Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

US-India research team completes analysis of X chromosome

04.04.2005


Dozens of new genes identified



By intensely and systematically comparing the human X chromosome to genetic information from chimpanzees, rats and mice, a team of scientists from the United States and India has uncovered dozens of new genes, many of which are located in regions of the chromosome already tied to disease.

Regions of the X chromosome, one of the two sex chromosomes (Y is the other), have been linked to mental retardation and numerous other disorders, but finding the particular genetic abnormalities involved has been difficult.


The team’s accomplishment, described in the April issue of Nature Genetics, should speed research into diseases associated with the X chromosome and encourage similar analyses of other chromosomes. "To our knowledge, this is the first time critical analysis of an entire chromosome has been done by a group that wasn’t involved in determining the chromosome’s genetic sequence," says study leader Akhilesh Pandey, M.D., Ph.D., an assistant professor in the McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins and chief scientific adviser to the Institute of Bioinformatics (IOB) in Bangalore, India, where the analyses took place. "We didn’t start small. We wanted to prove that complete annotation can be done, and done in a way that lets you find new and unexpected things."

For 18 months, 26 Indian scientists pored through the publicly available sequence of the X chromosome (information generated by the Wellcome Trust Sanger Institute in England and others) to identify genes and other important parts of its DNA.

But unlike other efforts, the team didn’t just "mine the data" by using computers to search for known patterns in the genetic sequence. Instead, Pandey decided they would look for similarities between the human X chromosome’s protein-encoding instructions and corresponding regions in the mouse. Regions that were identical or nearly so were then examined carefully by IOB biologists.

"We didn’t want to start out by saying that genes had to look a certain way," says Pandey. "So our only initial assumption was that if a genetic region is important and codes for a protein, the sequence will be conserved at the protein level. Thus, even if the genetic sequence is different here and there, the protein sequence could still be the same."

Essentially, the researchers took advantage of the redundancy inherent in the genetic code. DNA’s four building blocks -- A, T, C and G -- act as instructions for proteins in select three-block sets. These three-block sets each "code" for just one of the 20 possible protein building blocks, or amino acids, but some of the sets code for the same amino acid. For example, the DNA sequences TTGAGGAGC and CTACGATCA are quite different, but both specify the same three amino acids -- leucine, arginine and serine, in that order. "Instead of telling the computer what to look for, we let nature tell the computer what was important," says Pandey. "When you align the protein-encoding instructions of the human and mouse, the genes jump out at you."

In the regions that were the same between species, the scientists found 43 new "gene structures" that encode proteins. Some of the newly identified genes sit in regions long tied to X-linked mental retardation syndromes, which appear only in boys, or other disorders. Quite remarkably, Pandey says, almost half of the new genes don’t look like any previously known genes, nor do they look like each other.

"These would not be found any other way, because no one knew to look for them," he says. "No one had ever identified any aspect of their sequences as being important."

The IOB scientists and the U.S. members of the team experimentally investigated a few of the new genes to confirm the comparative approach’s validity. Their results, as well as data created by other scientists since the U.S-India team started working, confirm the existence of some of the newly identified genes. The team’s work also showed that some so-called pseudogenes on the X chromosome are actually expressed, or transcribed, which contradicts the widespread idea that they are functionless.

"We’re really trying to show that complete annotation of chromosomes can be done, and that doing it this way means you can find things you don’t expect to find," says Pandey. "It’s long, painstaking work, but it’s worth it."

Pandey hopes that researchers will take the initiative to annotate sequenced genetic information and validate regions used in their work.

Joanna Downer | EurekAlert!
Further information:
http://www.jhmi.edu
http://www.nature.com/ng

More articles from Life Sciences:

nachricht Are there sustainable solutions in dealing with dwindling phosphorus resources?
16.10.2017 | Leibniz-Institut für Nutzierbiologie (FBN)

nachricht Strange undertakings: ant queens bury dead to prevent disease
13.10.2017 | Institute of Science and Technology Austria

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Smart sensors for efficient processes

Material defects in end products can quickly result in failures in many areas of industry, and have a massive impact on the safe use of their products. This is why, in the field of quality assurance, intelligent, nondestructive sensor systems play a key role. They allow testing components and parts in a rapid and cost-efficient manner without destroying the actual product or changing its surface. Experts from the Fraunhofer IZFP in Saarbrücken will be presenting two exhibits at the Blechexpo in Stuttgart from 7–10 November 2017 that allow fast, reliable, and automated characterization of materials and detection of defects (Hall 5, Booth 5306).

When quality testing uses time-consuming destructive test methods, it can result in enormous costs due to damaging or destroying the products. And given that...

Im Focus: Cold molecules on collision course

Using a new cooling technique MPQ scientists succeed at observing collisions in a dense beam of cold and slow dipolar molecules.

How do chemical reactions proceed at extremely low temperatures? The answer requires the investigation of molecular samples that are cold, dense, and slow at...

Im Focus: Shrinking the proton again!

Scientists from the Max Planck Institute of Quantum Optics, using high precision laser spectroscopy of atomic hydrogen, confirm the surprisingly small value of the proton radius determined from muonic hydrogen.

It was one of the breakthroughs of the year 2010: Laser spectroscopy of muonic hydrogen resulted in a value for the proton charge radius that was significantly...

Im Focus: New nanomaterial can extract hydrogen fuel from seawater

Hybrid material converts more sunlight and can weather seawater's harsh conditions

It's possible to produce hydrogen to power fuel cells by extracting the gas from seawater, but the electricity required to do it makes the process costly. UCF...

Im Focus: Small collisions make big impact on Mercury's thin atmosphere

Mercury, our smallest planetary neighbor, has very little to call an atmosphere, but it does have a strange weather pattern: morning micro-meteor showers.

Recent modeling along with previously published results from NASA's MESSENGER spacecraft -- short for Mercury Surface, Space Environment, Geochemistry and...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

World Health Summit 2017: International experts set the course for the future of Global Health

10.10.2017 | Event News

Climate Engineering Conference 2017 Opens in Berlin

10.10.2017 | Event News

Conference Week RRR2017 on Renewable Resources from Wet and Rewetted Peatlands

28.09.2017 | Event News

 
Latest News

A single photon reveals quantum entanglement of 16 million atoms

16.10.2017 | Physics and Astronomy

The melting ice makes the sea around Greenland less saline

16.10.2017 | Earth Sciences

On the generation of solar spicules and Alfvenic waves

16.10.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>