Research sheds light on the mechanics of gene transcription

The molecular machinery behind gene transcription -- the intricate transfer of information from a segment of DNA to a corresponding strand of messenger RNA -- isn't stationed in special "transcription factories" within a cell nucleus, according to Cornell researchers. Instead, the enzyme RNA polymerase II (Pol II) and other key molecules can assemble at the site of an activated gene, regardless of the gene's position.

The findings, published in the Dec. 28, 2007, issue of the journal Molecular Cell, are the result of an ongoing collaboration between the laboratories of John T. Lis, the Barbara McClintock Professor of Molecular Biology and Genetics, and Watt W. Webb, professor of applied physics and the S.B. Eckert Professor in Engineering. Jie Yao, the paper's lead author, recently finished his Ph.D. at Cornell under Webb.

Using multiphoton microscopy, a technique developed by Webb that allows high-precision 3D imaging in living cells, the researchers observed polytene chromosomes -- giant, multistranded chromosomes in the salivary gland tissue of fruit flies that have hundreds of sets of the genome instead of the usual two sets in conventional cells.

They activated heat shock genes, which protect cells from sudden rises in temperature, and watched them in real time as they began to be transcribed. The researchers also tagged Pol II with a fluorescent marker to track its movements within the nucleus.

While some reports have suggested that activated genes move to a specific nuclear location for transcription, the Cornell research supports the traditional view that gene activation is not dependent on movement to special locations, or so-called "transcription factories," said Lis.

"You see the genes decondense and fill up with polymerase, but they're not moving anywhere -- they don't collect in a single place," he said. Instead, the transcription machinery assembles at the called-upon locus, regardless of its position in the nucleus.

To test the generality of the findings beyond polytene nuclei to common (but much smaller and more difficult to test) diploid cells, the researchers used a technique called fluorescence in situ hybridization, which allowed them to detect the location of specific DNA sequences along a chromosome in fixed cells.

Looking at the location of co-regulated heat shock genes (genes that are transcribed simultaneously), they found that co-regulated pairs that occupied distinct sites before heat shock were no closer together after heat shock. As in the polytene chromosomes, the genes did not move to a single site for transcription.

And using fluorescence recovery after photobleaching -- another method engineered by Webb -- the researchers found that over time Pol II began to recycle itself within newly formed "compartments" around the activated gene.

"At some point you accumulate enough polymerase that it feeds back, so in a sense you've created a factory de novo" said Lis. "This is, to our knowledge, the first demonstration of Pol II recycling at a specific gene in vivo."

Lis and colleagues are now looking at other molecules involved in transcription to see if they behave similarly. "We're hoping to develop new ways to really see, in vivo, how gene regulation works mechanistically," he said.

Source: Cornell University

Related stories:

Early-stage gene transcription creates access to DNA
A gene contained in laboratory yeast has helped an international team of researchers uncover new findings about the process by which protein molecules bind to control sequences in genes in order to initiate gene expression, according to findings reported in the journal Nature.
Study finds genetic variant plays role in cleft lip
University of Iowa researchers and collaborators have found, in a previously identified gene, a variation that likely contributes to one in five cases of isolated cleft lip. It is the first time a genetic variant has been associated with cleft lip alone, rather than both cleft lip and palate.
Simple twists of fate
A novel Brandeis University study this week in PLoS Biology reports on some of the molecular gymnastics performed by a protein involved in regulating DNA transcription. Using state-of-the art tools, researchers observed the shape and behavior of individual DNA molecules bent into tight loops by Lac repressor, a protein from the bacterium E.coli that switches on and off individual genes.
Researcher Discovers Molecules That Inhibit Important Gene Regulators
A North Carolina State University chemist has discovered a molecule that can potentially stop the production of cancer cells at the very beginning of the process by switching off the gene regulators responsible for turning healthy cells into cancer cells. The discovery could lead to the development of drugs that can treat some of the deadliest forms of cancer, including brain cancer.
Rodent studies suggest mother's diet can affect genes and offspring's risk of allergic asthma
A pregnant mouse's diet can induce epigenetic changes that increase the risk her offspring will develop allergic asthma, according to researchers at National Jewish Health and Duke University Medical Center. Pregnant mice that consumed diets high in supplements containing methyl-donors, such as folic acid, had offspring with more severe allergic airway disease than offspring from mice that consumed diets low in methyl-containing foods. The results of the study are being published Sept. 18, 2008, in the online version of the Journal of Clinical Investigation and will appear in the October print issue.
Scientists find 'redesigned hammer' that forged evolution of pregnancy in mammals
Yale researchers have shown that the origin and evolution of the placenta and uterus in mammals is associated with evolutionary changes in a single regulatory protein, according to a report in Proceedings of the National Academy of Sciences.
Different stem cell types defined by exclusive combinations of genes working together
In the new issue of Cell Stem Cell, scientists report that the same transcription factor, which is crucial for the survival of different stem cell types, can behave differently.
Benchmark cyanobacterium sequenced could be cheap renewable energy source
(PhysOrg.com) -- A team of researchers headed by biologists at Washington University in St. Louis has sequenced the genome of a unique bacterium that manages two disparate operations — photosynthesis and nitrogen fixation — in one little cell during two distinct cycles daily.

News discussion:

General Science news