Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

New Technique for Tracking Gene Regulators

29.12.2004


May help decipher regulator proteins’ roles in cell differentiation, cancer, and more



Finding out where gene-regulator proteins bind to DNA and identifying the genes they regulate just got a step easier thanks to a new technique developed by scientists at the U.S. Department of Energy’s Brookhaven National Laboratory. The technique could greatly speed the process of unraveling the role these proteins play in turning on and off the genes that establish the very identity of cells — be they brain cells, liver, or blood — as well as what might go awry in certain conditions like cancer.

The Brookhaven scientists, together with collaborators from Oregon Health & Science University, Emory School of Medicine, and Stony Brook University, have published the first results using their technique in the December 29, 2004 issue of Cell, where they describe the human-genome binding sites of a regulator protein known as CREB.


“Though scientists have now decoded almost all of the entire human genome — the series of nucleotide bases (labeled A, T, G, and C) that make up the source code for running the machinery of the cell — we are just beginning to decipher it,” said biologist John Dunn, who led Brookhaven’s role in the research. “It’s as if we have in our hands a giant book of life, but we are barely beginning to learn how to read it.” “Our technique gives us a new way to index the code, to find the places where regulators act — where the on/off switches are that determine which genes are at work in different types of cells under different conditions,” he said.

Previous, individual experiments have identified about 100 places where CREB binds to DNA and regulates genes in humans, so scientists know it is important, particularly in regulating cell differentiation, survival, and the function of nerve cells. But there has been no easy way to screen the entire genome. “We are the first to do a genome-wide survey,” says Dunn.

The problem has been the sheer magnitude of information in the genome: three billion nucleotides, and many tens of thousands genes. Trying to ascertain which of these genes CREB regulates by more traditional methods, evaluating one gene at a time, would be too labor-intensive, expensive, and take a very long time.

Scientists have been working on short cuts, but all so far have limits. For example, in one recent technique, scientists mix the regulator protein of interest (let’s say, CREB) with the entire genome of a cell and let it bind. Then they fragment the genome into smaller pieces, 500 to 1,500 nucleotide bases long. Using antibodies that specifically recognize and bind to CREB, they then isolate the pieces that have CREB attached, and wash all the others away. Scientists can use traditional gene-sequencing methods to decipher the sequence of A, T, G, and C on these fragments and then locate their original positions on the genome, but it is a slow and somewhat expensive process. Other methods, such as matching the pieces to their compliments on microarrays, are limited by the size of genome they can analyze.

Dunn’s team has come up with a technique to determine the positions of these 500-to-1,500-base-long pieces on an entire genome — even one as large as the human genome — relatively quickly and in very large numbers.

After isolating the CREB-bound fragments, they release the CREB and then cut the DNA with a “restriction” enzyme that recognizes a particular nucleotide base sequence, CATG. Further manipulation of the cut ends allows them to isolate 20-base-long-fragments, or “tags,” in each direction from these cut sites. This gives the scientists a large number of very short DNA “tag” sequences, which all have the same start sequence of CATG plus 16 additional unknown bases. The scientists then “glue” together the tags into chains and sequence them.

While small in length, the tags are large enough to allow computer searches to locate their specific positions on the complete genome in a manner that is analogous to a laser scanner reading barcodes on items in the grocery store. In this case the inventory isn’t cans of food but the database of the human, mouse, or rat genome sequences. And because the scientists know that each of these tags lies within, at most, 500 to 1,500 bases of a CREB-binding site, they are able to search the region around the specific locations for CREB binding sequences or genes that might be regulated by CREB.

Using this technique, the scientists have identified some 6,302 genome-binding sites for CREB, including many that are located near known genes. Genes identified as being regulated by CREB using this method include the gene responsible for causing Huntington’s disease in mice, which is important for making advances in understanding Huntington’s disease in humans, and genes that may play an important role in certain cancers. “This technique can be applied to any protein that binds to specific sequences in the DNA and promises to be a very useful tool,” says Dunn.

This research was funded by the Office of Biological and Environmental Research within the U.S. Department of Energy’s Office of Science, the National Institutes of Health, and the Howard Hughes Medical Institute. The Department of Energy’s Office of Science was a founder of the Human Genome Project, a nationwide effort to generate the instrumentation and biological and computational resources necessary to sequence the entire human genome, identify all functional genes, and help transfer this information and related technology to the private sector for the benefit of society (see DOEgenomes.org).

Karen McNulty Walsh | EurekAlert!
Further information:
http://www.bnl.gov

More articles from Life Sciences:

nachricht How brains surrender to sleep
23.06.2017 | IMP - Forschungsinstitut für Molekulare Pathologie GmbH

nachricht A new technique isolates neuronal activity during memory consolidation
22.06.2017 | Spanish National Research Council (CSIC)

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Can we see monkeys from space? Emerging technologies to map biodiversity

An international team of scientists has proposed a new multi-disciplinary approach in which an array of new technologies will allow us to map biodiversity and the risks that wildlife is facing at the scale of whole landscapes. The findings are published in Nature Ecology and Evolution. This international research is led by the Kunming Institute of Zoology from China, University of East Anglia, University of Leicester and the Leibniz Institute for Zoo and Wildlife Research.

Using a combination of satellite and ground data, the team proposes that it is now possible to map biodiversity with an accuracy that has not been previously...

Im Focus: Climate satellite: Tracking methane with robust laser technology

Heatwaves in the Arctic, longer periods of vegetation in Europe, severe floods in West Africa – starting in 2021, scientists want to explore the emissions of the greenhouse gas methane with the German-French satellite MERLIN. This is made possible by a new robust laser system of the Fraunhofer Institute for Laser Technology ILT in Aachen, which achieves unprecedented measurement accuracy.

Methane is primarily the result of the decomposition of organic matter. The gas has a 25 times greater warming potential than carbon dioxide, but is not as...

Im Focus: How protons move through a fuel cell

Hydrogen is regarded as the energy source of the future: It is produced with solar power and can be used to generate heat and electricity in fuel cells. Empa researchers have now succeeded in decoding the movement of hydrogen ions in crystals – a key step towards more efficient energy conversion in the hydrogen industry of tomorrow.

As charge carriers, electrons and ions play the leading role in electrochemical energy storage devices and converters such as batteries and fuel cells. Proton...

Im Focus: A unique data centre for cosmological simulations

Scientists from the Excellence Cluster Universe at the Ludwig-Maximilians-Universität Munich have establised "Cosmowebportal", a unique data centre for cosmological simulations located at the Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences. The complete results of a series of large hydrodynamical cosmological simulations are available, with data volumes typically exceeding several hundred terabytes. Scientists worldwide can interactively explore these complex simulations via a web interface and directly access the results.

With current telescopes, scientists can observe our Universe’s galaxies and galaxy clusters and their distribution along an invisible cosmic web. From the...

Im Focus: Scientists develop molecular thermometer for contactless measurement using infrared light

Temperature measurements possible even on the smallest scale / Molecular ruby for use in material sciences, biology, and medicine

Chemists at Johannes Gutenberg University Mainz (JGU) in cooperation with researchers of the German Federal Institute for Materials Research and Testing (BAM)...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Plants are networkers

19.06.2017 | Event News

Digital Survival Training for Executives

13.06.2017 | Event News

Global Learning Council Summit 2017

13.06.2017 | Event News

 
Latest News

Quantum thermometer or optical refrigerator?

23.06.2017 | Physics and Astronomy

A 100-year-old physics problem has been solved at EPFL

23.06.2017 | Physics and Astronomy

Equipping form with function

23.06.2017 | Information Technology

VideoLinks
B2B-VideoLinks
More VideoLinks >>>