Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Urgent! How genes tell cellular construction crews, 'Read me now!'

14.08.2013
Stowers researchers show that DNA sequences at the beginning of genes -- at least in fruit flies -- contain more information than previously thought

When egg and sperm combine, the new embryo bustles with activity. Its cells multiply so rapidly they largely ignore their DNA, other than to copy it and to read just a few essential genes. The embryonic cells mainly rely on molecular instructions placed in the egg by its mother in the form of RNA.


The dorsal-ventral patterning gene snail (shown in red) is one of the few genes that are active before as well as after the midblastula transition. The segmentation gene paired (shown in green) is turned on during the transition. Cell nuclei are shown in blue.

Credit: Image: Courtesy of Kai Chen

The cells translate these RNA molecules into proteins that manage almost everything in the first minutes or hours of the embryo's life. Then, during the so-called midblastula transition, cells start transcribing massive amounts of their own DNA. How embryonic cells prepare for this moment, and how they flag a small set of genes for transcription before that, holds important information about normal development and disease in animals and in humans.

A new study that sheds light on these questions appears in the Aug. 13 issue of eLife Sciences, authored by researchers at the Stowers Institute for Medical Research. The team, led by Associate Investigator Julia Zeitlinger, Ph.D., shows that in the fruit fly Drosophila melanogaster, genes active in the first two hours of a fertilized egg are read quickly due to special instructions at the beginning of each gene, in a region aptly named the "promoter."

Within each promoter region, different combinations of short control elements or "boxes" form a code that instructs specialized construction crews, called RNA polymerases, where and when to start transcribing. Researchers long thought that once an RNA polymerase appears at the worksite it would quickly finish the job.

"The most important result is that promoters are different," Zeitlinger says. "The general paradigm for a long time has been a promoter is a promoter. But really what we see is that they have different functions."

As a postdoctoral fellow at MIT, Zeitlinger unexpectedly discovered that sometimes RNA polymerase II pauses at the beginning of a gene as if taking a lunch break. More often than not, pausing occurred at genes important for development. Zeitlinger thought pausing may help get these molecular construction workers on site before a huge work order is due.

"We were wondering whether pausing was being used for preparing global gene activation during the midblastula transition," says Kai Chen, PhD, a former graduate student in Zeitlinger's lab and the study's first author. "We expected to see widespread pausing before that transition."

The fruit fly Drosophila melanogaster was a perfect test subject. This fly embryo takes two hours to reach the midblastula transition providing plenty of time to analyze what happens during this early period. Furthermore, decades of previous research on the flies provided context to guide the work.

Chen used a method called ChIP-seq, which can locate RNA polymerase II molecules on any gene. Paused polymerases would show up only at the beginning of genes. Working polymerases, on the other hand, would be found throughout the gene body.

The results took the Stowers team by surprise. Before the midblastula transition, RNA Polymerase II appeared to rarely pause as it transcribed roughly 100 early genes. And no construction crews were sitting idle on inactive genes in preparation for the midblastula transition. Pausing only became widespread only during the midblastula transition itself.

"What we found was not what we expected at all," Zeitlinger says. Before the midblastula transition, instead of preparing for a huge workload the construction crews were busy completing rush jobs. "The polymerase has to come to the promoter and immediately transcribe because there's so little time to do the job. That's one way of making transcription faster. "

When Chen and colleagues computationally compared the DNA sequences of promoters where pausing occurred with those where it didn't, a pattern emerged. They found that three different types of promoters correlated with the construction crew's pausing behavior.

The genes that RNA Polymerase II reads before the midblastula transition were often preceded by a promoter that seemed to yell, "Urgent! Don't even think about pausing." These promoters contain what's known as a TATA-box, named for its conserved arrangement of nucleotides, most commonly TATAA.

As cell division slows down during the midblastula transition, cells have the luxury of pausing, perhaps to fine-tune when transcription begins, Zeitlinger says.

These midblastula genes were regulated by promoters that contain a variety of specific promoter elements associated with paused RNA polymerase, including GAGA, Downstream Promoter Element (DPE), Motif Two Element (MTF) and Pause Button (PB).

The team also found a third type of promoter, which contained both the TATA-box and the pausing sequences. At these genes, RNA polymerase II does not pause initially but begins to pause during the midblastula transition.

Zeitlinger hopes learning more about promoters will give clues to the functions of unknown genes. Because these promoter sequences are not specific to flies, the differences among promoter types may be conserved in other animals as well.

"My lab is interested in understanding how development or even diseases are encoded in the genome," Zeitlinger says. "If we understand transcription, then we can predict a lot of what genomes encode, in terms of disease or differences between individuals."

"Promoters had been seen by some scientists as sort of boring," she adds, "but now, they are starting to get really interesting."

Other contributors include Jeff Johnston, Wanqing Shao, Samuel Meier and Cynthia Staber, all from the Stowers Institute.

The study was funded by the Stowers Institute for Medical Research, the Pew Charitable Trust and an NIH New Innovator Award.

About the Stowers Institute for Medical Research

The Stowers Institute for Medical Research is a non-profit, basic biomedical research organization dedicated to improving human health by studying the fundamental processes of life. Jim Stowers, founder of American Century Investments, and his wife Virginia opened the Institute in 2000. Since then, the Institute has spent over 900 million dollars in pursuit of its mission.

Currently the Institute is home to nearly 550 researchers and support personnel; over 20 independent research programs; and more than a dozen technology development and core facilities. Learn more about the Institute at http://www.stowers.org.

Gina Kirchweger | EurekAlert!
Further information:
http://www.stowers.org

More articles from Life Sciences:

nachricht Researchers identify potentially druggable mutant p53 proteins that promote cancer growth
09.12.2016 | Cold Spring Harbor Laboratory

nachricht Plant-based substance boosts eyelash growth
09.12.2016 | Fraunhofer-Institut für Angewandte Polymerforschung IAP

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Electron highway inside crystal

Physicists of the University of Würzburg have made an astonishing discovery in a specific type of topological insulators. The effect is due to the structure of the materials used. The researchers have now published their work in the journal Science.

Topological insulators are currently the hot topic in physics according to the newspaper Neue Zürcher Zeitung. Only a few weeks ago, their importance was...

Im Focus: Significantly more productivity in USP lasers

In recent years, lasers with ultrashort pulses (USP) down to the femtosecond range have become established on an industrial scale. They could advance some applications with the much-lauded “cold ablation” – if that meant they would then achieve more throughput. A new generation of process engineering that will address this issue in particular will be discussed at the “4th UKP Workshop – Ultrafast Laser Technology” in April 2017.

Even back in the 1990s, scientists were comparing materials processing with nanosecond, picosecond and femtosesecond pulses. The result was surprising:...

Im Focus: Shape matters when light meets atom

Mapping the interaction of a single atom with a single photon may inform design of quantum devices

Have you ever wondered how you see the world? Vision is about photons of light, which are packets of energy, interacting with the atoms or molecules in what...

Im Focus: Novel silicon etching technique crafts 3-D gradient refractive index micro-optics

A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.

Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...

Im Focus: Quantum Particles Form Droplets

In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.

“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ICTM Conference 2017: Production technology for turbomachine manufacturing of the future

16.11.2016 | Event News

Innovation Day Laser Technology – Laser Additive Manufacturing

01.11.2016 | Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

 
Latest News

Researchers identify potentially druggable mutant p53 proteins that promote cancer growth

09.12.2016 | Life Sciences

Scientists produce a new roadmap for guiding development & conservation in the Amazon

09.12.2016 | Ecology, The Environment and Conservation

Satellites, airport visibility readings shed light on troops' exposure to air pollution

09.12.2016 | Health and Medicine

VideoLinks
B2B-VideoLinks
More VideoLinks >>>