May 05, 2000
Genes Can Answer to More than One Master
Like discovering a car that has more than one engine under the hood,
cell biologists are learning to their surprise that alternate molecular
machines can drive the basic process of transcription that orchestrates
the expression of genes.
The core transcription machinery of RNA polymerase copies the
information found in DNA genes onto messenger RNA molecules that then
govern the production of proteins.
“The take-home lesson from these studies is that we're now appreciating more than ever before that the basic workhorse transcriptional apparatus is much more elaborate and probably more specific to organisms and tissues than we imagined.”
Robert Tjian
Although the reason for multiple transcriptional controls remains
mysterious, researchers speculate that the mechanism might allow the
same gene to be used for different purposes in different cells.
Now, Howard Hughes Medical Institute (HHMI) researchers have taken
an important step in understanding this phenomenon by pinpointing the
first gene in the fruit fly Drosophila melanogaster that is a
target of an alternate control molecule, called TRF1. They believe that
the discovery opens the way for a richer understanding of how gene
expression is regulated.
In an article in the May 5, 2000, issue of the journal
Science, HHMI investigator Robert Tjian and graduate
student Michael C. Holmes report that the Drosophila gene
tudor contains tandem promoter segments, one of which responds
to TRF1.
"The discovery of TRF has been intriguing because for perhaps the
last fifteen years we thought that the basal transcriptional machinery
of the cell was essentially invariant," said Tjian, who is at the
University of California, Berkeley. "We thought that only one set of
"general" proteins was involved, and that all the regulation was
directed by enhancer-binding proteins that were specific to a
particular gene sequence.
"It was like using the same engine over and over again, but just
putting different gearing systems into it. But then we discovered that
there were multiple engines."
The scientists had found evidence that TRF1 is apparently one of
several alternate transcriptional control molecules—called
recognition factors—that can replace the most prevalent control
element, called TATA-binding protein, or TBP.
"While past studies had proven that TRF1 was involved in
transcription, the big question was why was it particularly exciting
just finding another TBP-like molecule," said Tjian. "But then research
revealed, surprisingly, that this molecule was not evenly distributed
in every cell. Some cell types, particularly those in the central
nervous system, expressed high levels of this protein and others had
either very low levels or none at all."
To attempt to pinpoint a particular TRF1-responsive gene from among
the 12,000 known Drosophila genes, the researchers first
launched an "aerial reconnaissance" of Drosophila chromosomes.
Using a technique called polytene chromosome staining, they created an
antibody that specifically targeted and attached to TRF1. They then
bathed the giant salivary chromosomes from Drosophila in the
antibody. Since the antibody also included a staining molecule, they
could home in on potential TRF1-targeted genes by scanning the fly
genome for regions that were preferentially stained.
"We found that only about forty or fifty bands on the fly
chromosomes lit up," said Tjian. "This told us that our hypothesis that
TRF1 was specialized for certain genes was on the right track."
To find the TRF1-responsive genes, the scientists treated
preparations of fly chromosomes with chemicals that formed bonds
between TRF and the DNA. They then chopped up the chromosomes into
small pieces and identified those pieces that had attached to the
TRF1-specific antibodies.
Using the pieces of chromosomes as clues, they were able to work
their way up to identifying whole genes. Screening those genes revealed
that the Drosophila gene tudor is a potential target gene
that can be activated by TRF1. To validate the responsiveness of
tudor to TRF1, the scientists cloned the promoter region of
tudor and tested whether it responded to TRF1 in
vitro.
"The result of this test was more interesting than I anticipated,"
said Tjian. "We thought that these genes would either have a
TBP-responding promoter or a TRF-responding promoter. But tudor
had both—tandem promoters. I think this is perhaps the most
unexpected piece of data in the paper."
According to Tjian, the discovery of tandem promoters represents the
opening of a new terrain for the exploration of transcription
control.
"Right now, trying to explain these tandem promoters is total
speculation," he emphasized. "However, if you look at the genome of the
fly, it's about 12,000 genes. In contrast, the roundworm, C.
elegans, has about 18,000 genes. Now, the fly is at least as
complex, if not more complex than the worm, and one way to achieve that
higher complexity with fewer genes is to make the same gene-coding
capacity more versatile. One way this versatility could evolve is by
simply having more elaborate control mechanisms over a smaller number
of genes." Thus, said Tjian, the same gene might be governed by
alternate control schemes in different cells.
Tjian and his colleagues plan to look for other genes that have
multiple controls and to explore further this newfound diversity of
gene control.
"The take-home lesson from these studies is that we're now
appreciating more than ever before that the basic workhorse
transcriptional apparatus is much more elaborate and probably more
specific to organisms and tissues than we imagined," he said.
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