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 Nanoparticle Exposure Can Awaken Dormant Viruses in the Lungs
16.01.2017 | Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt

nachricht Cholera bacteria infect more effectively with a simple twist of shape
13.01.2017 | Princeton University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Interfacial Superconductivity: Magnetic and superconducting order revealed simultaneously

Researchers from the University of Hamburg in Germany, in collaboration with colleagues from the University of Aarhus in Denmark, have synthesized a new superconducting material by growing a few layers of an antiferromagnetic transition-metal chalcogenide on a bismuth-based topological insulator, both being non-superconducting materials.

While superconductivity and magnetism are generally believed to be mutually exclusive, surprisingly, in this new material, superconducting correlations...

Im Focus: Studying fundamental particles in materials

Laser-driving of semimetals allows creating novel quasiparticle states within condensed matter systems and switching between different states on ultrafast time scales

Studying properties of fundamental particles in condensed matter systems is a promising approach to quantum field theory. Quasiparticles offer the opportunity...

Im Focus: Designing Architecture with Solar Building Envelopes

Among the general public, solar thermal energy is currently associated with dark blue, rectangular collectors on building roofs. Technologies are needed for aesthetically high quality architecture which offer the architect more room for manoeuvre when it comes to low- and plus-energy buildings. With the “ArKol” project, researchers at Fraunhofer ISE together with partners are currently developing two façade collectors for solar thermal energy generation, which permit a high degree of design flexibility: a strip collector for opaque façade sections and a solar thermal blind for transparent sections. The current state of the two developments will be presented at the BAU 2017 trade fair.

As part of the “ArKol – development of architecturally highly integrated façade collectors with heat pipes” project, Fraunhofer ISE together with its partners...

Im Focus: How to inflate a hardened concrete shell with a weight of 80 t

At TU Wien, an alternative for resource intensive formwork for the construction of concrete domes was developed. It is now used in a test dome for the Austrian Federal Railways Infrastructure (ÖBB Infrastruktur).

Concrete shells are efficient structures, but not very resource efficient. The formwork for the construction of concrete domes alone requires a high amount of...

Im Focus: Bacterial Pac Man molecule snaps at sugar

Many pathogens use certain sugar compounds from their host to help conceal themselves against the immune system. Scientists at the University of Bonn have now, in cooperation with researchers at the University of York in the United Kingdom, analyzed the dynamics of a bacterial molecule that is involved in this process. They demonstrate that the protein grabs onto the sugar molecule with a Pac Man-like chewing motion and holds it until it can be used. Their results could help design therapeutics that could make the protein poorer at grabbing and holding and hence compromise the pathogen in the host. The study has now been published in “Biophysical Journal”.

The cells of the mouth, nose and intestinal mucosa produce large quantities of a chemical called sialic acid. Many bacteria possess a special transport system...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

12V, 48V, high-voltage – trends in E/E automotive architecture

10.01.2017 | Event News

2nd Conference on Non-Textual Information on 10 and 11 May 2017 in Hannover

09.01.2017 | Event News

Nothing will happen without batteries making it happen!

05.01.2017 | Event News

 
Latest News

Water - as the underlying driver of the Earth’s carbon cycle

17.01.2017 | Earth Sciences

Interfacial Superconductivity: Magnetic and superconducting order revealed simultaneously

17.01.2017 | Materials Sciences

Smart homes will “LISTEN” to your voice

17.01.2017 | Architecture and Construction

VideoLinks
B2B-VideoLinks
More VideoLinks >>>