome has revealed
itself to be far more complicated than anyone thought.
What many scientists overlooked for other, seemingly
sexier research topics has provided Page with a biological
challenge that is far from over.
“There are many points in the course of a line
of experiments where you choose to believe or disbelieve
something and you choose to follow it up or let it go,”
he says. “The history of Y chromosome research
is strewn with prematurely abandoned lines of work.”
But there was something about the chromosome that demanded
Page’s attention. As the sequence of the Y was
coming together, scientists learned bits and pieces
about the chromosome. But until the map was complete,
Page says, they were fumbling along in the dark. Now,
the team will use the human Y as a reference for the
study of the Y chromosomes of other organisms.
Already under way are projects to sequence the male-determining
chromosome in the chimpanzee and the mouse. The chimp
Y should be complete in 2004 and the mouse Y the following
year.
“We’ve seen the Y in humans and we’ve
started to see little bits in the chimp and we’re
beginning to see that there’s something a little
different,” Wilson says. Filling in those missing
pieces would go a long way toward understanding how
sex chromosomes have evolved and learning why different
organisms choose the specific type of reproductive strategy
they use.
Of course, the studies of the Y’s genetic self-repair
system will continue, as will plans to identify how
genes in the testes region function, and what happens
when they don’t.
When Page began this journey, he had no idea where
it would lead. It was a chance stab at a gene clone
that marked his first brush with what would become a
lifetime study. Today, he travels a more purposeful
path in his research. Still, he says, smiling, there
is much to be said for happenstance.
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