Navigation Links
New bioinformatics technique for systematically analyzing key regions in DNA that help control gene activity

Scientists at Lawrence Livermore National Laboratory (LLNL) and the Linnaeus Centre for Bioinformatics (LCB) at Uppsala University in Sweden have developed a new bioinformatics technique for systematically analyzing key regions in DNA that help control gene activity. The cooperative efforts were headed by Krzysztof Fidelis in the United States and by Jan Komorowski in Sweden.

Understanding the complex regulatory mechanisms that tell genes when to switch on and off is one of the toughest challenges facing researchers attempting to discover how life works. "Binding sites," or areas of DNA that interact with the proteins that help control gene expression, can be a long distance on the DNA strand from the genes they influence. Recent research also has shown that gene expression can be controlled by several regulatory proteins working together at a combination of different binding sites.

(Regulatory proteins are known as "transcription factors"; transcription is the first step in the process by which the genetic information in DNA is decoded by the cell to manufacture proteins, the building blocks of life.)

"It's difficult to experimentally observe how transcription factors bind to DNA at a distance from a gene, or how regulation happens," said Fidelis, a computational biologist in Livermore's Biosciences Directorate. "But you can identify their binding sites in a promoter or regulatory region - there are usually a few of these for each gene. We wanted to see if we could somehow deduce how many transcription factors at a time, or combinations of factors, are coming together physically and how these combinations regulate genes."

"To accomplish this," Komorowski said, "we used a machine learning technique called rough sets to mathematically model general rules that could associate known binding sites and gene expression in yeast, which is one of the most widely studied organisms." From the analysis of gene activity under a variety of environm ental conditions, the teams were able to develop a set of rules for predicting the location of binding site combinations based on limited binding site and gene expression data.

"We found that the same transcription factors, in slightly different combinations, could be responsible for the regulation of different genes," said Torgeir R. Hvidsten of the LCB. "Thus we now know that binding sites can be combined to allow a large number of expression outcomes using relatively few transcription factors."

Others collaborating in the project were Jerzy Tiuryn of the Faculty of Mathematics, Informatics, and Mechanics at Warsaw University in Poland; Bartosz Wilczynski of the Institute of Mathematics, Polish Academy of Sciences, and LLNL; and Andriy Kryshtafovych of LLNL. A report on the joint work appears in the June issue of the journal Genome Research.

The rough sets technique was developed by Zdzislaw Pawlak in Poland in the 1980s and is particularly suitable to build models from incomplete and uncertain data. It has been used in applications ranging from medical and financial data analysis to voice recognition and image processing. Applied to gene regulation, the approach was able to predict the location of regulatory sites for about one-third of the genes in the yeast genome - a success rate as good as or better than other current techniques.

"The next step is to test this approach on different organisms, including microbes and vertebrates," Fidelis said. The growing number of organisms whose genomes have been sequenced has generated a wealth of DNA sequence information that could provide the raw material for analysis.


'"/>

Source:LLNL


Related biology news :

1. European Commission funds EBI to do new research on synergies between bioinformatics and medical informatics
2. Pacific Rim researchers to collaborate on distributed bioinformatics analysis of avian flu
3. New lab technique identifies high levels of pathogens in therapy pool
4. Brain-mapping technique aids understanding of sleep, wakefulness
5. Study reveals new technique for fingerprinting environmental samples
6. Researchers pioneer new gene therapy technique using natural repair process
7. Newer imaging techniques may lead to over-treatment
8. Gene silencing technique offers new strategy for treating, curing disease
9. Mosaic mouse technique offers a powerful new tool to study diseases and genetics
10. Researchers devise new technique for creating human stem cells
11. New technique rapidly detects illness-causing bacteria
Post Your Comments:
*Name:
*Comment:
*Email:


(Date:1/25/2016)... Jan. 25, 2016  Glencoe Software, the world-leading supplier ... publication industries, will provide the data management solution OMERO ... Photo ... Phenotypic analysis measures the characteristics ... allowing comparisons between states such as health and disease, ...
(Date:1/20/2016)... , Jan. 20, 2016 A market ... to directly benefit from the explosion in genomics knowledge. ... Howe Sound Research. A range of dynamic trends are ... - personalized medicine - pharmacogenomics - pathogen evolution ... with large markets - greater understanding of the role ...
(Date:1/15/2016)... , Jan. 15, 2016 Recent publicized breaches ... to find new ways to ensure data security and ... iOS and Android that ties a ... transforming it into a hardware authorization token. Customer service ... their fingerprint on their KodeKey enabled device to verify ...
Breaking Biology News(10 mins):
(Date:2/10/2016)... -- NX Prenatal Inc., a US based molecular ... early warning of adverse pregnancy outcomes, announced today ... Dr. Thomas McElrath of Brigham & ... (SMFM) annual meeting held in Atlanta ... presentation reported initial positive top-line results regarding the ...
(Date:2/10/2016)... DUBLIN , Feb. 10, 2016  Allergan plc ... today announced that Brent Saunders , Allergan,s CEO ... in a fireside chat session at the RBC Capital ... 12:30 p.m. ET at The New York Palace Hotel ... presentation will be webcast live and can be accessed ...
(Date:2/10/2016)... Latham, NY (PRWEB) , ... February 10, 2016 , ... ... photodiode packages at the SPIE Photonics West conference in San Francisco’s Moscone ... and 14 in the same venue. , These latest InGaAs PIN diode standard ...
(Date:2/10/2016)... , ... February 10, 2016 , ... ... medicine, has announced a new agreement with Singapore-based Global Stem Cells Network (GSCN) ... the Philippines, Thailand and Singapore in the latest adipose and bone marrow therapies. ...
Breaking Biology Technology: