Researchers at the Johns Hopkins
High Throughput Biology Center
have invented two new gene "chip" technologies that can be
used to help identify otherwise elusive disease-causing
mutations in the 97 percent of the genome long believed to
be "junk."
A variety of DNA microarray technology, one of the two
new chips, called the TIP chip (transposable element
insertion point) can locate in the genome where so-called
jumping genes have landed and disrupted normal gene
function. This chip is described in the Proceedings of the
National Academy of Sciences' Online Early Edition
the week of Nov. 13-17.
The most commonly used gene chips are glass slides
that have arrayed on them neat grids of tiny dots
containing small sequences of only hand-selected nonjunk
DNA. TIP chips contain on them all DNA sequences. Because
each chip can hold thousands of these dots — even a
whole genome's worth of information — scientists in
the future may be able to rapidly and efficiently identify
exactly where mutations lie by comparing a DNA sample from
a patient with the DNA on the chip.
"With standard chips, we're missing a big piece of the
picture of mutations in humans because they look only at
the meaty parts of genes, but the human genome is only 3
percent meaty parts," said Jef Boeke, a professor of
molecular biology and genetics and director of the High
Throughput Biology Center, who spearheaded both studies at
the Institute of Basic Biomedical Sciences at Hopkins. "The
other 97 percent also can contain disease-causing mutations
and is often systematically ignored," he said.
Boeke and his team have focused particularly on
transposable elements, segments of DNA that hop around from
chromosome to chromosome. These elements can, depending on
where they land, wrongly turn on or off nearby genes,
interrupt a gene by lodging in the middle of it or cause
chromosomes to break. Transposable elements have long been
suspected of playing a role vital to disease-causing
mutations in people. Boeke hopes that the TIP chip
eventually can be used to look for such mutations in
people.
The new TIP chip contains evenly sized fragments of
the yeast genome arrayed in dots left to right in the same
order as they appear on the chromosome. Boeke's team used
the one-celled yeast genome as starting material because,
unlike the human genome, which contains hundreds of
thousands of transposable elements of which perhaps a few
hundred are actively moving around, the yeast genome
contains only a few dozen copies.
Like a word-find puzzle, where words are hidden in a
jumbled grid of letters, the TIP chip highlights exactly
where along the DNA sequence these elements have landed. By
chopping up the DNA, amplifying the DNA next to the
transposable elements and then applying these amplified
copies to the TIP chip, the researchers were able to map
more than 94 percent of the transposable elements to their
exact chromosome locations.
The second new chip, described in a separate report
published in the Nov. 3 issue of Nature Methods, contains
twice the amount of genetic information of current DNA
chips.
"This one lets us look at twice as much as we could in
the past, which means essentially that all chip experiments
become faster and cheaper and can be done on an even larger
scale," Boeke said. The chips his team currently uses cost
about $400 per experiment; if the amount of information can
be quadrupled, "it would be four experiments for the price
of one," he said.
Standard chips contain one layer of DNA dots that read
from left to right, like the "across" section of a
crossword puzzle. Boeke's new double-capacity chips hold
two layers of dots: a bottom layer that reads across and a
top layer that reads down, again using the crossword
analogy. So if an experiment lights up a horizontal row of
dots, the researchers learn that the data maps to the
region of the genome contained in the bottom layer;
likewise, if the experiment highlights a vertical row, the
data correspond to the top layer.
"It's so easy to differentiate the top and bottom
layers," Boeke said.
Next, he said, the team is going to try adding another
layer reading diagonally in order to triple the amount of
genomic information packed onto the tiny chips.
Researchers were supported by grants from the National
Institutes of Health.
Authors of the TIP chip and double-tiled DNA chip
papers are Sarah Wheelan, Lisa Scheifele, Francisco
Martinez Murillo, Rafael Irizarry and Boeke, all of Johns
Hopkins.
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