September 14, 2001
DNA Transcription is Tuned to Specific Cells
Researchers have found a new example of how the machinery that
controls the transcription of DNA to messenger RNA (mRNA) is tailored
to specific cells or genes.
In studies in mice, the researchers discovered that TAFII105, a key
component of the transcription machinery, is specific to egg-forming
cells in ovaries. The finding emphasizes a newly emerging theme in
molecular biology — that DNA transcription is not standardized
throughout cells but is instead adapted to control cell-specific gene
expression. The scientists believe that future research is likely to
reveal other cell-specific transcription components that ensure that
genes are expressed in a “customized” way according to the
needs of each cell.
“I believe that the field of transcription is entering a new phase of discovery. While it is true that the transcription machinery is universal in that every cell uses it, evolution has diversified this machinery to perform important specialized functions.”
Robert Tjian
The finding that TAFII105 is specifically involved in controlling
genes for egg formation also hints that some inherited forms of
sterility in women may be due to mutations in the TAFII105 gene, said
the scientists. In an article published in the September 14, 2001,
issue of the journal Science, Howard Hughes Medical Institute
investigator Robert
Tjian and colleagues Richard N. Freiman, Shane R. Albright, Shuang
Zheng, William C. Sha and Robert E. Hammer detailed how they traced the
transcriptional role of TAFII105 to granulosa cells in the ovaries of
mice. Granulosa cells surround the developing egg, called the oocyte,
and foster its development.
The scientists also used DNA microarrays to explore which genes were
switched off in knockout mice that lacked a functional copy of the
TAFII105 gene. The TAFII105 protein is one of a family of TAF proteins
that are subunits of a large complex called the transcription factor
TFIID.
"When TFIID and all its associated factors were discovered ten years
ago, we found it in every cell we looked at," said Tjian, who is at the
University of California at Berkeley. "We thought it would be invariant
from cell to cell, since it was so fundamental to the cells in
transcribing DNA," he said.
"So, when we discovered the TAF family of proteins, we never
anticipated that there would be cell-type-specific versions," said
Tjian. "But then five years or so after we made the initial discovery,
I had an intuition that maybe one of the ways that metazoan
[multicellular] organisms have been able to diversify their cell types
was to change the transcriptional machinery."
The concept of cell-type variations in transcriptional machinery was
considered radical when first proposed, said Tjian. But he believes
that evidence in favor of this idea, such as the findings reported by
Tjian and his colleagues in Science, is strengthening the case.
Tjian and his colleagues concentrated on TAFII105 as a possible
cell-type-specific subunit because they had originally discovered it
only in B cells of the immune system. Since the protein seemed
restricted to B cells, the scientists believed that knocking out the
TAFII105 gene in mice would likely not be lethal to the mice, and would
enable them to explore the protein's function. When they created the
knockout mice, however, they found no effect on the animals' immune
system, but noticed that the female knockout mice were invariably
sterile.
To pinpoint the reason for the sterility, Tjian's group collaborated
with Robert E. Hammer, a mouse reproductive biology expert at the
University of Texas Southwestern Medical Center. The researchers found
that the defect in the knockout mice affected the granulosa cells that
are part of the follicle surrounding developing eggs in the
ovaries.
"While that work nailed down the physiological defect in the
knockout mice, we really wanted to know which genes TAFII105 was
involved in regulating," said Tjian. To do that, Tjian and his
colleagues isolated mRNA from both wild-type and knockout mice and used
DNA microarrays to compare gene expression in the two types of mice.
The researchers treated separate DNA microarrays containing more than
11,000 mouse genes with ovarian mRNA from the two mouse strains, to
determine which genes were downregulated in the knockout mice.
Downregulation of a gene results in lower levels of mRNA.
"The results turned out to be interesting, because they revealed
that the knockout mice had downregulated exactly the kinds of genes one
would expect to be required for oocyte formation," said Tjian. "The
results enabled us to actually see why knocking out TAFII105 would
cause oocytes to be incorrectly developed." The findings offer a clear
pathway for further exploring the action of TAFII105, said Tjian.
"We now have a very good idea of which genes we should be studying
to understand the details of their transcription machinery and the role
of TAFII105," Tjian said. The findings might have clinical implications
in identifying the cause of some female sterility. "We suspect that if
we work with clinicians to begin examining the genetic identities of
the many forms of female sterility in the human population, it's likely
we're going to find mutations in TAFII105," he said.
Tjian also emphasized that the lessons learned from TAFII105 offer
insight into the complexity of the transcription machinery. "Our work
and that of others is revealing a multitude of cell-specific
differences in other components of the transcriptional machinery and in
different organisms," he said. "So, I believe that the field of
transcription is entering a new phase of discovery. While it is true
that the transcription machinery is universal in that every cell uses
it, evolution has diversified this machinery to perform important
specialized functions."
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