June 19, 2003
Finished Y-Chromosome Sequence Reveals a Genomic "Crystal Palace"
A team of 40 researchers has finished sequencing the Y chromosome,
the male sex chromosome once belittled as “the Rodney Dangerfield
of the human genome” because researchers believed it contained no
genes of interest.
The Y may gain a measure of respect now that researchers have
discovered that it is actually a genomic “crystal palace,”
containing genes that impact male fertility, vast stretches of
mirror-image DNA, and an assortment of functional and vestigial
genes.
“I have been told for years that the Y chromosome was full of junky repeats, a genetic wasteland.”
David C. Page
Most significantly, the new studies have unearthed a startling
mechanism that the Y chromosome uses to maintain its functionality. It
appears that the Y protects its genetic integrity by swapping multiple
copies of the same gene within its own structure.
“I have been told for years that the Y chromosome was full of
junky repeats, a genetic wasteland,” said senior author David C.
Page, a Howard Hughes Medical Institute investigator at MIT's
Whitehead Institute for Biomedical Research. “People would ask
why we would consider wasting our time mapping and sequencing it. But,
in fact, what we see is that it's a crystal palace.”
The researchers published their findings in two articles in the June
19, 2003, issue of the journal Nature. Page collaborated with
colleagues from the Whitehead Institute, Washington University School
of Medicine and the Academic Medical Center in Amsterdam.
According to Page, the team's detailed genomic sequence of the human
Y chromosome will contribute to a better understanding of male
infertility, as well as certain sex-linked genetic disorders in women.
He also speculated that their findings could lead to genomic
explanations for differences in disease susceptibility between men and
women.
Sex chromosomes in animals and humans include the X chromosome and
the much smaller Y chromosome. Females have a pair of X chromosomes and
males have both an X and Y chromosome.
Although the sequences of several organisms with Y chromosomes —
including fruit flies and mice — have been declared
“complete,” said Page, those genome sequences did not
include the Y chromosome. In the case of the human Y chromosome — and
likely those of other animals — standard sequencing techniques have
been confounded by the long stretches of nearly identical DNA that lack
the landmarks needed to guide the assembly of sequences from smaller
segments, said Page.
The Y is unique among chromosomes in that it bears long stretches of
mirror-image, or “palindromic,” DNA sequences that nearly
thwarted sequencing efforts. “Nobody has seen palindromes of this
scale and degree of precision anywhere in the genome,” said Page.
“Before we began this project, when asked why it would be so hard
to map and sequence the Y chromosome, I used to say it feels like a
hall of mirrors. I had no idea how accurate that analogy was, because
the Y literally is a hall of mirrors. Trying to sequence the Y
chromosome is, indeed, like entering a hall of mirrors, spinning
around, and after coming outside, being asked to draw the hall's floor
plan. You're disoriented.”
To overcome the disorienting duplications in DNA sequence, Page and
his colleagues employed an iterative method to get an overall picture
of the Y map. They later refined the technique to do more precise
sequencing of the individual segments of the Y chromosome. By
sequencing the Y chromosome in segments, they were able to detect
minute differences among the near-identical palindromes. They then
folded that sequence data back into their mapping to improve it.
In order to minimize complications due to normal genetic variability
among males, the sequencing was performed on the Y chromosome of one
male, whose identity remains anonymous.
Page said much of the credit for the high-precision sequencing goes
to the Washington University Genome Sequencing Center, whose
researchers achieved an overall accuracy in the Y-chromosome sequence
of one error in 100,000 to 1,000,000 DNA base pairs. This feat is even
more impressive when one considers that in order to deduce the
approximately 24-million-base-pair sequence of the Y chromosome, the
team had to sequence well over 50 million base pairs of DNA, according
to Page's estimates.
The final sequence reveals that the Y chromosome is a mosaic of two
kinds of genomic sequences: euchromatic sequences that represent active
genes, and heterochromatic sequences that are nonfunctional.
The functional euchromatic sequences included three classes, said
Page. “These three classes really shout out messages about the
evolution of the Y chromosome and sex chromosomes in general, and about
the function of the Y chromosome today,” he said.
The three classes are called “X-degenerate,”
“X-transposed” and “ampliconic” sequences.
X-degenerate sequences are relics from an ancient time when the X and Y
chromosomes first evolved from an ordinary, or autosomal, chromosome.
Genes within these sequences — which resemble genes on the X
chromosome — show evidence of steady decay due to mutation, and many
are non-functional. “We can see evidence that, whereas the gene
on the X is a functional working copy, in many cases the corresponding
gene on the Y is a rotted-out hulk that no longer does any
business,” said Page. “And that provides us a glimpse into
one aspect of the Y chromosome as a rotted-out X chromosome.”
The X-transposed sequences are genes that were swapped as a group
from the X chromosome roughly three to four million years ago, after
the ancestors of humans and chimpanzees diverged into separate lines.
There are few functional genes in this region, said Page.
Finally, the ampliconic sequences are those that exist within
multiple, repeated palindromic segments. “The ampliconic genes
are the big surprise,” said Page. “While the X-degenerate
genes tend to be expressed throughout the body and in many different
tissues and cell types, the genes in the ampliconic sequences are very
restricted to the testis in their expression. And to the extent that
we've studied them in detail, it looks like they're actually expressed
in only in the spermatogenic cells themselves.” Thus, said Page,
these genes are likely to play an extremely important role in
generating sperm. This role has been confirmed by earlier work showing
that mutations in the Y chromosome are the most common known genetic
causes of male infertility.
Perhaps the most fundamental insight arising from the sequencing of
the Y chromosome, said Page, is how ampliconic genes avoid degradation
due to mutation. Unlike the two X chromosomes in females, the Y
chromosome does not have a partner with which to swap genes during cell
division in order to replace genes that have suffered deleterious
mutations, said Page.
“This was the theoretical underpinning for the traditional
notion that the Y was a genetic wasteland — the Rodney Dangerfield of
the genome,” said Page. “But we believe we have found that
many of the genes on the Y, and virtually all the ampliconic genes,
occur in pairs. And so, pairs of genes on the Y can swap, not with
genes on another chromosome, but with a partner on the corresponding
identical palindrome. This Y-Y gene conversion is, I think, the most
important finding of our work.” However, he added, that same
internal recombination underlies the chromosomal aberrations that lead
to male infertility.
To confirm that the ampliconic genes on the Y chromosome palindromes
have been recombining over time, Page and his colleagues also performed
a comparative analysis of Y chromosomes of humans and chimpanzee
sequences in those regions. As reported in the second Nature
paper, that comparison, indeed, revealed that such recombination exists
in both species.
“The sex chromosomes represent a grand experiment of
nature,” added Page. “And in our work, every few years
we've caught a glimpse of some unexpected aspect of this experiment.
And of all these aspects, this Y-Y gene conversion is one of the
wildest.”
Page emphasized that the scientific and clinical implications of the
sequencing of the Y chromosome are profound. For example, comparative
sequencing of the Y chromosome among various human populations will
reveal much about its variation and functions.
More broadly, he said, “While the sequencing of the human
genome has been extraordinarily valuable, I think our work illustrates
that those hardest parts of the genome that remain to be sequenced
might house particular gems worth finding.” And further digging
in especially frustrating heterochromatic regions of DNA, which also
contain massively duplicated blocks of genetic material, might also
yield new genomic insights.
Clinicians are already using data from the Y-chromosome sequencing
to understand the genetic origins of male infertility, said Page. That
genomic data will aid in understanding Turner syndrome, one of the most
common chromosomal disorders in females. The disorder arises from the
lack of one sex chromosome, and the absent gene might well be an
X-degenerate gene or its counterpart on the X chromosome, said
Page.
On a more speculative note, Page said that genes on the Y chromosome
might play a role in influencing gender-specific differences in disease
susceptibility. Evidence has developed that the Y chromosome plays a
role in gonadal sex determination, skeletal growth, germ-cell
tumorigenesis and graft rejection, he said.
“We know that there are many diseases for which men or women
are at higher risk,” said Page. “It has been conventionally
assumed that these differences in disease susceptibility reflect the
action of sex hormones, and not the action of the sex chromosomes
directly.” But that assumption was set in place when some people
thought the Y didn't have any genes on it, said Page.
At one time, researchers believed that during development of
females, all genes on one X chromosome were inactivated, leaving only
one full complement of genes on the other X chromosome. And since the Y
supposedly harbored no genes other than reproductively related ones,
men and women were supposedly genetically equivalent.
“But now we know there are many genes on the X that escape
inactivation, so they are present in two copies in females and in one
copy in males. So, maybe we should rethink the roles of the second sex
chromosomes in these often dramatic differences in disease
susceptibility between males and females.”
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