Navigation Links
Evolutionary comparison finds new human genes
Date:11/20/2007

Using supercomputers to compare portions of the human genome with those of other mammals, researchers at Cornell have discovered some 300 previously unidentified human genes, and found extensions of several hundred genes already known.

The discovery is based on the idea that as organisms evolve, sections of genetic code that do something useful for the organism change in different ways.

The research is reported by Adam Siepel, Cornell assistant professor of biological statistics and computational biology, Cornell postdoctoral researcher Brona Brejova and colleagues at several other institutions in the online version of the journal Genome Research, and it will appear in the December print edition.

The complete human genome was sequenced several years ago, but that simply means that the order of the 3 billion or so chemical units, called bases, that make up the genetic code is known. What remains is the identification of the exact location of all the short sections that code for proteins or perform regulatory or other functions.

More than 20,000 protein-coding genes have been identified, so the Cornell contribution, while significant, doesn't dramatically change the number of known genes. What's important, the researchers say, is that their discovery shows there still could be many more genes that have been missed using current biological methods. These methods are very effective at finding genes that are widely expressed but may miss those that are expressed only in certain tissues or at early stages of embryonic development, Siepel said.

"What's exciting is using evolution to identify these genes," Siepel said. "Evolution has been doing this experiment for millions of years. The computer is our microscope to observe the results."

Four different bases -- commonly referred to by the letters G, C, A and T -- make up DNA. Three bases in a row can code for an amino acid (the building blocks of proteins), and a string of these three-letter codes can be a gene, coding for a string of amino acids that a cell can make into a protein.

Siepel and colleagues set out to find genes that have been "conserved" -- that are fundamental to all life and that have stayed the same, or nearly so, over millions of years of evolution.

The researchers started with "alignments" discovered by other workers -- stretches up to several thousand bases long that are mostly alike across two or more species. Using large-scale computer clusters, including an 850-node cluster at the Cornell Center for Advanced Computing, the researchers ran three different algorithms, or computing designs -- one of which Siepel created -- to compare these alignments between human, mouse, rat and chicken in various combinations.

Over millions of years, individual bases can be swapped -- C to G, T to A, for example -- by damage or miscopying. Changes that alter the structure of a protein can kill the organism or send it down a dead-end evolutionary path. But conserved genes contain only minor changes that leave the protein able to do its job. The computer looked for regions with those sorts of changes by creating a mathematical model of how the gene might have changed, then looking for matches to this model.

After eliminating predictions that matched already known genes, the researchers tested the remainder in the laboratory, proving that many of the genes could in fact be found in samples of human tissue and could code for proteins. The researchers were sometimes able to identify the proteins by comparison with databases of known proteins. The discovered genes mainly have to do with motor activity, cell adhesion, connective tissue and central nervous system development, functions that might be expected to be common to many different creatures.

The entire project, from building and testing the mathematical models to running final laboratory tests, took about three years, Siepel said. The work was supported by the National Cancer Institute, a National Science Foundation Early Career Development Grant and a University of California graduate research fellowship.


'/>"/>

Contact: Press Relations Office
pressoffice@cornell.edu
607-255-6074
Cornell University Communications
Source:Eurekalert

Related biology news :

1. Clones on task serve greater good, evolutionary study shows
2. Adaptation to parasites drive African fishes along different evolutionary paths
3. Old developmental pathways spawn revolutionary evolutionary changes
4. New study sheds light on Galápagos hawk evolutionary history
5. A new explanation for evolutionary changes in genetic sex-determination systems
6. Predators and parasites may increase evolutionary stability
7. Time-sharing tropical birds key to evolutionary mystery
8. Evolutionary biology research on plant shows significance of maternal effects
9. Genome comparison of 12 fruit fly species
10. University of Oregon researcher finds that on waters surface, nitric acid is not so tough
11. Study finds environmental tests help predict hospital-acquired Legionnaires disease risk
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:5/20/2016)... 20, 2016  VoiceIt is excited to announce ... By working together, VoiceIt and VoicePass ... and VoicePass take slightly different approaches to voice ... security and usability. ... new partnership. "This marketing and technology ...
(Date:5/12/2016)... WearablesResearch.com , a brand of Troubadour Research & ... Q1 wave of its quarterly wearables survey. A particular ... a program where they would receive discounts for sharing ... "We were surprised to see that so many ... CEO of Troubadour Research, "primarily because there are segments ...
(Date:5/3/2016)... Lithuania , May 3, 2016  Neurotechnology, ... released the MegaMatcher Automated Biometric Identification System ... of large-scale multi-biometric projects. MegaMatcher ABIS can process ... accuracy using any combination of fingerprint, face or ... MegaMatcher SDK and MegaMatcher Accelerator ...
Breaking Biology News(10 mins):
(Date:6/23/2016)... SANTA MONICA, Calif. , June 23, 2016  The Prostate Cancer ... to pioneer increasingly precise treatments and faster cures for prostate cancer. Members of ... 77 institutions across 15 countries. Read More About the ... ... ...
(Date:6/23/2016)... FRANCISCO , June 23, 2016   EpiBiome ... has secured $1 million in debt financing from Silicon ... ramp up automation and to advance its drug development ... its new facility. "SVB has been an ... beyond the services a traditional bank would provide," said ...
(Date:6/23/2016)... ... ... STACS DNA Inc., the sample tracking software company, today announced that Dr. Hays ... DNA as a Field Application Specialist. , “I am thrilled that Dr. Young ... DNA. “In further expanding our capacity as a scientific integrator, Hays brings a wealth ...
(Date:6/23/2016)... June 23, 2016 Apellis Pharmaceuticals, Inc. ... clinical trials of its complement C3 inhibitor, APL-2. ... multiple ascending dose studies designed to assess the ... subcutaneous injection in healthy adult volunteers. ... as a single dose (ranging from 45 to ...
Breaking Biology Technology: